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1

U-098: ISC BIND Deleted Domain Name Resolving Vulnerability | Department of  

Broader source: Energy.gov (indexed) [DOE]

098: ISC BIND Deleted Domain Name Resolving Vulnerability 098: ISC BIND Deleted Domain Name Resolving Vulnerability U-098: ISC BIND Deleted Domain Name Resolving Vulnerability February 8, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to bypass certain security restrictions. PLATFORM: ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ABSTRACT: The vulnerability is caused due to an error within the cache update policy. reference LINKS: Original Advisory Secunia Advisory SA47884 CVE-2012-1033 IMPACT ASSESSMENT: High Discussion: Researchers discovered a vulnerability affecting the large majority of popular DNS implementations which allows a malicious domain name to stay resolvable long after it has been removed from the upper level servers. The

2

U-183: ISC BIND DNS Resource Records Handling Vulnerability | Department of  

Broader source: Energy.gov (indexed) [DOE]

3: ISC BIND DNS Resource Records Handling Vulnerability 3: ISC BIND DNS Resource Records Handling Vulnerability U-183: ISC BIND DNS Resource Records Handling Vulnerability June 5, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to disclose potentially sensitive information or cause a DoS (Denial of Service). PLATFORM: Version(s): ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ISC BIND 9.9.x ABSTRACT: This problem was uncovered while testing with experimental DNS record types. It is possible to add records to BIND with null (zero length) rdata fields. Reference List: Secunia Advisory 49338 CVE-2012-1667 Original Advisory IMPACT ASSESSMENT: High Discussion: Recursive servers may crash or disclose some portion of memory to the

3

U-039: ISC Update: BIND 9 Resolver crashes after logging an error in  

Broader source: Energy.gov (indexed) [DOE]

9: ISC Update: BIND 9 Resolver crashes after logging an error 9: ISC Update: BIND 9 Resolver crashes after logging an error in query.c U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 2:30pm Addthis PROBLEM: ISC Update: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Versions of BIND, 9.4-ESV, 9.6-ESV, 9.7.x, 9.8.x ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

4

V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup  

Broader source: Energy.gov (indexed) [DOE]

7: McAfee Firewall Enterprise ISC BIND Record Handling Lockup 7: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability V-007: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability October 22, 2012 - 6:00am Addthis PROBLEM: McAfee Firewall Enterprise ISC BIND Record Handling Lockup Vulnerability PLATFORM: Versions 8.2.x prior to 8.2.1P06, and 8.3.x prior to 8.3.0P02 REFERENCE LINKS: Secunia Advisory SA51050 CVE-2012-5166 McAfee Corporate Knowledge Base IMPACT ASSESSMENT: Medium DISCUSSION: The vulnerability is caused due to an error when handling queries for certain records and can be exploited to cause the named process to lockup. IMPACT: If specific combinations of RDATA are loaded into a nameserver, either via cache or an authoritative zone, a subsequent query for a related record

5

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

Broader source: Energy.gov (indexed) [DOE]

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

6

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

Broader source: Energy.gov (indexed) [DOE]

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

7

U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service |  

Broader source: Energy.gov (indexed) [DOE]

0: ISC BIND RDATA Processing Flaw Lets Remote Users Deny 0: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service September 14, 2012 - 6:00am Addthis PROBLEM: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service PLATFORM: Version(s): 9.0.x -> 9.6.x, 9.4-ESV->9.4-ESV-R5-P1, 9.6-ESV->9.6-ESV-R7-P2, 9.7.0->9.7.6-P2, 9.8.0->9.8.3-P2, 9.9.0->9.9.1-P2 ABSTRACT: A vulnerability was reported in ISC BIND. reference LINKS: The vendor's advisory SecurityTracker Alert ID: 1027529 Bugtraq ID: 55522 Red Hat Bugzilla - Bug 856754 CVE-2012-4244 IMPACT ASSESSMENT: High Discussion: A remote user can send a query for a record that has RDATA in excess of 65535 bytes to cause named to exit. This can be exploited against recursive servers by causing the server to query for records provided by an

8

T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service |  

Broader source: Energy.gov (indexed) [DOE]

2: ISC BIND Packet Processing Flaw Lets Remote Users Deny 2: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service July 6, 2011 - 7:47am Addthis PROBLEM: A vulnerability was reported in ISC BIND. A remote user can cause denial of service conditions. PLATFORM: 9.6.3, 9.6-ESV-R4, 9.6-ESV-R4-P1, 9.6-ESV-R5b1 9.7.0, 9.7.0-P1, 9.7.0-P2, 9.7.1, 9.7.1-P1, 9.7.1-P2, 9.7.2, 9.7.2-P1, 9.7.2-P2, 9.7.2-P3, 9.7.3, 9.7.3-P1, 9.7.3-P2, 9.7.4b1 9.8.0, 9.8.0-P1, 9.8.0-P2, 9.8.0-P3, 9.8.1b1 ABSTRACT: A defect in the affected BIND 9 versions allows an attacker to remotely cause the "named" process to exit using a specially crafted packet. This defect affects both recursive and authoritative servers. The code location of the defect makes it impossible to protect BIND using ACLs configured

9

DsrR, a Novel IscA-Like Protein Lacking Iron- and Fe-S-Binding Functions, Involved in the Regulation of Sulfur Oxidation in Allochromatium vinosum  

Science Journals Connector (OSTI)

...sequence. IscA-like proteins without bound iron...DsrR and IscA-like proteins. This disordered region corresponds...site in IscA-like proteins. Several residues...convergence in the NMR ensemble, probably reflecting...

Frauke Grimm; John R. Cort; Christiane Dahl

2010-01-08T23:59:59.000Z

10

U-224: ISC DHCP Multiple Denial of Service Vulnerabilities | Department of  

Broader source: Energy.gov (indexed) [DOE]

4: ISC DHCP Multiple Denial of Service Vulnerabilities 4: ISC DHCP Multiple Denial of Service Vulnerabilities U-224: ISC DHCP Multiple Denial of Service Vulnerabilities July 31, 2012 - 7:00am Addthis PROBLEM: ISC DHCP Multiple Denial of Service Vulnerabilities PLATFORM: ISC DHCP before versions DHCP 4.1-ESV-R6 or DHCP 4.2.4-P1 ABSTRACT: ISC DHCP is prone to multiple denial-of-service vulnerabilities. reference LINKS: BIND and DHCP Security Updates Released Bugtraq ID: 54665 Secunia Advisory SA50018 CVE-2012-3571 CVE-2012-3570 CVE-2012-3954 IMPACT ASSESSMENT: Medium Discussion: Multiple vulnerabilities have been reported in ISC DHCP, which can be exploited by malicious people to cause a DoS (Denial of Service). 1) An error when handling client identifiers can be exploited to trigger an endless loop and prevent the server from processing further client requests

11

Institute for Sustainable Communities (ISC) | Open Energy Information  

Open Energy Info (EERE)

Sustainable Communities (ISC) Address: 535 Stone Cutters Way Montpelier, Vermont 05602 USA Place: Montpelier, Vermont Zip: 05602 Website: http:www.iscvt.org References: http:...

12

ISC-Reducing Congestion through Smart Parking Management | Open Energy  

Open Energy Info (EERE)

ISC-Reducing Congestion through Smart Parking Management ISC-Reducing Congestion through Smart Parking Management Jump to: navigation, search Tool Summary LAUNCH TOOL Name: ISC-Reducing Congestion through Smart Parking Management Agency/Company /Organization: Institute for Sustainable Communities (ISC) Sector: Climate, Energy Focus Area: Transportation Resource Type: Case studies/examples, Lessons learned/best practices Website: www.iscvt.org/resources/documents/san_francisco_sfpark.pdf Locality: San Francisco, California Cost: Free Language: English ISC-Reducing Congestion through Smart Parking Management Screenshot References: Reducing Congestion through Smart Parking Management[1] "The transit study concluded that congestion is a primary factor reducing the reliability and speed of onroad transit, which in turn is exacerbated

13

IMPERIAL INNOVATION STUDIES CENTRE (ISC) The Innovation Studies Centre (ISC) at Imperial College London is undertaking a  

E-Print Network [OSTI]

impact of innovative new approaches to this for the NHS and social care system. Director: Mr Oliver Wells#12;IMPERIAL INNOVATION STUDIES CENTRE (ISC) The Innovation Studies Centre (ISC) at Imperial of innovation processes and how scientific and engineering potential can be unlocked for future prosperity

Oakley, Jeremy

14

ISC Conventional Reading Rooms | U.S. DOE Office of Science ...  

Office of Science (SC) Website

IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Freedom of Information Act (FOIA) ISC Conventional...

15

Phospholipase A2 Engineering. Deletion of the C-Terminus Segment Changes Substrate Specificity and Uncouples Calcium and Substrate Binding at the  

E-Print Network [OSTI]

channel, and the calcium binding loop are perturbed, but the global conformation is not changed and Uncouples Calcium and Substrate Binding at the Zwitterionic Interface, Baohua Huang,,§ Bao-Zhu Yu,| Joseph and the uncoupling between substrate and calcium binding are interesting and significant. One of the important

Tsai, Ming-Daw

16

T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service | Department  

Broader source: Energy.gov (indexed) [DOE]

7: BIND RPZ Processing Flaw Lets Remote Users Deny Service 7: BIND RPZ Processing Flaw Lets Remote Users Deny Service T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service May 6, 2011 - 7:00am Addthis PROBLEM: A vulnerability has been reported in BIND, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: ISC BIND version 9.8.0. ABSTRACT: When a name server is configured with a response policy zone (RPZ), queries for type RRSIG can trigger a server crash. REFERENCE LINKS: ISC Advisory: CVE-2011-1907 Secunia Advisory: SA44416 Vulnerability Report: ISC BIND CVE-2011-1907 SecurityTracker Alert ID: 1025503 IMPACT ASSESSMENT: High Discussion: This advisory only affects BIND users who are using the RPZ feature configured for RRset replacement. BIND 9.8.0 introduced Response Policy Zones (RPZ), a mechanism for modifying DNS responses returned by a

17

A Generalized Deletion Machine  

E-Print Network [OSTI]

In this work we prescribe a more generalized quantum-deleting machine (input state dependent). The fidelity of deletion is dependent on some machine parameters such that on alteration of machine parameters we get back to standard deleting machines. We also carried out a various comparative study of various kinds of quantum deleting machines. We also plotted graphs, making a comparative study of fidelity of deletion of the deletion machines, obtained as particular cases on changing the machine parameters of our machine.

Indranil Chakrabarty; Satyabrata Adhikari

2005-11-22T23:59:59.000Z

18

Embargoed Deletion  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

PNAS proof PNAS proof Embargoed Deletion of Cel48S Q:1 from Clostridium thermocellum ; 2 Daniel G. Olson a,b,c , Shital A. Tripathi a,c , Richard J. Giannone c,d , Jonathan Lo b,c , Nicky C. Caiazza a,c , David A. Hogsett a,c , Robert Hettich c,d , Adam M. Guss b,c , Genia Dubrovsky b,c , and Lee R. Lynd a,b,c,e,1 a Mascoma Corporation, NH 03766; b Thayer School of Engineering and e Department of Biological Sciences, Dartmouth College, NH 03755; and c BioEnergy Science Center, d Oak Ridge National Laboratory, TN 37830 Q:3 Edited* by Lonnie O'Neal Ingram, University of Florida, Gainesville, FL, and approved August 16, 2010 (received for review April 9, 2010) Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cel- lulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, S S , and S8), the most abundant cellulosome

19

Integrated Support Center (ISC) Homepage | U.S. DOE Office of Science (SC)  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Home Home Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Categorical Exclusion Determinations Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Larry Kelly U.S. Department of Energy 200 Administration Road Oak Ridge, TN 37830 P: (865) 576-0885 Integrated Support Center The Office of Science Integrated Support Center proudly facilitates work across the ten Office of Science laboratories and site offices. Caption: The Hall D tagger area of the Continuous Electron Beam Accelerator Facility at Thomas Jefferson Laboratory. Hall D tagger area 1 of 2 Print Text Size: A A A RSS Feeds FeedbackShare Page The Office of Science's (SC) Integrated Support Center (ISC) provides

20

WORKING DOCUMENT for ISC -DRAFT -October 11th "Nanosciences, Nanotechnologies, Materials and new  

E-Print Network [OSTI]

WORKING DOCUMENT for ISC - DRAFT - October 11th 2006 Theme 4 "Nanosciences, Nanotechnologies ------------------------------------------------------------------------------- Table of contents I Context 1 II Content of Calls 5 Nanosciences and Nanotechnologies 7 Materials 18 New "Nanosciences, Nanotechnologies, Materials and new Production Technologies ­ NMP" is to fund research

Meju, Max

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service...  

Broader source: Energy.gov (indexed) [DOE]

service to legitimate users. This issue may also be exploited to disclose certain memory information to clients. Solution: The vendor has issued a fix. Addthis Related...

22

Improving the fidelity of deletion  

Science Journals Connector (OSTI)

In this work we study the quantum deletion machine with two transformers, and show that the deletion machine with a single transformer performs better than the deletion machine with more than two transformers. We also observe that the fidelity of deletion depends on the blank state used in the deleter, and so for different blank states the fidelity is different. Further, we study the Pati-Braunsein deleter with transformer.

Satyabrata Adhikari and B. S. Choudhury

2006-05-24T23:59:59.000Z

23

U-038: BIND 9 Resolver crashes after logging an error in query.c |  

Broader source: Energy.gov (indexed) [DOE]

8: BIND 9 Resolver crashes after logging an error in query.c 8: BIND 9 Resolver crashes after logging an error in query.c U-038: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 8:37am Addthis PROBLEM: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Multiple version of BIND 9. Specific versions under investigation ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

24

Microsoft Word - ORO ISC Functional Analysis and Inventory 3-6-07 FINAL.doc  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Table of Contents Page Introduction 1 Mission 1 Distinctive Characteristics 2 Assumptions 3 Staffing and Trends 4 Critical Skills Inventory 6 Significant Successes 7 Strategic Goals and Objectives 9 Conclusions 10 Appendix A: Functional Descriptions 11 Appendix B: SC ISC Staffing Levels by Occupational Groupings 16 Appendix C: Organizational Metrics 21 F U N C T I O N A L A N A L Y S I S A N D I N V E N T O R Y Introduction The Manager, Oak Ridge Office (ORO), has requested this Functional Analysis and Inventory to identify and present quantifiable performance metrics for various matrix support activities performed by ORO. This analysis will be used to describe the ORO operating model as a component of the Office of Science (SC) Integrated

25

isc golf, that is. The 4,560-foot course winds throughout the woods behind East Campus  

E-Print Network [OSTI]

D isc golf, that is. The 4,560-foot course winds throughout the woods behind East Campus Saturday 6:45 a.m. Spinning Spinning Spinning Noon Boot Camp R.I.P.P.E.D Power Yoga Yoga Pilates Total Body Toning R.I.P.P.E.D. Power Yoga Yoga Pilates Total Body Toning Power Yoga R.I.P.P.E.D. 4:30 p.m. Vinyasa

Suzuki, Masatsugu

26

Towards an InTerdIscIplInary approach To nexT-GeneraTIon BIofuels EnvironmEntal, tEchno-Economic, and GovErnancE  

E-Print Network [OSTI]

Towards an InTerdIscIplInary approach To nexT-GeneraTIon BIofuels EnvironmEntal, t. 2010. The Ecological Impact of Biofuels. Pages 351-377 in D. J. Futuyma, H. B. Shafer, and D. Huffer, S., Roche, C.M., Blanch, H.W., and Clark, D.S. (2012). Escherichia coli for biofuel production

Iglesia, Enrique

27

Help:Deleting pages | Open Energy Information  

Open Energy Info (EERE)

pages pages Jump to: navigation, search See Category:Proposed deletion for the listing of all articles currently proposed for deletion. Proposed deletion is the way to suggest that an article is a candidate for uncontroversial deletion. If nobody objects, the article is deleted after seven days. An article may not be proposed for deletion ("PRODed") if it has been PRODed before. Proposed deletion is only applicable to mainspace articles, lists, and disambiguation pages; it cannot be used with redirects, userspace pages, templates, categories, or pages in any other namespace. There are three steps to the PROD process An article or disambiguation page is nominated when an editor carefully reviews the article and inserts the {{subst:proposed deletion}} tag by placing {{subst:proposed deletion}} on the page. This lists the

28

V-204: A specially crafted query can cause BIND to terminate abnormally |  

Broader source: Energy.gov (indexed) [DOE]

V-204: A specially crafted query can cause BIND to terminate V-204: A specially crafted query can cause BIND to terminate abnormally V-204: A specially crafted query can cause BIND to terminate abnormally July 27, 2013 - 4:35am Addthis PROBLEM: A specially crafted query that includes malformed rdata can cause named to terminate with an assertion failure while rejecting the malformed query. PLATFORM: BIND 9.7 ABSTRACT: A specially crafted query sent to a BIND nameserver can cause it to crash (terminate abnormally). REFERENCE LINKS: ISC Knowledge Base CVE-2013-4854 IMPACT ASSESSMENT: High DISCUSSION: BIND is an implementation of the Domain Name System (DNS) protocols. Authoritative and recursive servers are equally vulnerable. Intentional exploitation of this condition can cause a denial of service in all nameservers running affected versions of BIND 9. Access Control Lists do

29

Help:Sysop deleting and undeleting | Open Energy Information  

Open Energy Info (EERE)

Sysop deleting and undeleting Sysop deleting and undeleting Jump to: navigation, search Deleting a page is a straightforward operation for anyone with sysop permissions. Users without such permissions can still remove text from wiki pages, or propose/request that a page should be deleted. See Help:Deleting a page. Contents 1 Before deleting 2 Use the 'delete' tab 3 Undeleting 4 Configuring deletion reasons Before deleting Sysops should also be aware of the general advice given on Help:Deleting a page (In particular, note that there are many situations where a deleting is too drastic. Often a redirect is more appropriate for example) Before deleting you could perform various checks: Use the "What links here" tool. This gives an indication as to how important a page is, and what subjects it relates to. Perhaps the page is

30

PartialDeletion for web.cdr  

Office of Legacy Management (LM)

States Department of Energy Grand Junction Office F A C T S H E E T Partial Deletion of Monticello Mill Tailings Site From the National Priorities List July 2003 The U.S....

31

Probabilistic cloning and deleting of quantum states Yuan Feng, Shengyu Zhang, and Mingsheng Ying*  

E-Print Network [OSTI]

, deleting unknown quantum states was also found to be impossible, where ``deleting'' means ``uncopy- ing

Zhang, Shengyu

32

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment in the context of a cloning vector which contains an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment. Also disclosed is a method for producing single-stranded DNA probes utilizing the same cloning vector. An optimal vector, PZIP is described. Methods for introducing unidirectional deletions into a terminal location of a cloned DNA sequence which is inserted into the vector of the present invention are also disclosed. These methods are useful for introducing deletions into either or both ends of a cloned DNA insert, for high throughput sequencing of any DNA of interest.

Dunn, John J. (Bellport, NY); Quesada, Mark A. (Horseheads, NY); Randesi, Matthew (New York, NY)

2001-01-01T23:59:59.000Z

33

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

1999-07-27T23:59:59.000Z

34

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

Dunn, J.J.; Quesada, M.A.; Randesi, M.

1999-07-27T23:59:59.000Z

35

The effect on chromosome stability of deleting replication origins.  

Science Journals Connector (OSTI)

...is the result of breakage of bubble-containing replication intermediates...deletion. The transition from bubble arc to Y arc characteristic...external origin and therefore BUBBLE D that deleting ARS309 removes...ARS elements to chromosome stability. It is part of the 200-kb...

A Dershowitz; C S Newlon

1993-01-01T23:59:59.000Z

36

Flag rates for deletion? | OpenEI Community  

Open Energy Info (EERE)

Flag rates for deletion? Flag rates for deletion? Home > Groups > Utility Rate I found some "rates" that don't belong; they are one-time connection fees instead of rates (e.g. with a $2,500 connection fee as a "fixed monthly charge"). Is there some way to flag rates for suggested deletion? Submitted by Ewilson on 22 June, 2012 - 11:27 1 answer Points: 1 Hi Ewilson, Thank you for pointing this out! We are currently working on a way for users to propose deletion: http://en.openei.org/wiki/Help:Deleting_pages. Let me know if you have any questions! Wzeng on 12 July, 2012 - 08:19 Groups Menu You must login in order to post into this group. Recent content There is currently no way to s... ranking of utilities by demand charge? FYI, OpenEI now accommodates t... Very useful information. Thank...

37

Help:Deleting a page | Open Energy Information  

Open Energy Info (EERE)

page page Jump to: navigation, search Contents 1 When not to delete a page 1.1 Proposing changes 1.2 Unlinking a page 2 Deletion itself 3 See also When not to delete a page Typically you would delete a page if the contents are entirely inappropriate and do not match the purposes of the Wiki. In other situations, you would take a less extreme course of action, for example: The page should have a different title -- See Help:Moving a page The contents should have been placed on a different page -- Add the contents to the other page, and then supply a redirect. See Help:Redirects The contents are already on a different page -- Delete the duplicate content and leave a redirect. That way, the page title, which made sense to somebody, will helpfully redirect to the information. See Help:Redirects

38

ISC2005v2.ppt  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

1989 The argument against massive parallelism (ca. 1988) From a presentation by Jim Hack at DOE Salishan High Speed Computing, 1988 Theoretical papers such as this "proved"...

39

Planar F-Deletion: Approximation and Optimal FPT Algorithms  

E-Print Network [OSTI]

Let F be a finite set of graphs. In the F-Deletion problem, we are given an n-vertex, m-edge graph G and an integer k as input, and asked whether at most k vertices can be deleted from G such that the resulting graph does not contain a graph from F as a minor. F-Deletion is a generic problem and by selecting different sets of forbidden minors F, one can obtain various fundamental problems such as Vertex Cover, Feedback Vertex Set or Treewidth t-Deletion. In this paper we obtain a number of generic algorithmic results about Planar F-Deletion, when F contains at least one planar graph. The highlights of our work are - A randomized O(nm) time constant factor approximation algorithm for the optimization version of Planar F-Deletion. - A randomized O(2^{O(k)} n) time parameterized algorithm for Planar F-Deletion when F is connected. Here a family F is called connected if every graph in F is connected. The algorithm can be made deterministic at the cost of making the polynomial factor in the running time n\\log^2 n ...

Fomin, Fedor; Misra, Neeldhara; Saurabh, Saket

2012-01-01T23:59:59.000Z

40

Targeted Genomic Deletion of the Lens-Specific Intermediate Filament Protein CP49  

E-Print Network [OSTI]

Targeted Genomic Deletion of the Lens-Specific Intermediate Filament Protein CP49 Azita Alizadeh,1, by blocking expression of the fiber cell­specific beaded filament protein CP49. METHODS. The first exon of the mouse CP49 gene was deleted by using targeted genomic deletion techniques. Gene deletion was assessed

Clark, John

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

PABPN1 polyalanine tract deletion and long expansions modify its aggregation pattern and expression  

Science Journals Connector (OSTI)

Expansions of a (GCN)10/polyalanine tract in the Poly(A) Binding Protein Nuclear 1 (PABPN1) cause autosomal dominant oculopharyngeal muscular dystrophy (OPMD). In OPMD muscles, as in models, PABPN1 accumulates in intranuclear inclusions (INIs) whereas in other diseases caused by similar polyalanine expansions, the mutated proteins have been shown to abnormally accumulate in the cytoplasm. This study presents the impact on the subcellular localization of PABPN1 produced by large expansions or deletion of its polyalanine tract. Large tracts of more than 24 alanines result in the nuclear accumulation of PABPN1 in SFRS2-positive functional speckles and a significant decline in cell survival. These large expansions do not cause \\{INIs\\} formation nor do they lead to cytoplasmic accumulation. Deletion of the polyalanine tract induces the formation of aggregates that are located on either side and cross the nuclear membrane, highlighting the possible role of the N-terminal polyalanine tract in PABPN1 nucleo-cytoplasmic transport. We also show that even though five other proteins with polyalanine tracts tend to aggregate when over-expressed they do not co-aggregate with PABPN1 INIs. This study presents the first experimental evidence that there may be a relative loss of function in OPMD by decreasing the availability of PABPN1 through an INI-independent mechanism.

Arnaud F. Klein; Mitsuru Ebihara; Christine Alexander; Marie-Jose Dicaire; A. Marie-Jose Sasseville; Yves Langelier; Guy A. Rouleau; Bernard Brais

2008-01-01T23:59:59.000Z

42

Detection of frame deletion for digital video forensics  

Science Journals Connector (OSTI)

The abundance of digital video forms a potential piece of evidence in courtrooms. Augmenting subjective assessment of digital video evidence by an automated objective assessment helps increase the accuracy of deciding whether or not to admit the digital ... Keywords: Digital forensics, Frame deletion, Video compression

Tamer Shanableh

2013-12-01T23:59:59.000Z

43

Sixth CREST Conference: 'Ctrl, Alt, Delete: Re-booting the State via  

E-Print Network [OSTI]

Sixth CREST Conference: 'Ctrl, Alt, Delete: Re-booting the State via E-Government in Europe, Delete: Re-booting the State via E-Government in Europe' Convenors: Dr Liki Koutrakou, UEA and Dr Paul

Feigon, Brooke

44

The effect of two deletion schemes upon the comprehension and reading rate of five levels of telegraphic prose  

E-Print Network [OSTI]

between the two deletion schemes that would involve a relative increase in comprehension, reading rate, and efficiency for the subject generated scheme with 1ncreasing percentages of deletion. (5) The index of agreement among subjects on the rank... Reduced Version of the Passage Based on 50% Deletion (S5) Randomly Reduced Version of the Passage Based on IOX Deletion (Rl) Randomly Reduced Version of the Passage Based on 20% Deletion (R2) Randomly Reduced Version of the Passage Based on 30K...

Pantalion, Charles Adrian

1972-01-01T23:59:59.000Z

45

Identification of interstitial deletions in human neoplasia by FISH-technique  

SciTech Connect (OSTI)

Undoubtedly, the discovery of the minute chromosome in chronic myelogenous leukemia (CML), termed the Philadelphia chromosome, has revolutionized cancer cytogenetics. Rowely`s seminal findings of a balanced translocation between chromosomes 9 and 22 opened new avenues where a simple deletion was clearly refuted. Even today, thousands of cases are being identified as simple terminal deletions by routine banding techniques in various human neoplasias. If these deletions are terminal, then how is the instability of the chromosome retained? Apparently, the precise characterization of telomeric ends has gone undetected in the past by conventional methods. It is evident that telomeres of chromosomes consist of short tandemly repeated DNA sequences (TTAGGG){sub n} which are conserved on both ends. The recent availability of chromosome-specific telomeric probes has become a cytogenetic icon for many perplexing questions. For example, we were referred a patient with acute myelogenous leukemia evolving from agnogenic myloid metaplasia. Routine cytogenetic techniques revealed a terminal deletion of one of the chromosomes 7 [del(7)(q21)]. When we hybridized the metaphases with chromosome 7q-specific telomeric probe [Oncor, Gaithersburg, MD], signal was detected at the distal q arms of the deleted chromosomes, apparently suggesting an interstial deletion. The cytogenetic diagnosis was changed to 46,SY,del(7)(q21.lq36.2). All deletions must be identified by FISH.

Gogineni, S.K.; Sanchez, M.A.; Elizalde, S.A. [Long Island College Hospital, Brooklyn, NY (United States)]|[New York Methodist Hospital, Brooklyn, NY (United States)] [and others

1994-09-01T23:59:59.000Z

46

Why did someone delete the Utility Rate Database Page? | OpenEI...  

Open Energy Info (EERE)

Why did someone delete the Utility Rate Database Page? Home > Groups > Utility Rate Can someone fix this? I can't access the Utility Rate Database Page It looks like someone...

47

Cold Urticaria, Immunodeficiency, and Autoimmunity Related to PLCG2 Deletions  

Science Journals Connector (OSTI)

...Supplementary Appendix) and generalized exposure to cold air, findings that are consistent with their reports that symptoms were often elicited by cold wind rather than contact with cold objects. Of the 27 subjects who were tested, 26 had immunologic abnormalities in addition to cold urticaria (Table S1... Analyses of families affected by cold urticaria, immunodeficiency, and autoimmunity implicate mutations that activate phospholipase C?2 (PLC?2), an enzyme pivotal to the translation of binding events at the cell surface to the intracellular milieu, as a cause of the disease.

Ombrello M.J.; Remmers E.F.; Sun G.

2012-01-26T23:59:59.000Z

48

Cloning and characterization of an alternatively spliced gene in proximal Xq28 deleted in two patients with intersexual genitalia and myotubular myopathy  

SciTech Connect (OSTI)

We have identified a novel human gene that is entirely deleted in two boys with abnormal genital development and myotubular myopathy (MTM1). The gene, F18, is located in proximal Xq28, approximately 80 kb centromeric to the recently isolated MTM1 gene. Northern analysis of mRNA showed a ubiquitous pattern and suggested high levels of expression in skeletal muscle, brain, and heart. A transcript of 4.6 kb was detected in a range of tissues, and additional alternate forms of 3.8 and 2.6 kb were present in placenta and pancreas, respectively. The gene extends over 100 kb and is composed of at least seven exons, of which two are non-coding. Sequence analysis of a 4.6-kb cDNA contig revealed two overlapping open reading frames (ORFs) that encode putative proteins of 701 and 424 amino acids, respectively. Two alternative spliced transcripts affecting the large open reading frame were identified that, together with the Northern blot results, suggest that distinct proteins are derived from the gene. No significant homology to other known proteins was detected, but segments of the first ORF encode polyglutamine tracts and proline-rich domains, which are frequently observed in DNA-binding proteins. The F18 gene is a strong candidate for being implicated in the intersexual genitalia present in the two MTM1-deleted patients. The gene also serves as a candidate for other disorders that map to proximal Xq28. 15 refs., 3 figs., 1 tab.

Laporte, J.; Hu, Ling-Jia; Kretz, C. [Institut de Genetique et de Biologie Moleculaire et Cellulaire, Strasbourg (France)] [and others] [Institut de Genetique et de Biologie Moleculaire et Cellulaire, Strasbourg (France); and others

1997-05-01T23:59:59.000Z

49

ISCED: International Standard Classification of Education ISCED Fields of Education and Training (2013)  

E-Print Network [OSTI]

ERA-Code 022 Humanities (except languages) 0223 Philosophy and ethics [Medizin/Ethik] 031 Social design and administration 0613 Software and applications development and analysis 0618 Inter Informationssystemtechnik [Communications Technology] [Energy Science & Technology] 524 523 06.0 | 06.2 | 06.5 091 Health

Pfeifer, Holger

50

Brief Report: Spermatogenesis in a Man with Complete Deletion of USP9Y  

Science Journals Connector (OSTI)

...guidelines. In order to define the extent of deletion, we used several sequence-tagged sites (sY82, sY88, sY83, G64723, AZFa-prox2, G66179, G66183, SHGC-3904, G65852, G49201, G65840, G66201, G49206, G66189, sY87, GY6, and G38346) and gene-specific primers to localize the breakpoints to an interval spanning... The azoospermia factor region A (AZFA) on chromosome Y contains two genes, one of which is USP9Y. Deletions in this region have been associated with male infertility. However, a man and his father and brother, all of whom carry a deletion that encompasses USP9Y, are normospermic, providing definitive evidence that USP9Y is not required for spermatogenesis.

Luddi A.; Margollicci M.; Gambera L.

2009-02-26T23:59:59.000Z

51

Quarkonium Binding and Entropic Force  

E-Print Network [OSTI]

A Q-Qbar bound state represents a balance between repulsive kinetic and attractive potential energy. In a hot quark-gluon plasma, the interaction potential experiences medium effects. Color screening modifies the attractive binding force between the quarks, while the increase of entropy with Q-Qbar separation gives rise to a growing repulsion. We study the role of these phenomena for in-medium Q-Qbar binding and dissociation. It is found that the relevant potential for Q-Qbar binding is the free energy F; with increasing Q-Qbar separation, further binding through the internal energy U is compensated by repulsive entropic effects.

Satz, Helmut

2015-01-01T23:59:59.000Z

52

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity  

E-Print Network [OSTI]

of Electrical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA 6Molecular nature of gene regulation. Unlike individual transcription factors, complexes of interacting factors bind cooperatively to genomic regions that contain a favorable configuration of binding sites (Johnson, 1995

Rohs, Remo

53

Electron Microscope Studies of Heteroduplex DNA from a Deletion Mutant of Bacteriophage ?X-174  

Science Journals Connector (OSTI)

...Accordingly, in Fig. 3 we depict the hetero- duplexes as having a nick in'the deleted strand.) Structure B can only occur for a...migration. Several points, however, are sufficiently clear to merit discussion. Since branch migration processes involve successive...

Jung-Suh Kim; Phillip A. Sharp; Norman Davidson

1972-01-01T23:59:59.000Z

54

Proposed FMP amendment language for GOA Amendment 72 Deletions are removed; additions are in bold.  

E-Print Network [OSTI]

Proposed FMP amendment language for GOA Amendment 72 Deletions are removed; additions are in bold. p. ES-4, Table ES-2: remove entire row tittles Bycatch Reduction Programs: Bycatch Reduction. The Council may recommend that NMFS initiate rulemaking to add or remove a fishery from shallow-water flatfish

55

Early Deletion of Fillers In Processing Conversational Speech Matthew Lease and Mark Johnson  

E-Print Network [OSTI]

Early Deletion of Fillers In Processing Conversational Speech Matthew Lease and Mark Johnson Brown to parsing has been shown to improve its accuracy (Charniak and Johnson, 2001). We ex- plore whether- pairs or evaluating our ability to do so (Charniak and Johnson, 2001). Moreover, this work showed

Lease, Matthew

56

The Frequency of DYT1 (GAG Deletion) Mutation in Primary Dystonia Patients from Iran  

E-Print Network [OSTI]

The Frequency of DYT1 (GAG Deletion) Mutation in Primary Dystonia Patients from Iran Mohammad Hamid. Molecular Medicine Division, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran 2. Medical Genetics Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran 3

Boyer, Edmond

57

Split Vertex Deletion meets Vertex Cover: New fixed-parameter and exact exponential-time algorithms  

Science Journals Connector (OSTI)

In the Split Vertex Deletion problem, given a graph G and an integer k, we ask whether one can delete k vertices from the graph G to obtain a split graph (i.e., a graph, whose vertex set can be partitioned into two sets: one inducing a clique and the second one inducing an independent set). In this paper we study exact (exponential-time) and fixed-parameter algorithms for Split Vertex Deletion. We show that, up to a factor quasipolynomial in k and polynomial in n, the Split Vertex Deletion problem can be solved in the same time as the well-studied Vertex Cover problem. By plugging in the currently best fixed-parameter algorithm for Vertex Cover due to Chen et al. [Theor. Comput. Sci. 411 (4042) (2010) 37363756], we obtain an algorithm that solves Split Vertex Deletion in time O ( 1.2738 k k O ( log k ) + n 3 ) . We show that all maximal induced split subgraphs of a given n-vertex graph can be listed in O ( 3 n / 3 n O ( log n ) ) time. To achieve our goals, we prove the following structural result that may be of independent interest: for any graph G we may compute a family P of size n O ( log n ) containing partitions of V ( G ) into two parts, such that for any two disjoint sets X C , X I ? V ( G ) where G [ X C ] is a clique and G [ X I ] is an independent set, there is a partition in P which contains all vertices of X C on one side and all vertices of X I on the other. Moreover, the family P can be enumerated in O ( n O ( log n ) ) time.

Marek Cygan; Marcin Pilipczuk

2013-01-01T23:59:59.000Z

58

Effect of GPD1 and GPD2 Deletion on the Production of Glycerol and Ethanol in the Yeast Saccharomyces cerevisiae  

Science Journals Connector (OSTI)

Glycerol is the main by-product in ethanol production during the very high gravity (VHG...Saccharomyces cerevisiae. This study investigates the effect of GPD1 or GPD...2 (encoding 3-phosphate dehydrogenase) delet...

Jingjing Yu; Jian Dong; Cuiying Zhang

2014-01-01T23:59:59.000Z

59

Skyrmions with low binding energies  

E-Print Network [OSTI]

Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ans\\"atze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

Gillard, Mike; Speight, Martin

2015-01-01T23:59:59.000Z

60

Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions  

SciTech Connect (OSTI)

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C(5) and C(6) sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of -xylosidase xylD slowed the growth of T. saccharolyticum on birchwood xylan and led to an accumulation of short-chain xylo-oligomers, no other single deletion, including the deletion of the previously characterized endoxylanase XynA, had a phenotype distinct from that of the wild type. This result indicates a multiplicity of xylanase enzymes which facilitate xylan degradation in T. saccharolyticum. Growth on xylan was prevented only when a previously uncharacterized endoxylanase encoded by xynC was also deleted in conjunction with xynA. Sequence analysis of xynC indicates that this enzyme, a low-molecular-weight endoxylanase with homology to glycoside hydrolase family 11 enzymes, is secreted yet untethered to the cell wall. Together, these observations expand our understanding of the enzymatic basis of xylan hydrolysis by T. saccharolyticum.

Podkaminer, Kara K [Thayer School of Engineering at Dartmouth; Guss, Adam M [ORNL; McKenzie, Heather [University of California, Riverside; Hogsett, David [Mascoma Corporation; Lynd, Lee R [Thayer School of Engineering at Dartmouth

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Erythropoietin binding protein from mammalian serum  

DOE Patents [OSTI]

Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

Clemons, G.K.

1997-04-29T23:59:59.000Z

62

Mutant ATP-binding RNA Aptamers Reveal the Structural Basis for Ligand Binding  

E-Print Network [OSTI]

Mutant ATP-binding RNA Aptamers Reveal the Structural Basis for Ligand Binding Thorsten Dieckmann1, Massachusetts General Hospital, Boston, MA 02114 USA The solution structure of the ATP-binding RNA aptamer has. The binding properties of ATP binder mutants and modi®ed ligand molecules are explored using NMR spectroscopy

Heller, Eric

63

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human  

E-Print Network [OSTI]

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across occupied by the insulator binding protein CTCF across the human genome. These nucleosomes are highly of CTCF function. Citation: Fu Y, Sinha M, Peterson CL, Weng Z (2008) The Insulator Binding Protein CTCF

Weng, Zhiping

64

Synthetic heparin-binding factor analogs  

DOE Patents [OSTI]

The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

Pena, Louis A. (Poquott, NY); Zamora, Paul O. (Gaithersburg, MD); Lin, Xinhua (Plainview, NY); Glass, John D. (Shoreham, NY)

2010-04-20T23:59:59.000Z

65

Atomic-binding-energy oscillations  

Science Journals Connector (OSTI)

We investigate the oscillatory supplement to the statistical nonrelativistic binding-energy formula for neutral atoms. The semiclassical approach proves capable of deriving these oscillations. It turns out that their amplitude is proportional to Z4/3 (Z is the number of electrons), and that their period is determined by the maximum angular momentum available in Thomas-Fermi atoms, i.e., 0.928Z1/3. Our calculation also provides an understanding of the peculiar shape of the oscillations, which show sharp minima and wide, structured maxima.

Berthold-Georg Englert and Julian Schwinger

1985-07-01T23:59:59.000Z

66

Binding of the Inhibitor Protein IF1 to Bovine F1-ATPase  

Science Journals Connector (OSTI)

In the structure of bovine F1-ATPase inhibited with residues 160 of the bovine inhibitor protein IF1, the ?-helical inhibitor interacts with five of the nine subunits of F1-ATPase. In order to understand the contributions of individual amino acid residues to this complex binding mode, N-terminal deletions and point mutations have been introduced, and the binding properties of each mutant inhibitor protein have been examined. The N-terminal region of IF1 destabilizes the interaction of the inhibitor with F1-ATPase and may assist in removing the inhibitor from its binding site when F1Fo-ATPase is making ATP. Binding energy is provided by hydrophobic interactions between residues in the long ?-helix of IF1 and the C-terminal domains of the ?DP-subunit and ?TP-subunit and a salt bridge between residue E30 in the inhibitor and residue R408 in the C-terminal domain of the ?DP-subunit. Several conserved charged amino acids in the long ?-helix of IF1 are also required for establishing inhibitory activity, but in the final inhibited state, they are not in contact with F1-ATPase and occupy aqueous cavities in F1-ATPase. They probably participate in the pathway from the initial interaction of the inhibitor and the enzyme to the final inhibited complex observed in the structure, in which two molecules of ATP are hydrolysed and the rotor of the enzyme turns through two 120 steps. These findings contribute to the fundamental understanding of how the inhibitor functions and to the design of new inhibitors for the systematic analysis of the catalytic cycle of the enzyme.

John V. Bason; Michael J. Runswick; Ian M. Fearnley; John E. Walker

2011-01-01T23:59:59.000Z

67

New Things For Windows 7 Old icons on the desktop that referenced Office 2007 applications will need to be deleted and  

E-Print Network [OSTI]

New Things For Windows 7 Old icons on the desktop that referenced Office 2007 applications will need to be deleted and replaced with icons for Office 2010. To do this, right click on the non-working icon and select delete or simply drag it to the Recycle Bin. To add the new icon, go to Start, then All

Bogaerts, Steven

68

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions  

Science Journals Connector (OSTI)

This 22q11 deletion patient was established to have a novel 2.3 Mb deletion with a proximal breakpoint located between genetic markers RH48663 and RH48348 and a distal breakpoint between markers D22S1138 and SHGC

Raihan K Uddin; Yang Zhang; Victoria Mok Siu; Yao-Shan Fan

2006-03-01T23:59:59.000Z

69

The hidden ties that bind | EMSL  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

hidden ties that bind EMSL advancements open new possibilities for characterizing nanoparticle interactions EMSL's sum-frequency generation vibrational spectrometer The Science...

70

Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules  

Science Journals Connector (OSTI)

......of hydrogen bonding in the interaction between a xylan binding module and xylan. Biochemistry (2001) 40:5700-5707. Yang...predicted ligand-binding residues residing on the surface in the hypothetical structures were verified to......

Wei-Yao Chou; Wei-I Chou; Tun-Wen Pai; Shu-Chuan Lin; Ting-Ying Jiang; Chuan-Yi Tang; Margaret Dah-Tsyr Chang

2010-04-15T23:59:59.000Z

71

Binding (or Cohesive) Energy Denition and Constraints  

E-Print Network [OSTI]

Binding (or Cohesive) Energy Denition and Constraints The binding or cohesive energy cof a substance (either liquid or solid) is the energy required to break all the bonds associated with one of its constituent molecules. It is, therefore a measure of the inter-molecular energy for a substance. We spend time

Nimmo, Francis

72

predictive information, multi-information, and binding  

E-Print Network [OSTI]

predictive information, multi-information, and binding information Samer Abdallah and Mark Plumbley.1 ­ December 9, 2010 Abstract We introduce an information theoretic measure of dependency between multiple random variables, called `binding information' and compare it with several previously proposed measures

Plumbley, Mark

73

Interstitial deletion of 8q21{yields}22 associated with minor anomalies, congenital heart defect, and Dandy-Walker variant  

SciTech Connect (OSTI)

We describe an infant with a deletion of 8q21{yields}22 who had distinct clinical manifestations including minor facial anomalies, a congenital heart defect, a Dandy-Walker variant, and mild to moderate developmental delay. Her facial characteristics included small, wide-spaced eyes, asymmetric bilateral epicanthal folds, a broad nasal bridge, a {open_quotes}carp-shaped{close_quotes} mouth, micrognathia, and prominent, apparently low-set ears. Three other reports describe children with larger proximal deletions of 8q that include 8q21 and q22. These four children all have similar facial appearance. Of the others reported, one had a congenital heart defect and one had craniosynostosis. This case, in addition to the previously noted three cases, helps in delineating a recognizable syndrome. 12 refs., 3 figs., 1 tab.

Donahue, M.L. [Medical Univ. of South Carolina, Charleston, SC (United States); Ryan, R.M. [Univ. of Rochester, NY (United States)

1995-03-13T23:59:59.000Z

74

Facile Dimer Synthesis for DNA-Binding Polyamide Ligands  

Science Journals Connector (OSTI)

Pyrrole-imidazole polyamide ligands are highly sequence specific synthetic DNA-binding ligands that bind with high affinity. ... Regulation of gene expression by synthetic DNA-binding ligands ...

Modi Wetzler; David E. Wemmer

2010-07-13T23:59:59.000Z

75

Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters  

E-Print Network [OSTI]

Evolutionary relationships of ATP-Binding Cassette (ABC)MH Jr: Membrane porters of ATP-binding cassette transportand exporters in the evolution of ATP-binding cassette (ABC)

Zheng, Wei Hao; Vstermark, ke; Shlykov, Maksim A; Reddy, Vamsee; Sun, Eric I; Saier, Milton H

2013-01-01T23:59:59.000Z

76

Single-Molecule Dynamics Reveals Cooperative Binding-Folding...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Abstract: The...

77

Coordinatively unsaturated Al3+ centers as binding sites for...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Coordinatively unsaturated Al3+ centers as binding sites for active catalyst phases on ?-Al2O3. Coordinatively unsaturated Al3+ centers as binding sites for active catalyst...

78

Final Report for the Account Creation/Deletion Reenginering Task for the Scientific Computing Department  

SciTech Connect (OSTI)

In October 2000, the personnel responsible for administration of the corporate computers managed by the Scientific Computing Department assembled to reengineer the process of creating and deleting users' computer accounts. Using the Carnegie Mellon Software Engineering Institute (SEI) Capability Maturity Model (CMM) for quality improvement process, the team performed the reengineering by way of process modeling, defining and measuring the maturity of the processes, per SEI and CMM practices. The computers residing in the classified environment are bound by security requirements of the Secure Classified Network (SCN) Security Plan. These security requirements delimited the scope of the project, specifically mandating validation of all user accounts on the central corporate computer systems. System administrators, in addition to their assigned responsibilities, were spending valuable hours performing the additional tacit responsibility of tracking user accountability for user-generated data. For example, in cases where the data originator was no longer an employee, the administrators were forced to spend considerable time and effort determining the appropriate management personnel to assume ownership or disposition of the former owner's data files. In order to prevent this sort of problem from occurring and to have a defined procedure in the event of an anomaly, the computer account management procedure was thoroughly reengineered, as detailed in this document. An automated procedure is now in place that is initiated and supplied data by central corporate processes certifying the integrity, timeliness and authentication of account holders and their management. Automated scripts identify when an account is about to expire, to preempt the problem of data becoming ''orphaned'' without a responsible ''owner'' on the system. The automated account-management procedure currently operates on and provides a standard process for all of the computers maintained by the Scientific Computing Department.

JENNINGS, BARBARA J.; MCALLISTER, PAULA L.

2002-04-01T23:59:59.000Z

79

Hardware device binding and mutual authentication  

DOE Patents [OSTI]

Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

Hamlet, Jason R; Pierson, Lyndon G

2014-03-04T23:59:59.000Z

80

Metal-binding polymesr as chelating agents  

E-Print Network [OSTI]

Abstract Metal chelating polymers are functional polymers that bear specified chemical groups capable of selectively binding metals. Heavy metal contamination is considered a serious problem because these metals, even at ...

Mohammadi, Zahra

2011-04-11T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Structural Basis for Metal Binding Specificity: the N-terminal Cadmium Binding Domain of the  

E-Print Network [OSTI]

In bacteria, P1-type ATPases are responsible for resistance to di- and monovalent toxic heavy metals by taking years and no common mechanism for resistance toward toxic heavy metals such as Cd(II), Zn(II), HgStructural Basis for Metal Binding Specificity: the N-terminal Cadmium Binding Domain of the P1

Scott, Robert A.

82

between ORC binding and nucleosome turnover, suggesting that turnover facilitates ORC binding.  

E-Print Network [OSTI]

between ORC binding and nucleosome turnover, suggesting that turnover facilitates ORC binding little if any de- pendence on ORC abundance (Fig. 3, H to P). Our findings support the hypothesis- titative correspondence of ORC to CATCH-IT data than to other chromatin measurements implies that the ORC

Pauly, Daniel

83

Predicting binding free energies in solution  

E-Print Network [OSTI]

Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also a...

Jensen, Jan H

2015-01-01T23:59:59.000Z

84

Homozygous deletions on the short arm of chromosome 9 in ovarian adenocarcinoma cell lines and loss of heterozygosity in sporadic tumors  

SciTech Connect (OSTI)

Rat ovarian surface epithelial cells transformed spontaneously in vitro have been found to have homozygous deletions of the interferon alpha (IFNA) gene. This suggests that inactivation of a tumor-suppressor gene in this region may be crucial for the development of ovarian cancer. The authors therefore used microsatellite markers and Southern analysis to examine the homologous region in humans - the short arm of chromosome 9 - for deletions in sporadic ovarian adenocarcinomas and ovarian tumor cell lines. Loss of heterozygosity occurred in 34 (37%) of 91 informative sporadic tumors, including some benign, low-malignant-potential and early-stage tumors, suggesting that it is an early event in the development of ovarian adenocarcinoma. Furthermore, homozygous deletions on 9p were found in 2 of 10 independent cell lines. Deletion mapping of the tumors and lines indicates that the candidate suppressor gene inactivated as a consequence lies between D9S171 and the IFNA locus, a region that is also deleted in several other tumors and that contains the melanoma predisposition gene, MLM. 52 refs., 4 figs., 1 tab.

Chenevix-Trench, G.; Kerr, J.; Hurst, T.; Sanderson, B.; Coglan, M.; Ward, B.; Khoo, S.K. (Univ. of Queensland, Brisbane (Australia)); Friedlander, M.; Leary, J.

1994-07-01T23:59:59.000Z

85

Structural Study of Lipid-binding Proteins  

E-Print Network [OSTI]

show stronger inhibition than the known inhibitor triclosan. The triclosan-like analogs with modification at the 5-position revealed a new binding site in PfENR that has great potential for improving the potency of inhibition. We found that two...

Tsai, Han-Chun

2013-08-09T23:59:59.000Z

86

Regulation of Gene Expression by Synthetic DNA-Binding Ligands  

E-Print Network [OSTI]

Regulation of Gene Expression by Synthetic DNA-Binding Ligands Peter B. Dervan ( ) · Adam T. Poulin

Dervan, Peter B.

87

Membrane porters of ATP-binding cassette transport systems are polyphyletic  

E-Print Network [OSTI]

in Membrane porters of ATP-binding cassette transportin Membrane porters of ATP-binding cassette transportin Membrane porters of ATP-binding cassette transport

Wang, Bin

2010-01-01T23:59:59.000Z

88

E-Print Network 3.0 - adiponectin retinol binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

retinol-binding protein 1; IRBP--interphotoreceptor retinoid-binding protein; LCA... Da protein; RBP--retinol-binding protein; RDH--retinol dehydrogenase Keywords:...

89

PATTERNS & PHENOTYPES ATP-Binding Cassette (ABC) Transporter  

E-Print Network [OSTI]

a PATTERNS & PHENOTYPES ATP-Binding Cassette (ABC) Transporter Expression and Localization in Sea Urchin Development Lauren E. Shipp and Amro Hamdoun* Background: ATP-binding cassette (ABC) transporters of polarized cells. Accepted 26 March 2012 INTRODUCTION ATP-binding cassette (ABC) trans- porters

90

Experimental study of exiton binding energy in semiconducting carbon nanotubes  

E-Print Network [OSTI]

Experimental study of exiton binding energy in semiconducting carbon nanotubes Nicolas Izard,1, 2 to the exciton binding energy of nanotubes. Electroabsorption is a powerfull technique which directly probe dimensional nanotube leads to strong electron-hole localiza- tion, with binding energy as high as 0.5 e

Maruyama, Shigeo

91

CCAAT/enhancer binding protein gene promoter: binding of nuclear factors during differentiation of 3T3-L1 preadipocytes.  

Science Journals Connector (OSTI)

...gene promoter: binding of nuclear factors during differentiation...these differentially expressed nuclear factors. The factor present...that play a central role in energy metabolism, particularly in...the differentiation- induced nuclear factor that binds specifically...

R J Christy; K H Kaestner; D E Geiman; M D Lane

1991-01-01T23:59:59.000Z

92

Respiratory Syncytial Virus Modified by Deletions of the NS2 Gene and Amino Acid S1313 of the L Polymerase Protein Is a Temperature-Sensitive, Live-Attenuated Vaccine Candidate That Is Phenotypically Stable at Physiological Temperature  

Science Journals Connector (OSTI)

...previously (38). Animal identification codes and vaccine virus are indicated on the...and (iv) the non-ts deletion of the NS2 gene. This resulted in 5 new cDNA-derived...and (ii) it bears the deletion of the NS2 protein, which is an antagonist of the...

Cindy Luongo; Christine C. Winter; Peter L. Collins; Ursula J. Buchholz

2012-12-12T23:59:59.000Z

93

Deletions of SKY1 or PTK2 in the Saccharomyces cerevisiae trk1Dtrk2D mutant cells exert dual effect on ion homeostasis  

E-Print Network [OSTI]

that regulate ion transport across the plasma membrane of Saccharomyces cerevisiae. We show here that deletion to spermine and salt ions. A model that integrates these results to explain the mechanism of ion transport on ion homeostasis Omri Erez and Chaim Kahana* Department of Molecular Genetics, Weizmann Institute

Kahana, Chaim

94

ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM DO BIOFUELS LIFE CYCLE  

E-Print Network [OSTI]

ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM 589 DO BIOFUELS LIFE CYCLE ANALYSES ACCURATELY QUANTIFY THE CLIMATE IMPACTS OF BIOFUELS-RELATED LAND USE CHANGE? Kristina J. Anderson in determining the sustainability of biofuels. To ensure that legal standards are effective in limiting climate

DeLucia, Evan H.

95

Identification of a Novel Homozygous Deletion Region at 6q23.1 in Medulloblastomas Using High-Resolution Array Comparative Genomic Hybridization Analysis  

Science Journals Connector (OSTI)

...homozygous deletion at 6q23.1 flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative reverse transcription-PCR...and flanked by the sequence-tagged site markers SHGC-13149 and SHGC-110551. B, quantitative reverse...

Angela B.Y. Hui; Hirokuni Takano; Kwok-Wai Lo; Wen-Lin Kuo; Cleo N.Y. Lam; Carol Y.K. Tong; Qing Chang; Joe W. Gray; Ho-Keung Ng

2005-07-01T23:59:59.000Z

96

Identification of a novel homozygous deletion region at 6q23.1 in medullobalstomas using high-resolution array CGH analysis  

Science Journals Connector (OSTI)

...markers confined a 0.887Mb minimal region of homozygous deletion at 6q23.1 which was flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative RT-PCR analysis showed complete loss of expression of 2 genes located...

Angela Bik-Yu Hui; Hirokuni Takano; Kwok Wai Lo; Wen Lin Kuo; Joe Gray; Ho Keung Ng

2005-05-01T23:59:59.000Z

97

Genetic deletion of Rnd3 results in aqueductal stenosis leading to hydrocephalus through up-regulation of Notch signaling  

Science Journals Connector (OSTI)

...signaling 10.1073/pnas.1219995110 Xi Lin Baohui Liu Xiangsheng Yang Xiaojing Yue...Huh MS Todd MA Picketts DJ ( 2009 ) SCO-ping out the mechanisms underlying the etiology of hydrocephalus...2853 2858 . 9 Riento K Guasch RM Garg R Jin B Ridley AJ ( 2003 ) RhoE binds to ROCK...

Xi Lin; Baohui Liu; Xiangsheng Yang; Xiaojing Yue; Lixia Diao; Jing Wang; Jiang Chang

2013-01-01T23:59:59.000Z

98

Synthetic DNA minor groove-binding drugs  

Science Journals Connector (OSTI)

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][1,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5?-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

B.S.Praveen Reddy; S.Murari Sondhi; J.William Lown

1999-01-01T23:59:59.000Z

99

JC3 Bulletin Archive | Department of Energy  

Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

June 7, 2013 V-173: Plesk 0-Day Vulnerability The vulnerability is caused due to PHP misconfiguration in the affected application June 6, 2013 V-172: ISC BIND RUNTIMECHECK...

100

Gene encoding herbicide safener binding protein  

DOE Patents [OSTI]

The cDNA encoding safener binding protein (SafBP), also referred to as SBP1, is set forth in FIG. 5 and SEQ ID No. 1. The deduced amino acid sequence is provided in FIG. 5 and SEQ ID No. 2. Methods of making and using SBP1 and SafBP to alter a plant's sensitivity to certain herbicides or a plant's responsiveness to certain safeners are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors and seeds from said plants.

Walton, Jonathan D. (East Lansing, MI); Scott-Craig, John S. (East Lansing, MI)

1999-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold  

Science Journals Connector (OSTI)

Two plant cytokinin-specific binding proteins were crystallized in complex with gibberellic acid (GA3), which is an entirely different plant hormone. The crystal structures, determined at high resolution, reveal a highly specific mode of GA3 binding, calling for a revision of the hormone specificity of plant proteins with the PR-10 fold.

Ruszkowski, M.

2014-06-29T23:59:59.000Z

102

Functionalized Polymers For Binding To Solutes In Aqueous Solutions  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. Available for thumbnail of Feynman Center (505) 665-9090 Email Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol

103

Hardware device to physical structure binding and authentication  

DOE Patents [OSTI]

Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

2013-08-20T23:59:59.000Z

104

Crown Ethers in Graphene Bring Strong, Selective Binding | ornl...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Materials Characterization Crown Ethers in Graphene Bring Strong, Selective Binding November 14, 2014 Schematic showing a graphene sheet containing an array of ideal crown ethers....

105

Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods P. Ganesh,* , Jeongnim Kim, Changwon...

106

Dissociative Binding of Carboxylic Acid Ligand on Nanoceria Surface...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Abstract: Carboxylic acid is a common ligand anchoring group to functionalize nanoparticle surfaces. Its binding structures and mechanisms as a function of the oxidation...

107

Crown Ethers Flatten in Graphene for Strong, Specific Binding...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Crown Ethers Flatten in Graphene for Strong, Specific Binding ORNL discovery holds potential for separations, sensors, batteries, biotech and more This sheet of graphene contains...

108

Biophysical Studies of Protein Folding and Binding Stability.  

E-Print Network [OSTI]

?? Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent (more)

Batra, Jyotica

2009-01-01T23:59:59.000Z

109

Designing artificial metal binding peptides | Center for Bio...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Designing artificial metal binding peptides 24 Oct 2012 Dong Wang is a graduate student in the Department of Chemistry and Biochemistry at Arizona State University. He is working...

110

Method and apparatus for detecting chemical binding  

DOE Patents [OSTI]

The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Miller, Thomasin C. (Los Alamos, NM); Wells, Cyndi A. (Los Alamos, NM)

2007-07-10T23:59:59.000Z

111

Triton binding energy with realistic precision  

E-Print Network [OSTI]

We compute the binding energy of triton with realistic statistical errors stemming from NN scattering data uncertainties and the deuteron and obtain $E_t=-7.638(15) \\, {\\rm MeV}$. Setting the numerical precision as $\\Delta E_t^{\\rm num} \\lesssim 1 \\, {\\rm keV}$ we obtain the statistical error $\\Delta E_t^{\\rm stat}= 15(1) \\, {\\rm keV}$ which is mainly determined by the channels involving relative S-waves. This figure reflects the uncertainty of the input NN data, more than two orders of magnitude larger than the experimental precision $\\Delta E_t^{\\rm exp}= 0.1 \\, {\\rm keV}$ and provides a bottleneck in the realistic precision that can be reached. This suggests an important reduction in the numerical precision and hence in the computational effort.

R. Navarro Perez; E. Garrido; J. E. Amaro; E. Ruiz Arriola

2014-07-29T23:59:59.000Z

112

Distal 8p deletion (8) (p23.1): An easily missed chromosomal abnormality that may be associated with congenital heart defect and mental retardation  

SciTech Connect (OSTI)

We describe the clinical manifestations and molecular cytogenetic analyses of three patients with a similar distal deletion of chromosome 8. Each child had mild developmental delay and subtle minor anomalies. Two had cardiac anomalies but no other major congenital anomalies were present. High resolution G and R banding showed in all three patients del(8)(p23.1), but the breakpoint in case 1 was distal to 8p23.1, in case 2 was in the middle of 8p23.1, and in case 3 proximal to 8p23.1. Fluorescence in situ hybridization (FISH) studies with a chromosome 8 paint probe confirmed that no other rearrangement had occurred. FISH with a chromosome 8-specific telomere probe indicated that two patients had terminal deletions. Chromosome analysis of the parents of case 1 and mother of case 2 were normal; the remaining parents were not available for study. Thirteen individual patients including the three in this study, and three relatives in one family with del(8)(p23.1), have been reported in the past 5 years. Major congenital anomalies, especially congenital heart defects, are most often associated with a breakpoint proximal to 8p23.1. Three patients were found within a 3-year period in this study and five cases were found within 4 years by another group, indicating that distal 8p deletion might be a relatively common chromosomal abnormality. This small deletion is easily overlooked (i.e., cases 1 and 2 were reported as normal at amniocentesis) and can be associated with few or no major congenital anomalies. 31 refs., 4 figs., 2 tabs.

Wu, Bai-Lin; Schneider, G.H.; Sabatino, D.E. [Harvard Medical School, Boston, MA (United States)] [and others] [Harvard Medical School, Boston, MA (United States); and others

1996-03-01T23:59:59.000Z

113

Architecture of a Fur Binding Site: a Comparative Analysis  

Science Journals Connector (OSTI)

...configuration). Although Fur can bind synthetic DNA sequences containing the F-F-F...the ability of Fur to recognize synthetic DNA sequences containing two to four...The ability of Fur to bind synthetic DNA fragments containing one to five...

Jennifer L. Lavrrar; Mark A. McIntosh

2003-04-01T23:59:59.000Z

114

Binding of Nucleobases with Single-Walled Carbon Nanotubes  

E-Print Network [OSTI]

We have calculated the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotubes (SWNTs) using ab-initio Hartre-Fock method (HF) together with force field calculations. The gas phase binding energies follow the sequence G $>$ A $>$ T $>$ C. We show that main contribution to binding energy comes from van-der Wall (vdW) interaction between nanotube and nucleobases. We compare these results with the interaction of nucleobases with graphene. We show that the binding energy of bases with SWNTs is much lower than the graphene but the sequence remains same. When we include the effect of solvation energy (Poisson-Boltzman (PB) solver at HF level), the binding energy follow the sequence G $>$ T $>$ A $>$ C $>$, which explains the experiment\\cite{zheng} that oligonucleotides made of thymine bases are more effective in dispersing the SWNT in aqueous solution as compared to poly (A) and poly (C). We also demonstrate experimentally that there is differential binding affinity of nucleobases with the single-walled carbon nanotubes (SWNTs) by directly measuring the binding strength using isothermal titration (micro) calorimetry. The binding sequence of the nucleobases varies as thymine (T) $>$ adenine (A) $>$ cytosine (C), in agreement with our calculation.

Anindya Das; A. K. Sood; Prabal K. Maiti; Mili Das; R. Varadarajan; C. N. R. Rao

2007-09-19T23:59:59.000Z

115

Molecular Mechanisms of Calcium and Magnesium Binding to Parvalbumin  

E-Print Network [OSTI]

between the coordinating residues of the EF-hand calcium binding loop of parvalbumin and the overallMolecular Mechanisms of Calcium and Magnesium Binding to Parvalbumin M. Susan Cates, Miguel L at EF loop position 12 results in a dramatically less tightly bound monodentate Ca2 coordination

Phillips, George N. Jr.

116

Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang*  

E-Print Network [OSTI]

Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang* Department of Biochemistry, University of Zurich, Zurich, Switzerland Abstract Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change

Caflisch, Amedeo

117

Synthesis and Characterization of Polyamine Bicycles for Anion Binding  

E-Print Network [OSTI]

. Binding studies and crystal structures are discussed within. Structural aspects of the binding of halides in the p-xylyl octaaza cryptand [1,4,11,14,17,24,29,36-octa-azapentacyclo [12.12.12.26,9.219,22.231,34]-tetratetraconta-6 (43), 7,9(44), 19(41), 20...

Morehouse, Paula Kay

2007-10-09T23:59:59.000Z

118

Unexpected Nondissociative Binding of N2O on Oxygen Vacancies...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Nondissociative Binding of N2O on Oxygen Vacancies on a Rutile TiO2(110)-11 . Unexpected Nondissociative Binding of N2O on Oxygen Vacancies on a Rutile TiO2(110)-11 ....

119

BPA FINAL Binding Arbitration policy | Department of Energy  

Broader source: Energy.gov (indexed) [DOE]

BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited

120

Disordered binding of small molecules to A12-28 DISORDERED BINDING OF SMALL MOLECULES TO A12-28  

E-Print Network [OSTI]

.vitalis@bioc.uzh.ch. Keywords: Alzheimer's disease; intrinsically disordered proteins; molecular dynamics; protein aggregation of Alzheimer's amyloid- protein in subtle but complex fashion. Conclusion: Intrinsic disorder of diseaseDisordered binding of small molecules to A12-28 DISORDERED BINDING OF SMALL MOLECULES TO A12

Caflisch, Amedeo

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Characterization of the ATP-Binding Domain of the Sarco(endo)plasmic Reticulum -ATPase: Probing Nucleotide Binding by Multidimensional NMR  

E-Print Network [OSTI]

Characterization of the ATP-Binding Domain of the Sarco(endo)plasmic Reticulum Ca2+ -ATPase cycle catalyzed by SERCA1a, we have studied the ATP-binding domain of SERCA1a in both nucleotide containing the nucleotide-binding domain of SERCA1a spanning residues Thr357-Leu600. ATP binding activity

Ikura, Mitsuhiko

122

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain  

E-Print Network [OSTI]

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa IIb xylan-binding domain 1 (XBD1) from Cellulomonas fimi xylanase D is shown to bind xylan of two four-stranded sheets that form a twisted ` sandwich'. The xylan-binding site is a groove made

Williamson, Mike P.

123

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes  

SciTech Connect (OSTI)

Cellulases hydrolyze {beta}-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.

Bu, L.; Nimlos, M. R.; Shirts, M. R.; Stahlberg, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

2012-07-13T23:59:59.000Z

124

XAS and Pulsed EPR Studies of the Copper Binding Site in Riboflavin Binding Protein  

SciTech Connect (OSTI)

Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 Angstroms, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a CuO3N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

Smith,S.; Bencze, K.; Wasiukanis, K.; Benore-Parsons, T.; Stemmler, T.

2008-01-01T23:59:59.000Z

125

The distal 8p deletion (8)(p23.1): A common syndrome associated with cogenital heart defect and mental retardation?  

SciTech Connect (OSTI)

We describe the clinical manifestations and molecular cytogenetic analysis of three patients with a similar distal deletion: del(8)(p23.1). Case 1: A nine-year-old girl who was the product of a normal pregnancy, with family history of recurrent miscarriages. She has an ASD, development delay and dysmorphic features. Case 2: A three-month-old female who died with a hypoplastic left heart and dysmorphic features. Her non-identical twin sister is healthy. No further family history is available. Case 3: A four-year-old boy who was the product of a normal pregnancy with family history of mental retardation. He has bifid uvula, delayed speech and language, and no major malformations or dysmorphic features. High resolution G and R banding revealed in all three patients del(8)(p23.1), but the breakpoint for case 1 and 2 was proximal to 8p23.1 and for case 3 distal to 8p23.1. FISH studies with a chromosome 8 paint probe confirmed that no other rearrangement was involved. Chromosome analysis of the parents of case 3 and mother of case 1 were normal; the remaining parents were not available for study. Eight individual patients and three members in one family with del(8)(p23.1) have been reported in the past five years. Major congenital anomalies, especially congenital heart defect, is most often associated with a breakpoint proximal to 8p23.1 Three patients were detected within a three year period in this study and five cases were found within a four year period by another group, suggesting that the distal 8p deletion may be a relatively common syndrome. This small deletion is easily overlooked (i.e. case 1 and 3 were reported as normal at amniocentesis) and can be associated with few or no major congenital anomalies.

Wu, B.L.; Schneider, G.H.; Sabatino, D.E. [Harvard Medical School, Boston, MA (United States)] [and others

1994-09-01T23:59:59.000Z

126

E-Print Network 3.0 - alix binding requirements Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

alix binding requirements Search Powered by Explorit Topic List Advanced Search Sample search results for: alix binding requirements Page: << < 1 2 3 4 5 > >> 1 3025Commentary...

127

Membrane Porters of ATP-Binding Cassette Transport Systems Are Polyphyletic  

E-Print Network [OSTI]

REVIEW Membrane Porters of ATP-Binding Cassette Transportat Springerlink.com Abstract The ATP-binding cassette (ABC)classi?ed according to the ATP hydrolyzing constituents,

Wang, Bin; Dukarevich, Maxim; Sun, Eric I.; Yen, Ming Ren; Saier, Milton H.

2009-01-01T23:59:59.000Z

128

E-Print Network 3.0 - affect stability binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

2011 Summer Research Program Summary: configuration. The annealing of the two primer binding site regions may: 1) Provide greater stability... of the primer binding sites...

129

E-Print Network 3.0 - active maltose-binding fusion Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

a Summary: . Keywords: Fusion protein; inclusion bodies; maltose-binding protein; protein folding; solubility; aggre... - gation Escherichia coli maltose-binding protein (MBP) is...

130

E-Print Network 3.0 - antithrombin iii binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

binding studies with low-affinity heparin... and a heparin tetrasaccharide suggest that PAA binds antithrombin in both the pentasaccharide- and the extended... weight; nd ) not...

131

E-Print Network 3.0 - adhesive binding mechanism Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

binding mechanism Page: << < 1 2 3 4 5 > >> 1 IOWA STATE UNIVERSITY DEPARTMENT OF MECHANICAL ENGINEERING Summary: in metastatic cancers. Adhesion is initiated by the binding of...

132

Regulation of Gene Expression by Synthetic DNA-Binding Ligands  

Science Journals Connector (OSTI)

During the past 20 years, polyamides have evolved from the natural product distamycin to a new class of programmable heterocyclic oligomers that bind a broad repertoire of DNA sequences with high affinity and ...

Peter B. Dervan; Adam T. Poulin-Kerstien

2005-01-01T23:59:59.000Z

133

Visually Relating Gene Expression and in vivo DNA Binding Data  

SciTech Connect (OSTI)

Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.

Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

2011-09-20T23:59:59.000Z

134

Synthesis Dependent Core Level Binding Energy Shift in the Oxidation...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Energy Shift in the Oxidation State ofPlatinum Coated on CeriaTitania and its Synthesis Dependent Core Level Binding Energy Shift in the Oxidation State ofPlatinum Coated...

135

Lighting Up Individual DNA Binding Proteins with Quantum Dots  

Science Journals Connector (OSTI)

Lighting Up Individual DNA Binding Proteins with Quantum Dots ... Department of Chemistry and Biochemistry, DOE Institute for Genomics and Proteomics, and Department of Physiology, Geffen Medical School, UCLA, Los Angeles, California 90095 ...

Yuval Ebenstein; Natalie Gassman; Soohong Kim; Josh Antelman; Younggyu Kim; Sam Ho; Robin Samuel; Xavier Michalet; Shimon Weiss

2009-03-16T23:59:59.000Z

136

Binding Graphene Sheets Together Using Silicon: Graphene/Silicon Superlattice  

Science Journals Connector (OSTI)

We propose a superlattice consisting of graphene and monolayer thick Si sheets and investigate ... not only strengthen the interlayer binding between the graphene sheets compared to that in graphite, but also inj...

Yong Zhang; Raphael Tsu

2010-05-01T23:59:59.000Z

137

Disordered binding regions of Ewings sarcoma fusion proteins  

Science Journals Connector (OSTI)

A relationship was found between the amino acid (AA) composition, intrinsic protein disorder (IPD) and protein binding regions (PBRs) of the functional regions of Ewings sarcoma protein (EWS) and oncogenic EWS f...

R. Todorova

2014-01-01T23:59:59.000Z

138

A binding energy in light hyperfragments (A?16)  

Science Journals Connector (OSTI)

? binding energy values of 103 uniquely identified mesonic hyperfragments, produced by the interactions of K?-mesons at rest and at momentum 1.5 GeV/c with emulsion nuclei, are presented. One of the events is a ...

B. Bhowmik; T. Chand; D. V. Chopra

1969-02-01T23:59:59.000Z

139

Molecular Binding Energies from Partition Density Functional Theory  

SciTech Connect (OSTI)

Approximate molecular calculations via standard Kohn-Sham density functional theory are exactly reproduced by performing self-consistent calculations on isolated fragments via partition density functional theory [P. Elliott, K. Burke, M. H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010)]. We illustrate this with the binding curves of small diatomic molecules. We find that partition energies are in all cases qualitatively similar and numerically close to actual binding energies. We discuss qualitative features of the associated partition potentials.

Nafziger, J.; Wu, Q.; Wasserman, A.

2011-12-21T23:59:59.000Z

140

Fatty acid-binding protein in bovine skeletal muscle  

E-Print Network [OSTI]

FATTY ACID-BINDING PROTEIN IN BOVINE SKELETAL MUSCLE A Thesis by KIMBERLY KIRBY MOORE Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE... December 1989 Major Subject: Nutrition FATTY ACID-BINDING PROTEIN IN BOVINE SKELETAL MUSCLE A Thesis by KIMBERLY KIRBY MOORE Approved as to style and content by: Ste en B. Smith (Chair of Committee) Karen S. Kubena (Member) Gary C. Smith (Head...

Moore, Kimberly Kirby

2012-06-07T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

NEM modication prevents high-anity ATP binding to the rst nucleotide binding fold of the sulphonylurea receptor, SUR1  

E-Print Network [OSTI]

NEM modi¢cation prevents high-a¤nity ATP binding to the ¢rst nucleotide binding fold, UK Received 7 July 1999; received in revised form 11 August 1999 Abstract Pancreatic LL-cell ATP WWM 8-azido- [KK-32 P]ATP or 8-azido-[QQ-32 P]ATP was inhibited by NEM with Ki of 1.8 WWM and 2.4 WWM

Tucker, Stephen J.

142

Impact on the steam electric power industry of deleting Section 316(a) of the Clean Water Act: Energy and environmental impacts  

SciTech Connect (OSTI)

Many power plants discharge large volumes of cooling water. In some cases, the temperature of the discharge exceeds state thermal requirements. Section 316(a) of the Clean Water Act (CWA) allows a thermal discharger to demonstrate that less stringent thermal effluent limitations would still protect aquatic life. About 32% of the total steam electric generating capacity in the United States operates under Section 316(a) variances. In 1991, the US Senate proposed legislation that would delete Section 316(a) from the CWA. This study, presented in two companion reports, examines how this legislation would affect the steam electric power industry. This report quantitatively and qualitatively evaluates the energy and environmental impacts of deleting the variance. No evidence exists that Section 316(a) variances have caused any widespread environmental problems. Conversion from once-through cooling to cooling towers would result in a loss of plant output of 14.7-23.7 billion kilowatt-hours. The cost to make up the lost energy is estimated at $12.8-$23.7 billion (in 1992 dollars). Conversion to cooling towers would increase emission of pollutants to the atmosphere and water loss through evaporation. The second report describes alternatives available to plants that currently operate under the variance and estimates the national cost of implementing such alternatives. Little justification has been found for removing the 316(a) variance from the CWA.

Veil, J.A.; VanKuiken, J.C.; Folga, S.; Gillette, J.L.

1993-01-01T23:59:59.000Z

143

A novel inactivated gE/gI deleted pseudorabies virus (PRV) vaccine completely protects pigs from an emerged variant PRV challenge  

Science Journals Connector (OSTI)

Abstract A highly virulent and antigenic variant of pseudorabies virus (PRV) broke out in China at the end of 2011 and caused great economic loss in the pig industry. In this study, an infectious bacterial artificial chromosome (BAC) clone containing the full-length genome of the emerged variant PRV ZJ01 strain was generated. The BAC-derived viruses, vZJ01-GFP?gE/gI (gE/gI deleted strain, and exhibiting green autofluorescence), vZJ01?gE/gI (gE/gI deleted strain), and vZJ01gE/gI-R (gE/gI revertant strain), showed similar in vitro growth to their parent strain. In pigs, inactivated vZJ01?gE/gI vaccine generated significantly high levels of neutralizing antibodies against ZJ01 compared with Bartha-K61 live vaccine (p<0.05). After fatal ZJ01 challenge, all five animals in the inactivated vZJ01?gE/gI vaccine group survived without exhibiting any clinical sings, but two of five animals exhibited central nervous signs in the Bartha-K61 group. Meanwhile, all the non-vaccinated control animals died at 7 days post-challenge. This indicates that the inactivated vZJ01?gE/gI vaccine is a promising vaccine candidate for controlling the variant strains of PRV now circulating in China.

Zhenqing Gu; Jing Dong; Jichun Wang; Chengcai Hou; Haifeng Sun; Wenping Yang; Juan Bai; Ping Jiang

2015-01-01T23:59:59.000Z

144

Targeted Gene Deletion Demonstrates that Cell Adhesion MoleculeICAM-4 is Critical for Erythroblastic Island Formation  

SciTech Connect (OSTI)

Erythroid progenitors differentiate in erythroblastic islands, bone marrow niches composed of erythroblasts surrounding a central macrophage. Evidence suggests that within islands adhesive interactions regulate erythropoiesis and apoptosis. We are exploring whether erythroid intercellular adhesion molecule-4 (ICAM-4), animmunoglobulin superfamily member, participates in island formation. Earlier, we identified alpha V integrins as ICAM-4 counter receptors. Since macrophages express alpha V, ICAM-4 potentially mediates island attachments. To test this, we generated ICAM-4 knockout mice and developed quantitative, live cell techniques for harvesting intact islands and for reforming islands in vitro. We observed a 47 percent decrease in islands reconstituted from ICAM-4 null marrow compared to wild type. We also found a striking decrease in islands formed in vivo in knockout mice. Further, peptides that block ICAM-4 alpha V adhesion produced a 53-57 percent decrease in reconstituted islands, strongly suggesting that ICAM-4 binding to macrophage alpha V functions in island integrity. Importantly, we documented that alpha V integrin is expressed in macrophages isolated from erythro blastic islands. Collectively, these data provide convincing evidence that ICAM-4 is critical in erythroblastic island formation via ICAM-4/alpha V adhesion and also demonstrate that the novel experimental strategies we developed will be valuable in exploring molecular mechanisms of erythroblastic island formation and their functional role in regulating erythropoiesis.

Lee, Gloria; Lo, Annie; Short, Sarah A.; Mankelow, Tosti J.; Spring, Frances; Parsons, Stephen F.; Mohandas, Narla; Anstee, David J.; Chasis, Joel Anne

2006-02-15T23:59:59.000Z

145

Triclosan-Loaded Tooth-Binding Micelles for Prevention and Treatment of Dental Biofilm  

Science Journals Connector (OSTI)

To develop tooth-binding micelle formulations of triclosan for the prevention and treatment of dental...

Fu Chen; Kelly C. Rice; Xin-Ming Liu; Richard A. Reinhardt

2010-11-01T23:59:59.000Z

146

ORIGINAL PAPER A bacterial ice-binding protein from the Vostok ice core  

E-Print Network [OSTI]

to produce a 54 kDa ice-binding protein (GenBank EU694412) that is similar to ice-binding proteins previously- vival at sub-zero temperatures by producing proteins that bind to and inhibit the growth of ice crystalsORIGINAL PAPER A bacterial ice-binding protein from the Vostok ice core James A. Raymond ? Brent C

Christner, Brent C.

147

1 Copyright 2012 by ASME Proceedings of the ASME/ISCE International Symposium on Flexible Automation  

E-Print Network [OSTI]

, USA ABSTRACT The popularity of forklifts that use fuel cells based on proton exchange membranes (PEMs designed for PEM forklifts tend to have lower material-handling costs, improved closeness ratings Automation ISFA12 June 18-20, 2012, St. Louis, MO, USA ISFA2012-7116 IMPACT OF USING PEM FORKLIFTS

Gosavi, Abhijit

148

Using ISC & GIS to predict sulfur deposition from coal-fired power plants  

E-Print Network [OSTI]

The goal of this research project was to determine if atmospheric sources have the potential of contributing significantly to the sulfur content of grazed forage. Sulfur deposition resulting from sulfur dioxide emissions from coal- fired power...

Lopez, Jose Ignacio

2012-06-07T23:59:59.000Z

149

Characterization of salivary alpha-amylase binding to Streptococcus sanguis  

SciTech Connect (OSTI)

The purpose of this study was to identify the major salivary components which interact with oral bacteria and to determine the mechanism(s) responsible for their binding to the bacterial surface. Strains of Streptococcus sanguis, Streptococcus mitis, Streptococcus mutans, and Actinomyces viscosus were incubated for 2 h in freshly collected human submandibular-sublingual saliva (HSMSL) or parotid saliva (HPS), and bound salivary components were eluted with 2% sodium dodecyl sulfate. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western transfer, alpha-amylase was the prominent salivary component eluted from S. sanguis. Studies with {sup 125}I-labeled HSMSL or {sup 125}I-labeled HPS also demonstrated a component with an electrophoretic mobility identical to that of alpha-amylase which bound to S. sanguis. Purified alpha-amylase from human parotid saliva was radiolabeled and found to bind to strains of S. sanguis genotypes 1 and 3 and S. mitis genotype 2, but not to strains of other species of oral bacteria. Binding of ({sup 125}I)alpha-amylase to streptococci was saturable, calcium independent, and inhibitable by excess unlabeled alpha-amylases from a variety of sources, but not by secretory immunoglobulin A and the proline-rich glycoprotein from HPS. Reduced and alkylated alpha-amylase lost enzymatic and bacterial binding activities. Binding was inhibited by incubation with maltotriose, maltooligosaccharides, limit dextrins, and starch.

Scannapieco, F.A.; Bergey, E.J.; Reddy, M.S.; Levine, M.J. (State Univ. of New York, Buffalo (USA))

1989-09-01T23:59:59.000Z

150

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

Broader source: Energy.gov (indexed) [DOE]

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

151

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

Broader source: Energy.gov (indexed) [DOE]

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

152

T-cadherin structures reveal a novel adhesive binding mechanism  

SciTech Connect (OSTI)

Vertebrate genomes encode 19 classical cadherins and about 100 nonclassical cadherins. Adhesion by classical cadherins depends on binding interactions in their N-terminal EC1 domains, which swap N-terminal {beta}-strands between partner molecules from apposing cells. However, strand-swapping sequence signatures are absent from nonclassical cadherins, raising the question of how these proteins function in adhesion. Here, we show that T-cadherin, a glycosylphosphatidylinositol (GPI)-anchored cadherin, forms dimers through an alternative nonswapped interface near the EC1-EC2 calcium-binding sites. Mutations within this interface ablate the adhesive capacity of T-cadherin. These nonadhesive T-cadherin mutants also lose the ability to regulate neurite outgrowth from T-cadherin-expressing neurons. Our findings reveal the likely molecular architecture of the T-cadherin homophilic interface and its requirement for axon outgrowth regulation. The adhesive binding mode used by T-cadherin may also be used by other nonclassical cadherins

Ciatto, Carlo; Bahna, Fabiana; Zampieri, Niccol; VanSteenhouse, Harper C.; Katsamba, Phini S; Ahlsen, Goran; Harrison, Oliver J.; Brasch, Julia; Jin, Xiangshu; Posy, Shoshana; Vendome, Jeremie; Ranscht, Barbara; Jessell, Thomas M.; Honig, Barry; Shapiro, Lawrence (Columbia); (Burnham)

2010-03-30T23:59:59.000Z

153

Accurate nuclear radii and binding energies from a chiral interaction  

E-Print Network [OSTI]

The accurate reproduction of nuclear radii and binding energies is a long-standing challenge in nuclear theory. To address this problem two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective 3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

Ekstrom, A; Wendt, K A; Hagen, G; Papenbrock, T; Carlsson, B D; Forssen, C; Hjorth-Jensen, M; Navratil, P; Nazarewicz, W

2015-01-01T23:59:59.000Z

154

Orientation-dependent binding energy of graphene on palladium  

SciTech Connect (OSTI)

Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

Kappes, Branden B.; Ebnonnasir, Abbas; Ciobanu, Cristian V. [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States)] [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States); Kodambaka, Suneel [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)] [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)

2013-02-04T23:59:59.000Z

155

Binding Energy of a ? Particle in Nuclear Matter  

Science Journals Connector (OSTI)

The binding energy of a ? particle in nuclear matter, B?(?), is calculated using a ?-nucleon two-body potential with a hard core, which reproduces the binding energies of light hypernuclei and the ?-nucleon scattering at intermediate energies. The simplified version of the Brueckner theory used in previous calculations is applied. The effective mass of the ? particle, M?*, is estimated to be about 0.9M?. The rearrangement energy is included in the calculation. The result obtained, B?(?)?31 MeV, is in good agreement with the measured value.

Janusz Dabrowski and H. S. Khler

1964-10-12T23:59:59.000Z

156

Invisibility in non-Hermitian tight-binding lattices  

E-Print Network [OSTI]

Reflectionless defects in Hermitian tight-binding lattices, synthesized by the intertwining operator technique of supersymmetric quantum mechanics, are generally not invisible and time-of-flight measurements could reveal the existence of the defects. Here it is shown that, in a certain class of non-Hermitian tight-binding lattices with complex hopping amplitudes, defects in the lattice can appear fully invisible to an outside observer. The synthesized non-Hermitian lattices with invisible defects possess a real-valued energy spectrum, however they lack of parity-time (PT) symmetry, which does not play any role in the present work.

Stefano Longhi

2010-08-31T23:59:59.000Z

157

Identification of peptides that bind to irradiated pancreatic tumor cells  

SciTech Connect (OSTI)

Purpose: Peptides targeting tumor vascular cells or tumor cells themselves have the potential to be used as vectors for delivering either DNA in gene therapy or antitumor agents in chemotherapy. We wished to determine if peptides identified by phage display could be used to target irradiated pancreatic cancer cells. Methods and Materials: Irradiated Capan-2 cells were incubated with 5 x 10{sup 12} plaque-forming units of a phage display library. Internalized phage were recovered and absorbed against unirradiated cells. After five such cycles of enrichment, the recovered phage were subjected to DNA sequencing analysis and synthetic peptides made. The binding of both phage and synthetic peptides was evaluated by fluorescence staining and flow cytometry in vitro and in vivo. Results: We identified one 12-mer peptide (PA1) that binds to irradiated Capan-2 pancreatic adenocarcinoma cells but not to unirradiated cells. The binding of peptide was significant after 48 h incubation with cells. In vivo experiments with Capan-2 xenografts in nude mice demonstrated that these small peptides are able to penetrate tumor tissue after intravenous injections and bind specifically to irradiated tumor cells. Conclusion: These data suggest that peptides can be identified that target tumors with radiation-induced cell markers and may be clinically useful.

Huang Canhui [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Liu, Xiang Y. [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Rehemtulla, Alnawaz [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Lawrence, Theodore S. [Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States)]. E-mail: tsl@med.umich.edu

2005-08-01T23:59:59.000Z

158

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis  

SciTech Connect (OSTI)

The annotation of protein function is almost completely performed by in silico approaches. However, computational prediction of protein function is frequently incomplete and error prone. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins. This lack of functional information severely limits our understanding of Mtb pathogenicity. Current tools for experimental functional annotation are limited and often do not scale to entire protein families. Here, we report a generally applicable chemical biology platform to functionally annotate bacterial proteins by combining activity-based protein profiling (ABPP) and quantitative LC-MS-based proteomics. As an example of this approach for high-throughput protein functional validation and discovery, we experimentally annotate the families of ATP-binding proteins in Mtb. Our data experimentally validate prior in silico predictions of >250 ATPases and adenosine nucleotide-binding proteins, and reveal 73 hypothetical proteins as novel ATP-binding proteins. We identify adenosine cofactor interactions with many hypothetical proteins containing a diversity of unrelated sequences, providing a new and expanded view of adenosine nucleotide binding in Mtb. Furthermore, many of these hypothetical proteins are both unique to Mycobacteria and essential for infection, suggesting specialized functions in mycobacterial physiology and pathogenicity. Thus, we provide a generally applicable approach for high throughput protein function discovery and validation, and highlight several ways in which application of activity-based proteomics data can improve the quality of functional annotations to facilitate novel biological insights.

Ansong, Charles; Ortega, Corrie; Payne, Samuel H.; Haft, Daniel H.; Chauvigne-Hines, Lacie M.; Lewis, Michael P.; Ollodart, Anja R.; Purvine, Samuel O.; Shukla, Anil K.; Fortuin, Suereta; Smith, Richard D.; Adkins, Joshua N.; Grundner, Christoph; Wright, Aaron T.

2013-01-24T23:59:59.000Z

159

Supplemental Data Directed Evolution of ATP Binding Proteins  

E-Print Network [OSTI]

Supplemental Data Directed Evolution of ATP Binding Proteins from a Zinc Finger Domain Using m TG 3'). Denaturing Ni-NTA was performed on the ATP-column elution for round 2, and then FLAG with the resin, but instead passed directly over the immobilized ATP. The selection was performed at room

Heller, Eric

160

Molecular Cell High-Affinity Binding of Chp1 Chromodomain  

E-Print Network [OSTI]

Molecular Cell Article High-Affinity Binding of Chp1 Chromodomain to K9 Methylated Histone H3, Chp1, and siRNAs derived from centro- meric repeats. Recruitment of RITS to centromeres has been establishment. Our crystal structure of Chp1's chromodomain in complex with a trimethylated lysine 9 H3 peptide

Halazonetis, Thanos

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Similarity of Position Frequency Matrices for Transcription Factor Binding Sites  

E-Print Network [OSTI]

approximating the binding energy of the profiled transcription factor. Comparison tools for TFBS PFMs: Software is available to use over the web at http://rulai.cshl.edu/MatCompare Contact: dschones, sumazin to the average log likelihood ratio method and the Pearson correlation coef- ficient method on simulated data

162

Functional implications of multistage copper binding to the prion protein  

Science Journals Connector (OSTI)

...and Wells et al. (26). These workers proposed similar models of Cu 2+ binding...previous work (23) as well as by other workers (24). Using insights from these studies, we now analyze the...Center for Computational Sciences at Oak Ridge National Laboratory. The authors...

Miroslav Hodak; Robin Chisnell; Wenchang Lu; J. Bernholc

2009-01-01T23:59:59.000Z

163

Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites  

E-Print Network [OSTI]

Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites Justin H Ruoslahtifg and Sangeeta N. Bhatia*ah The success of nanoparticle-based cancer therapies ultimately depends on their ability to selectively and efficiently accumulate in regions of disease. Outfitting nanoparticles

Bhatia, Sangeeta

164

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

DNA-Binding Mechanism in DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere site (parS) on the plasmid DNA and two proteins, ParA and ParB. The initial formation of the so-called partition complex between ParB and the centromere is a critical step in partition. To understand the DNA-binding mechanism utilized by ParB, Schumacher and Funnell determined crystal structures of the C-terminal region of ParB, known as ParB(142-333), bound to centromere sites.

165

Computer Forensics: you can hide but you canComputer Forensics: you can hide but you can''t deletet delete Dr. Nazli Hardy, 2009Reference: Computer Forensics: Principles and Practice  

E-Print Network [OSTI]

1 Computer Forensics: you can hide but you canComputer Forensics: you can hide but you can''t deletet delete Dr. Nazli Hardy, 2009Reference: Computer Forensics: Principles and Practice Volonino Anzaldua Godwin Computer Forensics April 10, 2009 Presentation for Dr. Maria Schiza's Forensics class

Hardy, Christopher R.

166

Specificity of O-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules  

Science Journals Connector (OSTI)

...lignocellulosic biomass to fuels and chemicals . Annu...investigation of glycosylation effects on a family 1 carbohydrate-binding...1357 1360 . 28 Price JL ( 2010 ) Context-dependent...The spectra are the average of 4 scans with an averaged...each CBM analog are the average of the results of the...

Liqun Chen; Matthew R. Drake; Michael G. Resch; Eric R. Greene; Michael E. Himmel; Patrick K. Chaffey; Gregg T. Beckham; Zhongping Tan

2014-01-01T23:59:59.000Z

167

T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of...  

Broader source: Energy.gov (indexed) [DOE]

77: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability July 27, 2011 -...

168

T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets...  

Broader source: Energy.gov (indexed) [DOE]

33: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service May 31,...

169

High-Affinity Binding and Direct Electron Transfer to Solid Metals...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Binding and Direct Electron Transfer to Solid Metals by the Shewanella oneidensis MR-1 Outer Membrane c-type High-Affinity Binding and Direct Electron Transfer to Solid Metals...

170

E-Print Network 3.0 - atp-binding rna aptamer Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

aptamer Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding rna aptamer Page: << < 1 2 3 4 5 > >> 1 Mutant ATP-binding RNA Aptamers Reveal...

171

E-Print Network 3.0 - arabidopsis atp-binding cassette Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

atp-binding cassette Search Powered by Explorit Topic List Advanced Search Sample search results for: arabidopsis atp-binding cassette Page: << < 1 2 3 4 5 > >> 1 BioMed Central...

172

Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies  

Science Journals Connector (OSTI)

We have investigated the binding of the biologically important flavonoid fisetin with the carrier protein bovine serum albumin...4M?1...and the number of binding sites was determined as one. MALDI-TOF analyses s...

Atanu Singha Roy; Nitin Kumar Pandey; Swagata Dasgupta

2013-04-01T23:59:59.000Z

173

ANCHOR: web server for predicting protein binding regions in disordered proteins  

Science Journals Connector (OSTI)

......involved in protein-protein interactions. Disordered binding regions...segments differ from protein interaction sites of globular proteins due to their distinct...flexible structural ensemble in isolation and...indicative of disordered binding regions......

Zsuzsanna Dosztnyi; Blint Mszros; Istvn Simon

2009-10-15T23:59:59.000Z

174

E-Print Network 3.0 - affinity brain membrane-binding Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

brain membrane-binding Search Powered by Explorit Topic List Advanced Search Sample search results for: affinity brain membrane-binding Page: << < 1 2 3 4 5 > >> 1 Inositol...

175

E-Print Network 3.0 - allosteric modulator binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

by Force Distribution Analysis Summary: bind distal to the active site 2,3. A fundamental question is how the allosteric perturbation... .g., the binding of a cofactor, from...

176

Characterization of the FNR Protein of Escherichid coli, an Iron-Binding Transcriptional Regulator  

Science Journals Connector (OSTI)

...coli, an Iron-Binding Transcriptional Regulator Jeffrey Green Martin Trageser Stephan...John R. Guest FNR is a transcriptional regulator mediating the activation or repression...coli, an iron-binding transcriptional regulator. | FNR is a transcriptional regulator...

1991-01-01T23:59:59.000Z

177

E-Print Network 3.0 - antidepressant binding site Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

423 J. Biosci. 31(3), September 2006 Summary: the composition of the transcription factors that bind to the CRE sites prior and post-training for learned... binding sites, is...

178

Metal binding in an aluminum based metal-organic framework for...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Metal binding in an aluminum based metal-organic framework for carbon dioxide capture Link to article...

179

E-Print Network 3.0 - atp-binding cassette transporters Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

transporters Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette transporters...

180

E-Print Network 3.0 - atp-binding cassette transporter Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

transporter Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette transporter...

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

E-Print Network 3.0 - atp-binding cassette transport Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

transport Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette transport...

182

Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh  

Science Journals Connector (OSTI)

Crystal structures of the Ffh NG GTPase domain at < 1.24 resolution reveal multiple overlapping nucleotide binding modes.

Ramirez, U.D.

2008-09-19T23:59:59.000Z

183

Yukawa potential approach to the nuclear binding energy formula  

Science Journals Connector (OSTI)

The volume and surface contributions to the nuclear binding energy of a nucleus are calculated from first principles. Yukawas mesontheory of the nucleonnucleon interaction is used to show that the potential energy contains a volume term that is linear in the nucleon number A and asurface term that varies as A 2 / 3 for A sufficiently large. The kinetic energy contribution is accounted for in the usual way. The results are used to estimate the strong force coupling constant. The present approach could be used to discuss the binding energy of a nucleus in terms that are more fundamental than the customary analogy with the case of a drop of liquid.

N. Gauthier

1990-01-01T23:59:59.000Z

184

Improved value for the silicon free exciton binding energy  

SciTech Connect (OSTI)

The free exciton binding energy is a key parameter in silicon material and device physics. In particular, it provides the necessary link between the energy threshold for valence to conduction band optical absorption and the bandgap determining electronic properties. The long accepted low temperature binding energy value of 14.7 0.4 meV is reassessed taking advantage of developments subsequent to its original determination, leading to the conclusion that this value is definitely an underestimate. Using three largely independent experimental data sets, an improved low temperature value of 15.01 0.06 meV is deduced, in good agreement with the most comprehensive theoretical calculations to date.

Green, Martin A., E-mail: m.green@unsw.edu.au [Australian Centre for Advanced Photovoltaics, School of Photovoltaic and Renewable Energy Engineering, University of New South Wales, Sydney, Australia 2052 (Australia)

2013-11-15T23:59:59.000Z

185

Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site  

SciTech Connect (OSTI)

c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the {alpha}I helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the {alpha}I helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

Yang, Jingsong; Campobasso, Nino; Biju, Mangatt P.; Fisher, Kelly; Pan, Xiao-Qing; Cottom, Josh; Galbraith, Sarah; Ho, Thau; Zhang, Hong; Hong, Xuan; Ward, Paris; Hofmann, Glenn; Siegfried, Brett; Zappacosta, Francesca; Washio, Yoshiaki; Cao, Ping; Qu, Junya; Bertrand, Sophie; Wang, Da-Yuan; Head, Martha S.; Li, Hu; Moores, Sheri; Lai, Zhihong; Johanson, Kyung; Burton, George; Erickson-Miller, Connie; Simpson, Graham; Tummino, Peter; Copeland, Robert A.; Oliff, Allen (GSKPA)

2014-10-02T23:59:59.000Z

186

High molecular weight polysaccharide that binds and inhibits virus  

DOE Patents [OSTI]

This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods on inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

Konowalchuk, Thomas W

2014-01-14T23:59:59.000Z

187

Accelerated Articles Direct Electrical Transduction of Antibody Binding  

E-Print Network [OSTI]

Using Electrochemical Impedance Li-Mei C. Yang, Juan E. Diaz, Theresa M. McIntire, Gregory A. Weiss-2025 Electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kDa antibody to a "covalent virusM but noise compromised the reproducibility of the p-Ab measurement at frequencies below 40 Hz. A "signal-to-noise

Weiss, Gregory A.

188

Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to -cyclodextrin  

E-Print Network [OSTI]

starch strands apart thus increasing the hydrolyzable surface, or alternatively it may localize to the catalytic domain is attached is flexible, allowing the catalytic site to access a large surface area Cellulomonas fimi has two noncatalytic binding domains that clearly bind to different ligands; xylan binds only

Williamson, Mike P.

189

Solution Structure of the CBM10 Cellulose Binding Module from Pseudomonas Xylanase A,  

E-Print Network [OSTI]

residues (Tyr8, Trp22, and Trp24), which are exposed and form a flat surface on one face, in a classical). Although there are domains that bind specifically to xylan (denoted xylan-binding modules or XBMs) (4), many xylanases contain domains that bind specifically to cellulose rather than xylan (5). It has been

Williamson, Mike P.

190

Journal of Cellular Biochemistry 80:580588 (2001) Characterization of Nuclear Factors Binding to  

E-Print Network [OSTI]

). It was suggested that these elements might play a role in deter- mining the activity of the p53 promoter [Bienz that the binding proteins did not require divalent cation for DNA-binding activity. In addition, the binding. The mutations of the gene have been observed in over 50% of all human cancers [Hollstein et al., 1991; Levine et

Park, Jong-Sang

191

Stereoselective Binding of Ruthenium Complexes to Cytochrome c  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Complexes to Histidine Side Chains in Horse Heart Cytochrome c Jian Luo, James F. Wishart, and Stephan S. Isied J. Am. Chem. Soc. 120, 12970-12971 (1998) [Find paper at ACS Publications] Abstract: Stereoselective covalent binding of the ruthenium complexes cis-[Ru(bpy)2(H2O)2]2+ (bpy = 2,2'-bipyridine) and cis-[Ru(dmbpy)2(H2O)2]2+ (dmbpy = 4,4'-dimethyl-2,2'-bipyridine) to the surface His 33 residue and the more buried His 26 residues of Horse heart cytochrome c (Hh cyt c) to form large enantiomeric excess of D-[Ru(dmbpy)2(H2O)]-His 26-cyt c (38%), but little or no excess of D-[Ru(bpy)2(H2O)]-His 26-cyt c (6%). At the surface exposed His 33 site, equal entiomeric excess of L-[Ru(dmbpy)2(H2O)]-His 33-cyt c and L-[Ru(bpy)2(H2O)]-His 33-cyt c (34%)

192

Bounds to binding energies from the concavity of thermodynamical functions  

E-Print Network [OSTI]

Sequences of experimental ground-state energies are mapped onto concave patterns cured from convexities due to pairing and/or shell effects. The same patterns, completed by a list of excitation energies, can be used to give numerical estimates of the grand potential $\\Omega(\\beta,\\mu)$ for a mixture of nuclei at low or moderate temperatures $T=\\beta^{-1}$ and at many chemical potentials $\\mu.$ The average nucleon number $(\\beta,\\mu)$ then becomes a continuous variable, allowing extrapolations towards nuclear masses closer to drip lines. We study the possible concavity of several thermodynamical functions, such as the free energy and the average energy, as functions of $.$ Concavity, when present in such functions, allows trivial interpolations and extrapolations providing upper and lower bounds, respectively, to binding energies. Such bounds define an error bar for the prediction of binding energies. An extrapolation scheme for such concave functions is tested. We conclude with numerical estimates of the binding energies of a few nuclei closer to drip lines.

B. K. Jennings; B. R. Barrett; B. G. Giraud

2007-08-22T23:59:59.000Z

193

Binding of cobalt and iron to cavities in silicon  

SciTech Connect (OSTI)

The chemisorption binding of Co and Fe to cavity walls in Si was quantitatively characterized in the temperature range 973{endash}1273 K in order to evaluate the efficacy of cavities for impurity gettering. The cavities were formed by He ion implantation and annealing. Then, with the solution concentration of Co or Fe being held at the solid solubility through prior formation of excess metal-silicide phase, the equilibrium number of metal atoms bound to the cavities was measured. Using this information in conjunction with published solubilities, a binding free energy relative to interstitial solution was extracted. The binding free energies for cavity-wall chemisorption of Co and Fe were found to be less than those for precipitation of the respective silicide phases, a reversal of the ordering previously observed by us for Cu and Au. Nevertheless, model calculations indicate that the chemisorption mechanism is important together with silicide precipitation for cavity gettering of all four elements. The results of this work, taken with the known thermal stability and the anticipated device-side compatibility of cavities, suggest that these sinks will prove attractive for gettering.

Myers, S.M.; Petersen, G.A.; Seager, C.H. [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-1056 (United States)] [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-1056 (United States)

1996-10-01T23:59:59.000Z

194

Structures of the spectrin-ankyrin interaction binding domains  

SciTech Connect (OSTI)

As key components of the erythrocyte membrane skeleton, spectrin and ankyrin specifically interact to tether the spectrin cytoskeleton to the cell membrane. The structure of the spectrin binding domain of ankyrin and the ankyrin binding domain of spectrin have been solved to elucidate the structural basis for ankyrin-spectrin recognition. The structure of repeats 14 and 15 of spectrin shows that these repeats are similar to all other spectrin repeats. One feature that could account for the preference of ankyrin for these repeats is the presence of a conserved, negatively charged patch on one side of repeat 14. The structure of the ankyrin ZU5 domain shows a novel structure containing a {beta} core. The structure reveals that the canonical ZU5 consensus sequence is likely to be missing an important region that codes for a {beta} strand that forms part of the core of the domain. In addition, a positively charged region is suggestive of a binding surface for the negatively charged spectrin repeat 14. Previously reported mutants of ankyrin that map to this region lie mostly on the surface of the protein, although at least one is likely to be part of the core.

Ipsaro, Jonathan J.; Huang, Lei; Mondragn, Alfonso; (NWU)

2010-01-07T23:59:59.000Z

195

Thermodynamics and Kinetics of Carbon Dioxide Binding to Two Stereoisomers  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Binding to Stereoisomers of a Cobalt(I) Macrocycle Binding to Stereoisomers of a Cobalt(I) Macrocycle Carol Creutz, Harold A. Schwarz, James F. Wishart, Etsuko Fujita and Norman Sutin J. Am. Chem. Soc. 113, 3361-3371 (1991) Abstract: The thermodynamics and kinetics of binding of CO2, CO, and H+ to N-racemic and N-meso stereoisomers of the cobalt(I) macrocycle CoL+ (L=5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene) have been determined in aqueous media with use of the pulse radiolysis technique and transient ultraviolet-visible spectroscopy. N-rac or N-meso-CoL+ was produced by the hydrated electron reduction of N-rac or N-meso-CoL2+, with tert-butyl alcohol generally added to scavenge hydroxyl radicals. Reactions of both N-rac- and N-meso CoL+ are readily followed by the disappearance of intense ([epsilon] 1 x 104 M-1 cm-1) absorption bands

196

Page not found | Department of Energy  

Broader source: Energy.gov (indexed) [DOE]

81 - 25790 of 28,904 results. 81 - 25790 of 28,904 results. Article V-079: ISC BIND AAAA Record Lookup Handling Assertion Failure Vulnerability ISC has learned of the potential for an error condition to occur in BIND 9 http://energy.gov/cio/articles/v-079-isc-bind-aaaa-record-lookup-handling-assertion-failure-vulnerability Article EM Helps Military Families in Need LAS VEGAS - Six families from Nellis Air Force Base in Las Vegas recently received nearly $4,000 in donations - funds that helped provide a welcome relief during the holidays. http://energy.gov/em/articles/em-helps-military-families-need Download CX-009224: Categorical Exclusion Determination Project L-718, Electrical Utilities Transformer Management Support Facility CX(s) Applied: B1.15 Date: 09/04/2012 Location(s): Washington

197

Somatic mutational analysis of FAK in breast cancer: A novel gain-of-function mutation due to deletion of exon 33  

SciTech Connect (OSTI)

Highlights: A novel FAK splicing mutation identified in breast tumor. FAK-Del33 mutation promotes cell migration and invasion. FAK-Del33 mutation regulates FAK/Src signal pathway. -- Abstract: Focal adhesion kinase (FAK) regulates cell adhesion, migration, proliferation, and survival. We identified a novel splicing mutant, FAK-Del33 (exon 33 deletion, KF437463), in both breast and thyroid cancers through colony sequencing. Considering the low proportion of mutant transcripts in samples, this mutation was detected by TaqMan-MGB probes based qPCR. In total, three in 21 paired breast tissues were identified with the FAK-Del33 mutation, and no mutations were found in the corresponding normal tissues. When introduced into a breast cell line through lentivirus infection, FAK-Del33 regulated cell motility and migration based on a wound healing assay. We demonstrated that the expression of Tyr397 (main auto-phosphorylation of FAK) was strongly increased in FAK-Del33 overexpressed breast tumor cells compared to wild-type following FAK/Src RTK signaling activation. These results suggest a novel and unique role of the FAK-Del33 mutation in FAK/Src signaling in breast cancer with significant implications for metastatic potential.

Fang, Xu-Qian [Department of Clinical Laboratory, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai (China)] [Department of Clinical Laboratory, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai (China); Liu, Xiang-Fan [Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai (China)] [Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai (China); Yao, Ling [Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai (China)] [Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai (China); Chen, Chang-Qiang; Gu, Zhi-Dong [Department of Clinical Laboratory, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai (China)] [Department of Clinical Laboratory, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai (China); Ni, Pei-Hua [Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai (China)] [Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai (China); Zheng, Xin-Min [Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai (China) [Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai (China); Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY (United States); Fan, Qi-Shi, E-mail: qishifan@126.com [Department of Clinical Laboratory, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai (China)] [Department of Clinical Laboratory, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai (China)

2014-01-10T23:59:59.000Z

198

Clostridium thermocellum Xyn10B Carbohydrate-Binding Module 22-2: The Role of Conserved Amino Acids in Ligand Binding,  

E-Print Network [OSTI]

study [Charnock, S. J., et al. (2000) Biochemistry 39, 5013-5021] and revealed a surface cleft which studies have shown that CBMs appended to xylanase catalytic modules often bind prefer- entially to xylan (4-11). CBM families whose members bind xylan include CBM2b, CBM4, CBM6, CBM13, and CBM22

Williamson, Mike P.

199

Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA  

SciTech Connect (OSTI)

Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

2011-12-09T23:59:59.000Z

200

Tight-binding model for hydrogen-silicon interactions  

SciTech Connect (OSTI)

We have developed an empirical tight-binding model for use in molecular-dynamics simulations to study hydrogen-silicon systems. The hydrogen-silicon interaction is constructed to reproduce the electronic energy levels and vibration frequencies of silane (SiH{sub 4}). Further use of the model in the studies of disilane (Si{sub 2}H{sub 6}) and of hydrogen on the Si(111) surface also yields results in good agreement with first-principles calculations and experiments.

Min, B.J.; Lee, Y.H.; Wang, C.Z.; Chan, C.T.; Ho, K.M. (Microelectronics Research Center, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States) Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States))

1992-03-15T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

Hydroxyapatite-binding peptides for bone growth and inhibition  

DOE Patents [OSTI]

Hydroxyapatite (HA)-binding peptides are selected using combinatorial phage library display. Pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains in every two or three amino acid sequences are obtained. These sequences resemble the (Gly-Pro-Hyp).sub.x repeat of human type I collagen, a major component of extracellular matrices of natural bone. A consistent presence of basic amino acid residues is also observed. The peptides are synthesized by the solid-phase synthetic method and then used for template-driven HA-mineralization. Microscopy reveal that the peptides template the growth of polycrystalline HA crystals .about.40 nm in size.

Bertozzi, Carolyn R. (Berkeley, CA); Song, Jie (Shrewsbury, MA); Lee, Seung-Wuk (Walnut Creek, CA)

2011-09-20T23:59:59.000Z

202

Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Defining How Botulinum Toxin Binds to Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and Creating Improved Therapeutics to Block Toxicity Botulinum neurotoxin (BoNT), the most potent toxin known, induces a potentially fatal paralytic condition known as "botulism". Botulism can occur when toxin-producing bacteria infect wounds (wound botulism) or the intestinal tract (infant/intestinal botulism), or following the ingestion of contaminated food in which toxin has been produced (food-borne botulism). In the USA, infant botulism represents the most common manifestation of the disease, where its prevalence has led to speculation of a link to sudden infant death syndrome. BoNTs are subdivided into seven distinct serotypes (types A through G), and an increasingly large number of subtypes continue to be identified within each serotype, highlighting the need to produce broad-spectrum therapeutics. BoNT variants are an important biochemical set of tools for understanding nerve function, and important therapeutic agents in current clinical use to provide relief to patients with a wide spectrum of neurological disorders.

203

Contrasting binding of fisetin and daidzein in ?-cyclodextrin nanocavity  

Science Journals Connector (OSTI)

Steady state and time resolved fluorescence along with anisotropy and induced circular dichroism (ICD) spectroscopy provide useful tools to observe and understand the behavior of the therapeutically important plant flavonoids fisetin and daidzein in ?-cyclodextrin (?-CDx) nanocavity. BenesiHildebrand plots indicated 1:1 stoichiometry for both the supramolecular complexes. However, the mode of the binding of fisetin significantly differs from daidzein in ?-CDx, as is observed from ICD spectra which is further confirmed by docking studies. The interaction with ?-CDx proceeds mainly by the phenyl ring and partly by the chromone ring of fisetin whereas only the phenyl ring takes part for daidzein. A linear increase in the aqueous solubility of the flavonoids is assessed from the increase in the binding of the flavonoids with the ?-CDx cavity, which are determined by the gradual increase in the ICD signal, fluorescence emission as well as increase in fluorescence anisotropy with increasing (?-CDx). This confirms ?-CDx as a nanovehicle for the flavonoids fisetin and daidzein in improving their bioavailability.

Biswapathik Pahari; Bidisha Sengupta; Sandipan Chakraborty; Briannica Thomas; Dyffreyon McGowan; Pradeep K. Sengupta

2013-01-01T23:59:59.000Z

204

Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies  

E-Print Network [OSTI]

We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-heavy and heavy nuclei, including binding energies, charge radii, deformation parameters, neutron skin thickness, and excitation energies of giant multipole resonances.

T. Niksic; D. Vretenar; P. Ring

2008-09-08T23:59:59.000Z

205

Impact of the [delta]F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure  

SciTech Connect (OSTI)

Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.

Lewis, Hal A.; Zhao, Xun; Wang, Chi; Sauder, J. Michael; Rooney, Isabelle; Noland, Brian W.; Lorimer, Don; Kearins, Margaret C.; Conners, Kris; Condon, Brad; Maloney, Peter C.; Guggino, William B.; Hunt, John F.; Emtage, Spencer (SG); (Columbia); (JHU)

2010-07-19T23:59:59.000Z

206

Phosphorylation of the DNA-binding domain of nonhistone high-mobility group I protein by cdc2 kinase: Reduction of binding affinity  

SciTech Connect (OSTI)

Mammalian high-mobility group I nonhistone protein (HMG-I) is a DNA-binding chromatin protein that has been demonstrated both in vitro and in vivo to be localized to the A + T-rich sequenced of DNA. Recently an unusual binding domain peptide, the A{center dot}T-hook motif, that mediates specific interaction of HMG-I with the minor groove of DNA in vitro has been described. Inspection of the A{center dot}T-hook region of the binding domain showed that it matches the consensus sequence for phosphorylation by cdc2 kinase. Here the authors demonstrate that HMG-I is a substrate for phosphorylation by purified mammalian cdc2 kinase in vitro. The site of phosphorylation by this enzyme is a threonine residue at the amino-terminal end of the principal binding-domain region of the protein. Labeling of mitotically blocked mouse cells with ({sup 32}P)phosphate demonstrates that this same threonine residue in HMG-I is also preferentially phosphorylated in vivo. These finding indicate that cdc2 phosphorylation may significantly alter the DNA-binding properties of the HMG-I proteins. Becuase many cdc2 substrated are DNA-binding proteins, these results further suggest that alteration of the DNA-binding affinity of a variety of proteins is an important general component of the mechanism by which cdc2 kinase regulates cell cycle progression.

Reeves, R.; Nissen, M.S. (Washington State Univ., Pullman (United States)); Langan, T.A. (Univ. of Colorado, Denver (United States))

1991-03-01T23:59:59.000Z

207

Investigation of the Copper Binding Site And the Role of Histidine As a Ligand in Riboflavin Binding Protein  

SciTech Connect (OSTI)

Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 {angstrom}, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a Cu-O{sub 3}N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

Smith, S.R.; Bencze, K.Z.; Russ, K.A.; Wasiukanis, K.; Benore-Parsons, M.; Stemmler, T.L.

2009-05-26T23:59:59.000Z

208

E-Print Network 3.0 - altered lectin-binding sites Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

lectin binding sites in river biofilms. Neu... systems. At present the most prom- ising ... Source: Hitchcock, Adam P. - Department of Chemistry, McMaster University...

209

E-Print Network 3.0 - a1 binding site Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Materials Science 4 Stochastic evolution of transcription factor binding sites Johannes Berg and Michael Lassig Summary: . There is typically one particular nucleotide a i...

210

E-Print Network 3.0 - alpha -bungarotoxin binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Limited Keywords: binding sites; protein structure; geometry; alpha... CPA, 4CPA, 5CPA, alpha-amylase 6TAA) their ... Source: Engelman, Donald M.- Department of Molecular...

211

Energy landscapes for protein folding, binding, and aggregation : simple funnels and beyond  

E-Print Network [OSTI]

coordinates capture protein folding on smooth landscapes.in the Prediction of Protein Folding Kinetics. Proc. Natl.Landscapes for Protein Folding, Binding, and Aggregation:

Cho, Samuel Sung-Il

2007-01-01T23:59:59.000Z

212

E-Print Network 3.0 - acid-binding protein predicts Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Summary: and nucleic-acid binding proteins from eukaryotic cell lysates 12;2 Qproteome Nuclear Protein Handbook 07... Preparation of the cytosolic fraction 8 Preparation of the...

213

E-Print Network 3.0 - atp binding cassette Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding cassette Page: << < 1 2 3 4 5 > >> 1 12-13( Humulus Lupulus,...

214

Reversible CO Binding Enables Tunable CO/H2 and CO/N2 Separations...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

2,5-dioxido-1,4-benzenedicarboxylate) structure type are demonstrated to bind carbon monoxide reversibly and at high capacity. Infrared spectra indicate that, upon coordination of...

215

E-Print Network 3.0 - atomic binding energy Sample Search Results  

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energy Search Powered by Explorit Topic List Advanced Search Sample search results for: atomic binding energy Page: << < 1 2 3 4 5 > >> 1 Extended Xray Absorption Fine Structure...

216

E-Print Network 3.0 - androgen binding protein Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

data showing that androgen binding increases AR protein stability (Kemppainen et al., 1992... and protein biosynthesis. Androgen levels in CRPC appear adequate to stimulate AR...

217

E-Print Network 3.0 - a-binding protein acbp6 Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Biology and Medicine 3 Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding Summary: kinetics using FRET with acyl-CoA binding protein. In protein folding,...

218

E-Print Network 3.0 - abrogates son binding Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

at San Diego Collection: Biology and Medicine 68 Selective Small Molecules Blocking HIV-1 Tat and Coactivator PCAF Association Summary: in binding (9 vs 5). Surprisingly,...

219

E-Print Network 3.0 - adipocyte fatty acid-binding Sample Search...  

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Biochemistry 221: 127132, 2001. 2001 Kluwer Academic Publishers. Printed in the Netherlands. Summary: acid, gene regulation Introduction Fatty acid-binding proteins (FABPs)...

220

E-Print Network 3.0 - aptamer binding inducing Sample Search...  

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while... , formamidopyrimidine with an RNA aptamer whose binding to ... Source: Beal, Peter A. - Department of Chemistry, University of Utah Collection: Chemistry 32...

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While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Tight-Binding Models of Amorphous Systems: Liquid Metals  

Science Journals Connector (OSTI)

A tight-binding approach to the electronic structure of disordered systems is developed for a simple one-orbital model of a liquid metal. An equation is derived for a one-electron continuum Green's function from which the electronic density of states can be obtained. Utilizing an analogy between this Green's function and the T matrix of multiple-scattering theory, results are obtained corresponding to the quasicrystalline approximation (QCA) of Lax and the self-consistent approximation (SCA) of Schwartz and Ehrenreich. Moments of the spectral function are also analyzed. Calculations were made using random and hard-sphere pair distribution functions. The QCA in this model is quite inadequate, and the SCA, while a considerable improvement, proves to involve a questionable approximation to the three-body distribution function.

Laura M. Roth

1973-05-15T23:59:59.000Z

222

ATP binding to a multisubunit enzyme: statistical thermodynamics analysis  

E-Print Network [OSTI]

Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics, a simple model is presented. In this model, we assume that the binding of ATP will change the potential of the corresponding enzyme subunit, and the degree of this change depends on the state of its adjacent subunits. The probability of enzyme in a given state satisfies the Boltzmann's distribution. Although it looks much simple, this model can fit the recent experimental data of chaperonin TRiC/CCT well. From this model, the dominant state of TRiC/CCT can be obtained. This study provided a new way to understand biophysical processes by statistical thermodynamics analysis.

Yunxin Zhang

2012-03-22T23:59:59.000Z

223

ATP binding to a multisubunit enzyme: statistical thermodynamics analysis  

E-Print Network [OSTI]

Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics, a simple model is presented. In this model, we assume that the binding of ATP will change the potential of the corresponding enzyme subunit, and the degree of this change depends on the state of its adjacent subunits. The probability of enzyme in a given state satisfies the Boltzmann's distribution. Although it looks much simple, this model can fit the recent experimental data of chaperonin TRiC/CCT well. From this model, the dominant state of TRiC/CCT can be obtained. This study provided a new way to understand biophysical processes by statistical thermodynamics analysis.

Zhang, Yunxin

2012-01-01T23:59:59.000Z

224

On the nuclear interaction. Potential, binding energy and fusion reaction  

E-Print Network [OSTI]

The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

I. Casinos

2008-05-22T23:59:59.000Z

225

Characterization of Selective Binding of Alkali Cations with Carboxylate  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Characterization of Selective Characterization of Selective Binding of Alkali Cations with Carboxylate Characterization of Selective Binding of Alkali Cations with Carboxylate Print Wednesday, 24 September 2008 00:00 During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions has been known since the early 20th century, when Franz Hofmeister observed that some salts (ionic compounds) aided the solution of proteins in egg, some caused proteins to destabilize and precipitate, and others ranged in activity between the two extremes. Hofmeister then ranked "salt-out" (destabilizing) ions versus "salt-in" (stabilizing) ions according to the magnitude of their effects (the "Hofmeister effects"). However, despite enormous effort, why certain interactions are preferred over others is not completely understood. Recently, a team of researchers from UC Berkeley used the model systems of acetate and formate (two simple carboxylic acids) with a series of cations to test predictions made in the literature for preferential interactions. Near-edge x-ray absorption fine structure (NEXAFS) spectroscopy was used as this technique is highly sensitive to the chemical environments around a molecule. Experiments at ALS Beamline 8.0.1 confirmed strengthening of the interaction between the cations and the carboxylate group in the following order: potassium, sodium, and lithium.

226

Isolation and characterizations of oxalate-binding proteins in the kidney  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer The first large-scale characterizations of oxalate-binding kidney proteins. Black-Right-Pointing-Pointer The recently developed oxalate-conjugated EAH Sepharose 4B beads were applied. Black-Right-Pointing-Pointer 38 forms of 26 unique oxalate-binding kidney proteins were identified. Black-Right-Pointing-Pointer 25/26 (96%) of identified proteins had 'L-x(3,5)-R-x(2)-[AGILPV]' domain. -- Abstract: Oxalate-binding proteins are thought to serve as potential modulators of kidney stone formation. However, only few oxalate-binding proteins have been identified from previous studies. Our present study, therefore, aimed for large-scale identification of oxalate-binding proteins in porcine kidney using an oxalate-affinity column containing oxalate-conjugated EAH Sepharose 4B beads for purification followed by two-dimensional gel electrophoresis (2-DE) to resolve the recovered proteins. Comparing with those obtained from the controlled column containing uncoupled EAH-Sepharose 4B (to subtract the background of non-specific bindings), a total of 38 protein spots were defined as oxalate-binding proteins. These protein spots were successfully identified by quadrupole time-of-flight mass spectrometry (MS) and/or tandem MS (MS/MS) as 26 unique proteins, including several nuclear proteins, mitochondrial proteins, oxidative stress regulatory proteins, metabolic enzymes and others. Identification of oxalate-binding domain using the PRATT tool revealed 'L-x(3,5)-R-x(2)-[AGILPV]' as a functional domain responsible for oxalate-binding in 25 of 26 (96%) unique identified proteins. We report herein, for the first time, large-scale identification and characterizations of oxalate-binding proteins in the kidney. The presence of positively charged arginine residue in the middle of this functional domain suggested its significance for binding to the negatively charged oxalate. These data will enhance future stone research, particularly on stone modulators.

Roop-ngam, Piyachat; Chaiyarit, Sakdithep; Pongsakul, Nutkridta [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand)] [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand); Thongboonkerd, Visith, E-mail: vthongbo@yahoo.com [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand)] [Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok (Thailand)

2012-08-03T23:59:59.000Z

227

NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse  

Science Journals Connector (OSTI)

......experimental and predicted nuclear receptor binding...experiments. All datasets are processed using...derived from different datasets are comparable...edu 1 INTRODUCTION Nuclear receptors (NRs...experimental and predicted nuclear receptor binding...experiments. All datasets are processed using......

Yaping Fang; Hui-Xin Liu; Ning Zhang; Grace L. Guo; Yu-Jui Yvonne Wan; Jianwen Fang

2013-01-15T23:59:59.000Z

228

ATP Hydrolysis and DNA Binding by the Escherichia coli RecF Protein*  

E-Print Network [OSTI]

ATP Hydrolysis and DNA Binding by the Escherichia coli RecF Protein* (Received for publication ATP hydrolytic activity. ATP hydrolysis leads to RecF dissociation from double-stranded (ds to DNA. A mutant RecF protein that can bind but cannot hydrolyze ATP (RecF K36R) does not readily

Cox, Michael M.

229

Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein  

E-Print Network [OSTI]

Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein Sheref S. Mansy1 sequence into a stably folded, high affinity ATP binding protein structure. While the evolutionarily and functional data was then used to interpret the significance of each amino acid mutation. The enhanced ATP

Heller, Eric

230

Exciton binding energies in carbon nanotubes from two-photon photoluminescence J. Maultzsch,1,  

E-Print Network [OSTI]

Exciton binding energies in carbon nanotubes from two-photon photoluminescence J. Maultzsch,1, * R; their energy splitting is the fingerprint of excitonic interactions in carbon nanotubes. By ab initio experiment and theory we find binding energies of 0.3­0.4 eV for nanotubes with diameters between 6.8 and 9

Nabben, Reinhard

231

Geometric Binding Site Design for Surface-Tension Driven Self-Assembly  

E-Print Network [OSTI]

Geometric Binding Site Design for Surface-Tension Driven Self-Assembly Xiaorong Xiong, Sheng 98195-2500 Email: xrxiong@u.washington.edu Abstract-- Surface-tension driven self-assembly techniques-assembly, micro assembly, MEMS, hy- drophobic, hydrophilic, surface energy, surface tension force, binding site

232

Origin of the Variation of Exciton Binding Energy in Semiconductors Marc Dvorak,1  

E-Print Network [OSTI]

Origin of the Variation of Exciton Binding Energy in Semiconductors Marc Dvorak,1 Su-Huai Wei,2 Renewable Energy Laboratory, Golden, Colorado 80401, USA (Received 13 July 2012; revised manuscript received, and the exciton binding energy Eb in technologically important semiconductors varies from merely a few me

Wu, Zhigang

233

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces  

E-Print Network [OSTI]

, while identification of a hot spot by alanine scanning establishes the potential to generate substantial, termed "hot spots", that comprise the subset of residues that contribute the bulk of the binding free proposed as prime targets for drug binding.1,4 The established approach to the identification of such hot

Vajda, Sandor

234

Regulation of Single Stranded DNA Binding by the C-termini of E. coli SSB protein.  

E-Print Network [OSTI]

Regulation of Single Stranded DNA Binding by the C-termini of E. coli SSB protein. Alexander G@biochem.wustl.edu The homotetrameric E. coli single stranded DNA binding (SSB) protein plays a central role in DNA replication, repair domain (5). The E. coli SSB protein is the prototypical example of the homotetrameric class of SSB

Lohman, Timothy M.

235

Membrane binding of SRP pathway components in the halophilic archaea Haloferax volcanii  

E-Print Network [OSTI]

Membrane binding of SRP pathway components in the halophilic archaea Haloferax volcanii Tovit LichiY, the prokaryal signal recognition particle receptor, and SRP54, a central component of the signal recognition par-terminal GTP-binding domain (NG domain) or SRP54, were com- bined separately or in different combinations

Eichler, Jerry

236

Host Range and Variability of Calcium Binding by Surface Loops in the Capsids of Canine and  

E-Print Network [OSTI]

Host Range and Variability of Calcium Binding by Surface Loops in the Capsids of Canine and Feline, consisting of residues 359 to 375 of the capsid protein. This loop binds a divalent calcium ion in FPV and in the presence or absence of Ca2 . The largest structural difference was found to occur in a ¯exible surface loop

Rossmann, Michael G.

237

A Calmodulin Binding Protein from Arabidopsis Is Induced by Ethylene and Contains  

E-Print Network [OSTI]

A Calmodulin Binding Protein from Arabidopsis Is Induced by Ethylene and Contains a DNA- acting with other proteins. To isolate CaM binding proteins involved in ethylene signal transduction, we screened an expression library prepared from ethylene-treated Arabidopsis seedlings with 35 S- labeled Ca

Reddy, A.S.N

238

-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism  

Science Journals Connector (OSTI)

Structural analysis of apo and DNA-bound HU from S. aureus (SHU) revealed that conformational changes occur in both the protein and DNA upon DNA binding. Base-readout and shape-readout mechanisms are involved in DNA binding and recognition by SHU, in which -arm flexibility is a major determinant.

Kim, D.-H.

2014-11-28T23:59:59.000Z

239

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group  

E-Print Network [OSTI]

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group Stephen P within the center of the Fis­DNA complex narrows to about half the mean minor groove width of canonical B by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through

Rohs, Remo

240

Binding of a high-energy substrate conformer in antibody catalysis  

Science Journals Connector (OSTI)

...Utilization of binding energy to orient a substrate molecule...4 kcal*mol-1 higher in energy than the pseudodiequatorial...is able to exploit binding energy to preor- ganize its flexible...S. H., Nared, K. D. & Auditor, M.-T. M. (1988) Proc...

A P Campbell; T M Tarasow; W Massefski; P E Wright; D Hilvert

1993-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Cellular/Molecular An Arginine Involved in GABA Binding and Unbinding But  

E-Print Network [OSTI]

on the two interrelated processes of binding (the interaction of re- ceptor and ligand) and gating measures that depend on the interplay of many processes and cannot resolve individualmicroscopictransitions microscopic processes of ligand binding­ unbinding, channel opening­closing, and desensitization

Kemnitz, Joseph

242

Cable-Piliated Burkholderia cepaciaBinds to Cytokeratin 13 of Epithelial Cells  

Science Journals Connector (OSTI)

...ARTICLE MOLECULAR AND CELLULAR PATHOGENESIS Cable-Piliated Burkholderia cepacia Binds to...Canada. This strain expresses surface cable (Cbl) pili and is thought to be the major...epithelial cell (BEC) protein that binds cable pilus-positive B. cepacia. N-terminal...

Umadevi S. Sajjan; Francisco A. Sylvester; Janet F. Forstner

2000-04-01T23:59:59.000Z

243

Sorption of proteins to charged microgels: characterizing binding isotherms and driving forces  

E-Print Network [OSTI]

We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound reactants (charged proteins). Application of this approach to lysozyme sorption to oppositely charged core-shell microgels allows us to extract the intrinsic, binding affinity of the protein to the gel, which is salt-concentration independent and mostly hydrophobic in nature. The total binding affinity is found to be mainly electrostatic in nature, changes many orders of magnitude during the sorption process, and is significantly influenced by osmotic deswelling effects. The intrinsic binding affinity is determined to be about 7 kBT for our system. We additionally show that Langmuir binding models and those based on excludedvolume interactions are formally equivalent for low to moderate protein packing, if the nature of the bound state is consistently defined. Having appre...

Yigit, Cemil; Ballauff, Matthias; Dzubiella, Joachim

2012-01-01T23:59:59.000Z

244

Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change  

Office of Scientific and Technical Information (OSTI)

Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change Mechanism Resources with Additional Information Paul D. Boyer Courtesy of UCLA 'For Paul Boyer, the Nobel Prize was "an unexpected pleasure." It had been 20 years since he formulated a hypothesis to describe what he calls "the most prominent chemical reaction in the whole world." It is the process by which molecules produce ATP (adenosine triphosphate), thereby transmuting light, air, water and food into the energy required for both plant and animal life. Boyer had been greeted with disbelief when he theorized that the previously mysterious process is the work of a "beautiful little machine" that operates within enzymes on the molecular level. ... Boyer experienced "one of the warmest moments of my life" when he learned that British biochemist John Walker had worked out the methodology required to demonstrate whether Boyer had been right or wrong. ... Using Walker's methodology, one of Boyer's former graduate students "did some elegant chemical work to demonstrate that the molecular rotation actually occurred." Boyer's hypothesis, finally, had been proven correct. For work that so enriched understanding of the life process itself, he and Walker were jointly awarded the Nobel prize [in Chemistry] in 1997.'

245

Invisible surface defects in a tight-binding lattice  

E-Print Network [OSTI]

Surface Tamm states arise in one-dimensional lattices from some defects at the lattice edge and their energy generally falls in a gap of the crystal. The defects at the surface change rather generally the phase of propagative Bloch waves scattered off at the lattice edge, so that an observer, far from the surface, can detect the existence of edge defects from e.g. time-of-flight measurements as a delay or an advancement of a Bloch wave packet. Here we show that a special class of defects can sustain surface Tamm states which are invisible, in a sense that reflected waves acquire the same phase as in a fully homogeneous lattice with no surface state. Surface states have an energy embedded into the tight-binding lattice band and show a lower than exponential (algebraic) localization. Like most of bound states in the continuum of von Neumann - Wigner type, such states are fragile and decay into resonance surface states in presence of perturbations or lattice disorder. The impact of structural lattice imperfections and disorder on the invisibility of the defects is investigated by numerical simulations.

Stefano Longhi

2014-06-24T23:59:59.000Z

246

Conformational changes in polyelectrolytes and the effect on metal binding  

SciTech Connect (OSTI)

There has been considerable interest in the complexation of metals and other cations by natural humic and fulvic acids, as well as synthetic polyelectrolytes. In order to explain the binding observed for metals, and other species by organic polyelectrolytes, steric effects have been proposed. In this work, the effects of pH changes in aqueous solution on two synthetic polyelectrolytes, polymaleic acid (PMA) and polyacrylic acid (PAA), have been examined by laser Raman spectroscopy and turbidity measurements. These results are compared to Fourier-transform infrared (FTIR) and (/sup 13/C) nuclear magnetic resonance (NMR) spectra for solid samples of PMA, PAA, and fulvic and humic acids. Two types of carboxylic acid groups were detected for PMA in aqueous solution. Crystallization of PMA in a narrow pH range was observed. These data are consistent with strong intramolecular hydrogen bonding occurring in PMA at a pH of approximately 4. This implication of these results on the use of these compounds as models for fulvic and humic acids is discussed. 27 refs., 3 figs., 1 tab.

Marley, N.A.; Gaffney, J.S.; Minai, Y.; Choppin, G.R.

1988-09-01T23:59:59.000Z

247

Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects  

Science Journals Connector (OSTI)

...is to bind soluble xylans and xylooligosaccharides on the surface of the endogenous...2009 ) Enzymatic treatments reveal differential capacities for xylan recognition and degradation...Receptors, Cell Surface 0 Xylans 0 saccharide-binding...

Ccile Herv; Artur Rogowski; Anthony W. Blake; Susan E. Marcus; Harry J. Gilbert; J. Paul Knox

2010-01-01T23:59:59.000Z

248

Rhizobial and Fungal Symbioses Show Different Requirements for Calmodulin Binding to Calcium Calmodulin??Dependent Protein Kinase in Lotus japonicus  

Science Journals Connector (OSTI)

...in binding buffer at room temperature for 1 h. Binding of biotinylated...leghaemoglobin synthesis in snake beans. Biochem. J. 125...regulating symbiotic nodule development. Nature 417 : 962-966...for cortical endosymbiotic development. Plant Cell 22 : 2509-2526...

Yoshikazu Shimoda; Lu Han; Toshimasa Yamazaki; Rintaro Suzuki; Makoto Hayashi; Haruko Imaizumi-Anraku

2012-01-17T23:59:59.000Z

249

Effect of primer binding probability on amplified misprimed DNA by means of a computational study on the polymerase chain reaction  

E-Print Network [OSTI]

parameters are provided and the effects discussed. Finally, the conclusions are presented. It is noted that there was effect of the primer binding probability on the production of amplified DNA of interest in the presence of multiple binding sites...

Gopalakrishnan, Sanjay

1999-01-01T23:59:59.000Z

250

Ebolavirus VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression  

SciTech Connect (OSTI)

Ebolavirus causes a severe hemorrhagic fever and is divided into five distinct species, of which Reston ebolavirus is uniquely nonpathogenic to humans. Disease caused by ebolavirus is marked by early immunosuppression of innate immune signaling events, involving silencing and sequestration of double-stranded RNA (dsRNA) by the viral protein VP35. Here we present unbound and dsRNA-bound crystal structures of the dsRNA-binding domain of Reston ebolavirus VP35. The structures show that VP35 forms an unusual, asymmetric dimer on dsRNA binding, with each of the monomers binding dsRNA in a different way: one binds the backbone whereas the other caps the terminus. Additional SAXS, DXMS, and dsRNA-binding experiments presented here support a model of cooperative dsRNA recognition in which binding of the first monomer assists binding of the next monomer of the oligomeric VP35 protein. This work illustrates how ebolavirus VP35 could mask key recognition sites of molecules such as RIG-I, MDA-5, and Dicer to silence viral dsRNA in infection.

Kimberlin, Christopher R.; Bornholdt, Zachary A.; Li, Sheng; Woods, Jr., Virgil L.; MacRae, Ian J.; Saphire, Erica Ollmann (Scripps); (UCSD)

2010-03-12T23:59:59.000Z

251

Assessing Energetic Contributions to Binding from a Disordered Region in a Protein-Protein Interaction  

SciTech Connect (OSTI)

Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.

S Cho; C Swaminathan; D Bonsor; M Kerzic; R Guan; J Yang; C Kieke; P Anderson; D Kranz; et al.

2011-12-31T23:59:59.000Z

252

Two Cooperating Helices Constitute the Lipid-binding Domain of the Bacterial SRP Receptor  

Science Journals Connector (OSTI)

Protein targeting by the bacterial signal recognition particle requires the specific interaction of the signal recognition particle (SRP)ribosomenascent chain complex with FtsY, the bacterial SRP receptor. Although FtsY in Escherichia coli lacks a transmembrane domain, the membrane-bound FtsY displays many features of an integral membrane protein. Our data reveal that it is the cooperative action of two lipid-binding helices that allows this unusually strong membrane contact. Helix I comprises the first 14 amino acids of FtsY and the second is located at the interface between the A- and the N-domain of FtsY. We show by site-directed cross-linking and binding assays that both helices bind to negatively charged phospholipids, with a preference for phosphatidyl glycerol. Despite the strong lipid binding, helix I does not seem to be completely inserted into the lipid phase, but appears to be oriented parallel with the membrane surface. The two helices together with the connecting linker constitute an independently folded domain, which maintains its lipid binding even in the absence of the conserved NG-core of FtsY. In summary, our data reveal that the two consecutive lipid-binding helices of FtsY can provide a membrane contact that does not differ significantly in stability from that provided by a transmembrane domain. This explains why the bacterial SRP receptor does not require an integral ?-subunit for membrane binding.

David Braig; Constance Br; Jrg-Oliver Thumfart; Hans-Georg Koch

2009-01-01T23:59:59.000Z

253

Role of the Kaposi's Sarcoma-Associated Herpesvirus K15 SH3 Binding Site in Inflammatory Signaling and B-Cell Activation  

Science Journals Connector (OSTI)

...1698-1707. 39 Reference deleted. 40 Zoeteweij, J. P., A. V. Moses, A. S. Rinderknecht, D. A. Davis, W. W. Overwijk, R. Yarchoan, J. M. Orenstein, and A. Blauvelt. 2001. Targeted inhibition of calcineurin signaling blocks calcium-dependent...

Marcel Pietrek; Melanie M. Brinkmann; Ilona Glowacka; Anette Enlund; Anika Hvemeier; Oliver Dittrich-Breiholz; Michael Kracht; Marc Lewitzky; Kalle Saksela; Stephan M. Feller; Thomas F. Schulz

2010-06-09T23:59:59.000Z

254

Identification of Small Molecule Binding Molecules by Affinity Purification Using a Specific Ligand Immobilized on PEGA Resin  

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A synthetic ligand for FK506-binding protein 12 (SLF) was immobilized on various resins, and the binding assays between the SLF-immobilized resins and FK506-binding protein 12 (FKBP12) were performed. ... This matrix enabled the isolation of FKBP12 from a cell lysate, and the identification of SLF-binding peptides from a phage cDNA library. ... We confirmed the interaction between SLF and these peptides using a cuvette type quartz crystal microbalance (QCM) apparatus. ...

Kouji Kuramochi; Yuka Miyano; Yoshihiro Enomoto; Ryo Takeuchi; Kazutomo Ishi; Yoichi Takakusagi; Takeki Saitoh; Keishi Fukudome; Daisuke Manita; Yoshifumi Takeda; Susumu Kobayashi; Kengo Sakaguchi; Fumio Sugawara

2008-11-26T23:59:59.000Z

255

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality  

E-Print Network [OSTI]

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner structure model for the ATP binding site were obtained by the analysis of functional sequences selected from

Heller, Eric

256

A Two-site Kinetic Mechanism for ATP Binding and Hydrolysis by E. coli Rep Helicase Dimer Bound to a  

E-Print Network [OSTI]

A Two-site Kinetic Mechanism for ATP Binding and Hydrolysis by E. coli Rep Helicase Dimer Bound that are coupled to ATP binding and hydrolysis. We have investi- gated the kinetic mechanism of ATP binding 17(?2) s?1 ; KM 3 mM), pre-steady-state studies provide evidence for a two-ATP site mechanism

Lohman, Timothy M.

257

Contribution of a Xylan-Binding Module to the Degradation of a Complex Cellulosic Substrate by Designer Cellulosomes  

Science Journals Connector (OSTI)

...ENGINEERING Contribution of a Xylan-Binding Module to the Degradation...The intrinsic cellulose/xylan-binding module (XBM) of...adaptor protein and a cell-surface anchoring protein. J. Bacteriol...121-124. Contribution of a xylan-binding module to the degradation...

Sarah Moras; Yoav Barak; Jonathan Caspi; Yitzhak Hadar; Raphael Lamed; Yuval Shoham; David B. Wilson; Edward A. Bayer

2010-04-16T23:59:59.000Z

258

Roles of the Tetrahymena thermophila type I element binding factor, TIF1, in DNA replication and genome stability  

E-Print Network [OSTI]

element that is essential for replication initiation, fork progression and promoter activation. TIF1 is a non-ORC single strand-binding protein that binds the type I element in vivo. TIF1 binds opposing strands at the origin and promoter regions indicating...

Morrison, Tara Laine

2005-11-01T23:59:59.000Z

259

Z .Biochimica et Biophysica Acta 1342 1997 164174 Calcium binding to recoverin: implications for secondary structure and  

E-Print Network [OSTI]

a calcium-binding loop com- 0167-4838r97r$17.00 q 1997 Elsevier Science B.V. All rights reserved. Z .PII SZ .Biochimica et Biophysica Acta 1342 1997 164­174 Calcium binding to recoverin: implications Received 15 May 1997; accepted 30 May 1997 Abstract Recoverin is an EF-hand calcium-binding protein

Palczewski, Krzysztof

260

Positron binding to atoms and apolar molecules: A convergence of theory and experiment  

Science Journals Connector (OSTI)

The problem of the bound states of a positron with atoms and apolar molecules is studied with a regularized polarization potential V=Vrc??r?42, where Vrc is a repulsive hard-core potential. A continuous relation between the core radius and the target polarizability is identified for alkanes, leading to the observed linear relation between their experimental binding energies and polarizabilities. New values for the binding energies for I and Pt atoms are suggested. Some predictions for related molecules are made, suggesting positron binding to GeH4 and, possibly, to C2F6.

Paulo H. R. Amaral and Jos R. Mohallem

2012-10-25T23:59:59.000Z

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While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Method for detecting binding events using micro-X-ray fluorescence spectrometry  

DOE Patents [OSTI]

Method for detecting binding events using micro-X-ray fluorescence spectrometry. Receptors are exposed to at least one potential binder and arrayed on a substrate support. Each member of the array is exposed to X-ray radiation. The magnitude of a detectable X-ray fluorescence signal for at least one element can be used to determine whether a binding event between a binder and a receptor has occurred, and can provide information related to the extent of binding between the binder and receptor.

Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Mann, Grace (Hong Kong, HK)

2010-12-28T23:59:59.000Z

262

V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets  

Broader source: Energy.gov (indexed) [DOE]

8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw 8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code December 31, 2012 - 6:58am Addthis PROBLEM: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code PLATFORM: Version(s): 6, 7, 8 ABSTRACT: A vulnerability was reported in Microsoft Internet Explorer. A remote user can cause arbitrary code to be executed on the target user's system. REFERENCE LINKS: SecurityTracker Alert ID: 1027930 Secunia Advisory SA51695 CVE-2012-4792 IMPACT ASSESSMENT: High DISCUSSION: A remote user can create specially crafted HTML that, when loaded by the target user, will trigger a memory corruption error and execute arbitrary

263

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application  

Science Journals Connector (OSTI)

Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of proteinligand complexes. However, these methods rely on several sophisticated command scripts ...

Sunhwan Jo; Wei Jiang; Hui Sun Lee; Beno??t Roux; Wonpil Im

2012-12-04T23:59:59.000Z

264

E-Print Network 3.0 - alpha 1-adrenoceptor binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

of alpha-methyl d-glucopyranoside. Biochem J 109... binding site in hog pancreatic alpha-amylase. Biochemistry 15, 1987-93. 57 Sevilla, N., Steer, M. L... ., Helmreich, E....

265

The neutron binding energy in the neutron-rich nucleus93Sr  

Science Journals Connector (OSTI)

The neutron binding energy in93Sr has been determined to (52306) keV from energy correspondences between levels defined by ?-ray transitions and ?-delayed neutron emission.

K. -L. Kratz; H. Ohm

1980-01-01T23:59:59.000Z

266

E-Print Network 3.0 - atp-binding cassette subfamily Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette subfamily Page: << < 1 2 3 4 5 > >> 1 PharmGKB Submission Update: IV....

267

E-Print Network 3.0 - atp-binding protein evolved Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

evolved Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding protein evolved Page: << < 1 2 3 4 5 > >> 1 Chemistry & Biology, Vol. 11,...

268

E-Print Network 3.0 - atp-binding cassette abc Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

abc Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette abc Page: << < 1 2 3 4 5 > >> 1 PharmGKB Submission Update: IV. PMT...

269

E-Print Network 3.0 - atp-binding cassette multidrug Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette multidrug Page: << < 1 2 3 4 5 > >> 1 LIST OF PUBLICATONS Sakamoto, K....

270

E-Print Network 3.0 - atp binding residues Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding residues Page: << < 1 2 3 4 5 > >> 1 Asymmetric deceleration of ClpB or Hsp104...

271

E-Print Network 3.0 - atp binding domain Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

domain Search Powered by Explorit Topic List Advanced Search Sample search results for: atp binding domain Page: << < 1 2 3 4 5 > >> 1 ATP Utilization by Yeast Replication Factor C...

272

E-Print Network 3.0 - atp-binding motifs play Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

play Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding motifs play Page: << < 1 2 3 4 5 > >> 1 Chemistry & Biology, Vol. 11, 865874,...

273

E-Print Network 3.0 - atp-binding cassette systems Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

systems Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding cassette systems Page: << < 1 2 3 4 5 > >> 1 PharmGKB Submission Update: IV....

274

E-Print Network 3.0 - atp-binding site lesions Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

lesions Search Powered by Explorit Topic List Advanced Search Sample search results for: atp-binding site lesions Page: << < 1 2 3 4 5 > >> 1 NEM modication prevents high-anity ATP...

275

E-Print Network 3.0 - amino-terminal dna binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Nucleic Acid Copying using 2-amino-2, 3- Summary: -labeled-2-amino-terminated DNA primer, 0.5M template (5- GGGUp Up Up -3-primer binding site), 100mM MES... Figure S1. Acid...

276

E-Print Network 3.0 - allele specific binding Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

2009 http:www.cstl.nist.govbiotechstrbaseNISTpub.htm 1 Summary: dropout* *Due to primer binding site mutation All allele calls with MiniFiler for CSF1PO, D7S820, D13S317... ....

277

Purification and Properties of a Xylan-Binding Endoxylanase from Alkaliphilic Bacillus sp. Strain K-1  

Science Journals Connector (OSTI)

...rates that varied with their xylan content and structural complexity. The xylan-binding region, which exhibits high affinity to insoluble xylan, appears to be a potential...the xylanase directly to the surface of the insoluble hemicellulose-containing...

Khanok Ratanakhanokchai; Khin Lay Kyu; Morakot Tanticharoen

1999-02-01T23:59:59.000Z

278

Binding Kinetics of Triclosan (Irgasan) to Alloplastic Vascular Grafts: An In Vitro Study  

Science Journals Connector (OSTI)

The aim of this study was to investigate the binding kinetics of triclosan (Irgasan) to alloplastic vascular grafts and ... . Grafts were incubated in 10 g/L triclosan (Irgasan), dried, sterilized, and incubated...

T. Hernndez-Richter; H.M. Schardey; F. Lhlein

2000-07-01T23:59:59.000Z

279

PEVK Domain of Titin: An Entropic Spring with Actin-Binding Properties  

E-Print Network [OSTI]

as an entropic spring with the properties of a random coil exhibiting mechanical conforma- tions of differentPEVK Domain of Titin: An Entropic Spring with Actin-Binding Properties Wolfgang A. Linke,*,1

Fernandez, Julio M.

280

A redox-regulated chloroplast protein phosphatase binds to starch diurnally and functions in its accumulation  

Science Journals Connector (OSTI)

...linear and branched glucans (amylose and amylopectin) that determine the properties of...the activity and binding of {alpha}-glucan, water dikinase...possibly the activity of {beta}-amylase (21). However, to our knowledge...

Lubomir N. Sokolov; Jose R. Dominguez-Solis; Anne-Laure Allary; Bob B. Buchanan; Sheng Luan

2006-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

E-Print Network 3.0 - albumin impaired drug-binding Sample Search...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

acid concentrations and variants on Summary: such as quinidine to ORM1 S and* 5 * ORM1 F1 ( , ). drug-binding studies are warranted to determine the possible... . Drug Metab...

282

PDB-wide collection of binding data: current status of the PDBbind database  

Science Journals Connector (OSTI)

......characteristic interaction patterns on protein-protein binding interfaces. J. Chem...SA on true conformational ensembles of protein-ligand complexes. J. Chem...quantitative theory of intrinsically disordered proteins and their function......

Zhihai Liu; Yan Li; Li Han; Jie Li; Jie Liu; Zhixiong Zhao; Wei Nie; Yuchen Liu; Renxiao Wang

2014-10-01T23:59:59.000Z

283

Binding to Cellular Macromolecules as a Possible Mechanism for the Cytotoxicity of Misonidazole  

Science Journals Connector (OSTI)

...Varghese G. F. Whitmore Physics Division, Ontario Cancer Institute...Varghese and G. F. Whitmore Physics Division. Ontario Cancer Institute...derivative of misonida zole does not bind to DNA.3 Hence...R. Gillette (eds.), Handbook of Experimental Pharmacology...

A. J. Varghese and G. F. Whitmore

1980-07-01T23:59:59.000Z

284

E-Print Network 3.0 - assisted binding site Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Press 4994--5002 Nucleic Acids Research, 1997, Vol. 25, No. 24 Summary: analysis of Fis binding sites Paul N. Hengen 1 , Stacy L. Bartram 1,2,+ , Lisa E. Stewart 1 and Thomas...

285

E-Print Network 3.0 - angiostatin binds atp Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Sciences and Ecology 30 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: . The effect of ATP binding to recA...

286

E-Print Network 3.0 - atp binding site Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Physics ; Biology and Medicine 27 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: . The effect of ATP binding to recA...

287

E-Print Network 3.0 - abcc9-encoded nucleotide binding Sample...  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Chemistry ; Biology and Medicine 37 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: DNA binding affinity by nucleotide...

288

E-Print Network 3.0 - atp binding protein Sample Search Results  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Collection: Biology and Medicine 5 Biochemistry 1988, 27, 1205-1212 1205 Ogata, R. T., & Gilbert, W. (1979) J. Mol. Biol. 132, 709. Summary: . The effect of ATP binding to recA...

289

Specific binding of a fungal glucan phytoalexin elicitor to membrane fractions from soybean Glycine max  

Science Journals Connector (OSTI)

...arabinogalactan from larch wood, chitosan from crab shells, glucan...cerevisiae), dextran, chitosan, xylan, arabinogalactan...and xylan from larch wood, chitosan from crab shells, glucan...binding assay of the competitive inhibitor of f3-glucosidase, 1...

Walter E. Schmidt; Jrgen Ebel

1987-01-01T23:59:59.000Z

290

A Rationally-designed Fluorescence Competitive Binding Assay for Continuous Glucose Monitoring Applications  

E-Print Network [OSTI]

on the protein, Concanavalin A. However, to date, this assay has continually shown problems with sensitivity, stability, and reversibility in free solution. This work uses rational design to generate a new version of the competitive binding assay that can...

Cummins, Brian Michael

2014-03-18T23:59:59.000Z

291

2D IR spectroscopy and computational modeling : application to protein folding and binding  

E-Print Network [OSTI]

In this thesis, dynamics experiments are developed that can be used to study protein conformational changes such as folding and binding. Every functional motion of a protein is inextricably linked to conformational dynamics. ...

Ganim, Ziad

2010-01-01T23:59:59.000Z

292

Lis1 Acts as a ``Clutch'' between the ATPase and Microtubule-Binding  

E-Print Network [OSTI]

and single-particle electron micro- scopy. We show that rather than binding to the main ATPase site within, even during cycles of ATP hydro- lysis that would canonically induce detachment. Thus, Lis1 operates

293

Molecular Binding in Post-KohnSham Orbital-Free DFT  

Science Journals Connector (OSTI)

Alex Borgoo *, James A. Green , and David J. Tozer * ... Molecular binding in post-KohnSham orbital-free DFT is investigated, using noninteracting kinetic energy functionals that satisfy the uniform electron gas condition and which are inhomogeneous under density scaling. ... A parameter is introduced that quantifies binding, and a series of functionals are determined from fits to near-exact effective homogeneities and/or KohnSham noninteracting kinetic energies. ...

Alex Borgoo; James A. Green; David J. Tozer

2014-10-30T23:59:59.000Z

294

Purification and expression of fatty acid binding proteins in chicken liver and intestine  

E-Print Network [OSTI]

PURIFICATION AND EXPRESSION OF FATTY ACID BINDING PROTEINS IN CHICKEN LIVER AND INTESTINE A Thesis by JULIA ELLEN SEWELL Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements for the degree... of MASTER OF SCIENCE August 1988 Major subject: Nutrition PURIFICATION AND EXPRESSION OF FATTY ACID BINDING PROTEINS IN CHICKEN LIVER AND INTESTINE A Thesis by JULIA ELLEN SEWELL Approved as to style and content by: Pamela S. Hargi (Chair of Committ...

Sewell, Julia Ellen

1988-01-01T23:59:59.000Z

295

Modeling the chemical shift of lanthanide 4f electron binding energies  

Science Journals Connector (OSTI)

Lanthanides in compounds can adopt the tetravalent [Xe]4fn?1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4fn+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical environment A. Experimental data on three environments (i.e., the bare lanthanide ions where A=vacuum, the pure lanthanide metals, and the lanthanides in aqueous solutions) are employed to determine the 4f-electron binding energies in all divalent and trivalent lanthanides. The action of the chemical environment on the 4f-electron binding energy will be represented by an effective ambient charge QA=?Q at an effective distance from the lanthanide. This forms the basis of a model that relates the chemical shift of the 4f-electron binding energy in the divalent lanthanide with that in the trivalent one. Eu will be used as the lanthanide of reference, and special attention is devoted to the 4f-electron binding energy difference between Eu2+ and Eu3+. When that difference is known, the model provides the 4f-electron binding energies of all divalent and all trivalent lanthanide ions relative to the vacuum energy.

Pieter Dorenbos

2012-04-06T23:59:59.000Z

296

Binding of He{sub n}V clusters to ?-Fe grain boundaries  

SciTech Connect (OSTI)

The objective of this research is to explore the formation/binding energetics and length scales associated with the interaction between He{sub n}V clusters and grain boundaries in bcc ?-Fe. In this work, we calculated formation/binding energies for 18 He atoms in a monovacancy at all potential grain boundary (GB) sites within 15? of the ten grain boundaries selected (122106 simulations total). The present results provide detailed information about the interaction energies and length scales of 18 He atoms with grain boundaries for the structures examined. A number of interesting new findings emerge from the present study. First, the ?3(112) twin GB has significantly lower binding energies for all He{sub n}V clusters than all other boundaries in this study. For all grain boundary sites, the effect of the local environment surrounding each site on the He{sub n}V formation and binding energies decreases with an increasing number of He atoms in the He{sub n}V cluster. Based on the calculated dataset, we formulated a model to capture the evolution of the formation and binding energy of He{sub n}V clusters as a function of distance from the GB center, utilizing only constants related to the maximum binding energy and the length scale.

Tschopp, M. A., E-mail: mark.a.tschopp.civ@mail.mil [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); Gao, F. [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Solanki, K. N. [Arizona State University, Tempe, Arizona 85287 (United States)

2014-06-21T23:59:59.000Z

297

Sorption of proteins to charged microgels: characterizing binding isotherms and driving forces  

E-Print Network [OSTI]

We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound reactants (charged proteins). Application of this approach to lysozyme sorption to oppositely charged core-shell microgels allows us to extract the intrinsic, binding affinity of the protein to the gel, which is salt-concentration independent and mostly hydrophobic in nature. The total binding affinity is found to be mainly electrostatic in nature, changes many orders of magnitude during the sorption process, and is significantly influenced by osmotic deswelling effects. The intrinsic binding affinity is determined to be about 7 kBT for our system. We additionally show that Langmuir binding models and those based on excludedvolume interactions are formally equivalent for low to moderate protein packing, if the nature of the bound state is consistently defined. Having appreciated this, a more quantitative interpretation of binding isotherms in terms of separate physical interactions is possible in future for a wide variety of experimental approaches.

Cemil Yigit; Nicole Welsch; Matthias Ballauff; Joachim Dzubiella

2012-09-13T23:59:59.000Z

298

Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum  

E-Print Network [OSTI]

From opportunistic protist Cryptosporidium parvum we identified and functionally assayed a fatty acyl-CoA-binding protein (ACBP) gene. The CpACBP1 gene encodes a protein of 268 aa that is three times larger than typical ~10 KD ACBPs of humans...

Zeng, Bin

2009-05-15T23:59:59.000Z

299

Site-Specific Characterization of the Association of Xylooligosaccharides with the CBM13 Lectin-like Xylan Binding Domain from Streptomyces liVidans Xylanase  

E-Print Network [OSTI]

-like Xylan Binding Domain from Streptomyces liVidans Xylanase 10A by NMR Spectroscopy Manuela Scha binding sites (R, , and ) for a variety of small sugars, xylooligosaccharides, and xylan polymers surfaces, type B CBMs bind to polysaccharides, and type C CBMs bind to mono- and disaccharides (3). Within

McIntosh, Lawrence P.

300

T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users  

Broader source: Energy.gov (indexed) [DOE]

3: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets 3: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service May 31, 2011 - 3:35pm Addthis PROBLEM: A vulnerability was reported in BIND. A remote user can cause denial of service conditions. PLATFORM: BIND Version(s): 9.4-ESV-R3 and later, 9.6-ESV-R2 and later, 9.6.3, 9.7.1 and later, 9.8.0 and later; prior to 9.4-ESV-R4-P1, 9.6-ESV-R4-P1, 9.7.3-P1, 9.8.0-P2 ABSTRACT: A remote DNS server can supply very large RRSIG RRsets in a negative response to trigger an off-by-one error in a buffer size check and cause the target requesting named process to crash. A remote user can cause named to crash. reference LINKS: SecurityTracker Alert ID: 1025575 SecurityTracker Alert ID: 1025572

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Association of Copper to Riboflavin Binding Protein; Characterization by EPR and XAS  

SciTech Connect (OSTI)

The association of copper to Riboflavin Binding Protein (RBP) from egg white has been studied by electron paramagnetic resonance (EPR) and X-ray absorption (XAS) spectroscopies. The type II site contains a mix of copper I and II in an oxygen rich environment. The association of copper to Riboflavin Binding Protein (RBP) from egg white has been studied by electron paramagnetic resonance (EPR) and X-ray absorption (XAS) spectroscopies in order to provide insight into how this essential protein may transport and store copper in avian embryos. Riboflavin Binding Protein, RBP, purified from avian egg white, has been shown to bind copper in a 1:1 molar ratio when dialyzed against copper(II) [1]. While the egg is a unique environment and quite rich in copper, the mechanisms by which this copper is delivered during development and stored for eventual use remain unclear [2]. Since RBP is already identified in the active transport of the cofactor riboflavin to the egg, evidence of its copper binding ability may suggest an additional role for RBP in the transport and storage of copper.

Smith,S.; Bencze, K.; Wasiukanis, K.; Stemmler, T.; Benore-Parsons, M.

2008-01-01T23:59:59.000Z

302

The effect of heat stress on 1,25-dihydroxycholecalciferol induced calcium-binding protein in laying hens  

E-Print Network [OSTI]

atoms of calcium per molecule of protein (Wasserman and Taylor, 1968), and although it has a high specificity for calcium, it may also bind strontium and barium. A mammalian intestinal calcium- binding protein having a molecular weight...THE EFFECT OF HEAT STRESS ON 1, 25-DIHYDROXYCHOLECALCIFEROL INDUCED CALCIUM-BINDING PROTEIN IN LAYING HENS A Thesis by BONNIE HARRIET KAY SCHAEFFER Submitted to the Office of Graduate Studies Texas AErM University in partial fulfillment...

Schaeffer, Bonnie Harriet Kay

2012-06-07T23:59:59.000Z

303

A model for the hypolipidemic effect of chitosan : in vitro binding of bile acids and mixed micelles  

E-Print Network [OSTI]

lipids in the micelles or microemulsions are then incapable of being absorbed by the intestines. The proposal was tested in vitro by binding pure bile salts, mixed micelles, and model microemulsions to chitosan. The free lipids were separated from... the chitosan-lipid complex by rapid ultrafiltration and analyzed by either a colorimetric determina- tion or radioactive labeling. Chitosan was found to be an excellent binding agent for pure bile salts, binding up to 5 mg of bile salt per mg chitosan...

Nauss, Jeffrey Lynn

2012-06-07T23:59:59.000Z

304

U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free  

Broader source: Energy.gov (indexed) [DOE]

1: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding 1: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free Vulnerability U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding Use-After-Free Vulnerability February 13, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in multiple Mozilla products. PLATFORM: Mozilla Firefox 10.x Mozilla SeaMonkey 2.x Mozilla Thunderbird 10.x ABSTRACT: A vulnerability has been reported in multiple Mozilla products, which can be exploited by malicious people to compromise a user's system. reference LINKS: Vendor Advisory Secunia Advisory SA48008 CVE-2012-0452 IMPACT ASSESSMENT: High Discussion: A remote user can create HTML that, when loaded by the target user, will execute arbitrary code on the target user's system. The vulnerability is caused due to a use-after-free error in the

305

The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Unique Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A Markus Alahuhta, Qi Xu, Yannick J. Bomble, Roman Brunecky, William S. Adney, Shi-You Ding, Michael E. Himmel and Vladimir V. Lunin⁎ National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA Received 26 April 2010; received in revised form 12 July 2010; accepted 14 July 2010 Available online 21 July 2010 The crystal structure of the carbohydrate-binding module (CBM) 4 Ig fused domain from the cellulosomal cellulase cellobiohydrolase A (CbhA) of Clostridium thermocellum was solved in complex with cellobiose at 2.11 Å resolution. This is the first cellulosomal CBM4 crystal structure reported to date. It is similar to the previously solved noncellulosomal soluble oligosaccharide-binding CBM4 structures. However, this new structure possesses a significant

306

Different antagonist binding properties of rat pancreatic and cardiac muscarinic receptors  

SciTech Connect (OSTI)

The antagonist binding properties of rat pancreatic and cardiac muscarinic receptors were compared. In both tissues pirenzepine (PZ) had a low affinity for muscarinic receptors labelled by (/sup 3/H)N-methylscopolamine ((/sup 3/)NMS) (K/sub D/ values of 140 and 280nM, respectively, in pancreatic and cardiac homogenates). The binding properties of pancreatic and cardiac receptors were, however, markedly different. This was indicated by different affinities for dicyclomine, (11-(/(2-((diethylamino)-methyl)-1-piperidinyl/acetyl)-5, 11-dihydro-6H-pyrido(2,3-b)(1,4) benzodiazepin-6-on)(AFDX-116), 4-diphenylacetoxy-N-methyl-piperidine methobromide (4-DAMP) and hexahydrosiladifenidol (HHSiD). Pancreatic and cardiac muscarinic receptros also showed different (/sup 3/H)NMS association and dissociation rates. These results support the concept of M2 receptor subtypes have different binding kinetic properties. 20 references, 3 figures, 1 table.

Waelbroeck, M.; Camus, J.; Winand, J.; Christophe, J.

1987-11-09T23:59:59.000Z

307

Structural Plasticity Underpins Promiscuous Binding of the Prosurvival Protein A1  

SciTech Connect (OSTI)

Apoptotic pathways are regulated by protein-protein interactions. Interaction of the BH3 domains of proapoptotic Bcl-2 family proteins with the hydrophobic groove of prosurvival proteins is critical. Whereas some BH3 domains bind in a promiscuous manner, others exhibit considerable selectivity and the sequence characteristics that distinguish these activities are unclear. In this study, crystal structures of complexes between the prosurvival protein A1 and the BH3 domains from Puma, Bmf, Bak, and Bid have been solved. The structure of A1 is similar to that of other prosurvival proteins, although features, such as an acidic patch in the binding groove, may allow specific therapeutic modulation of apoptosis. Significant conformational plasticity was observed in the intermolecular interactions and these differences explain some of the variation in affinity. This study, in combination with published data, suggests that interactions between conserved residues demarcate optimal binding.

Smits,C.; Czabotar, P.; Hinds, M.; Day, C.

2008-01-01T23:59:59.000Z

308

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint  

SciTech Connect (OSTI)

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

2014-10-02T23:59:59.000Z

309

LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins  

SciTech Connect (OSTI)

Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U. (MIT); (ETH Zurich)

2012-08-31T23:59:59.000Z

310

Molecular imaging of water binding state and diffusion in breast cancer using diffuse optical spectroscopy and diffusion weighted MRI  

E-Print Network [OSTI]

Molecular imaging of water binding state and diffusion inChung et al. , In vivo water state measurements in breastby measuring tis- sue water state using diffuse optical

Chung, So Hyun; Yu, Hon; Su, Min-Ying; Cerussi, Albert E.; Tromberg, Bruce J.

2012-01-01T23:59:59.000Z

311

Expansion of the NRL Tight-Binding Method to Include f-orbitals and Application in Thorium and Actinium .  

E-Print Network [OSTI]

??The current NRL Tight-Binding suite of programs was designed to only include s, p, and d orbitals in the basis. Because of this limitation, materials (more)

Durgavich, Joel

2012-01-01T23:59:59.000Z

312

Ethylene oxides as hydrogen storage material with pockets in the electronic binding energy distribution  

Science Journals Connector (OSTI)

Using ab initio calculations, we have found that the oxygen atoms in oligomers of ethylene oxide have optimal binding with hydrogen molecules for hydrogen storage. Our theoretical model and molecular-dynamics simulations predict that adsorption-desorption process for such a candidate material occurs under unprecedented ambient conditions, T?300?K and P=113?atm, achieving gravimetric storage capacity of hydrogen up to 6.2?wt?%. We have also uncovered the special binding mechanism between a hydrogen molecule and an oxygen-embedded material which is enhanced by electron donation and back-donation.

Sungjong Woo and Young-Kyun Kwon

2009-02-02T23:59:59.000Z

313

Studies on immunoglobulins and complement binding to the surface of Schistosoma mansoni  

E-Print Network [OSTI]

. , Texas A&M University Chairman of Advisory Committee: Walter Michael Kemp (Ph. D. ) An indirect assay was used to detect binding of Fc associated specific anti-schistosome antibody (homospec1fic antibody) to adult male schistosomes. Binding... of this homospecific antibody could be demonstrated by utilizing freeze thaw antigen, anti-schistosome ~ ntihody a d iiuoresceinated ~Sta h iococcus au eus tnBI which h d to the Fc reg1on of the second antibody. Control experiments w1th reconstitution of eluted...

Rasmussen, Kathleen Ruth

2012-06-07T23:59:59.000Z

314

Importance of the Doppler Effect to the Determination of the Deuteron Binding Energy  

E-Print Network [OSTI]

The deuteron binding energy extracted from the reaction ${}^1H(n,\\gamma){}^2H$ is reviewed with the exact relativistic formula, where the initial kinetic energy and the Doppler effect are taken into account. We find that the negligible initial kinetic energy of the neutron could cause a significant uncertainty which is beyond the errors available up to now. Therefore, we suggest an experiment which should include the detailed informations about the initial kinetic energy and the detection angle. It could reduce discrepancies among the recently reported values about the deuteron binding energy and pin down the uncertainty due to the Doppler broadening of $\\gamma$ ray.

Yongkyu Ko; Myung Ki Cheoun; Il-Tong Cheon

1999-04-01T23:59:59.000Z

315

New Mathematical Method Reveals Where Proteins Bind with DNA to Switch  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Mathematical Mathematical Method Reveals Where Genes Switch On or Off New Mathematical Method Reveals Where Genes Switch On or Off "Compressed sensing" determines atomic-level energy potentials with accuracy approaching experimental measurement February 22, 2012 | Tags: Biological and Environmental Research (BER), Carver, Chemistry, Life Sciences, Math & Computer Science, NISE John Hules, JAHules@lbl.gov, +1 510 486 6008 Figure 1. Helix-turn-helix (HTH) proteins are the most widely distributed family of DNA-binding proteins, occurring in all biological kingdoms. This image shows a lambda repressor HTH transcription factor (green) binding to a lambda operator DNA sequence (blue and red) of the virus bacteriophage lambda. Image: Richard Wheeler, Wikipedia

316

Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon  

E-Print Network [OSTI]

Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon (Cdc6)/Origin Replication Complex subunit 1 (Orc1) proteins share sequence homology with eukaryotic DNA under- stand whether Cdc6/Orc1 functions in an eukaryotic or bacterial-like manner, we have

Berger, James M.

317

A beta 3 integrin mutation abolishes ligand binding and alters divalent cation-dependent conformation  

Science Journals Connector (OSTI)

...Dean, L. Kincla, H. R. Sykes, A. R. Lehmann, I. A. Wise, Exp. Cell Res. 183, 473 (1989)]. 15. S. J. Baker...JOSEPH C. LOFTUS,* TIMOTHY E. O'TOOLE, EDWARD F. PLOW, ALISON GLASs, ANDREW L. FRELINGER III, MARK H. GINSBERG The ligand-binding...

JC Loftus; TE O'Toole; EF Plow; A Glass; AL Frelinger 3rd; MH Ginsberg

1990-08-24T23:59:59.000Z

318

Disordered graphene and boron nitride in a microwave tight-binding analogue S. Barkhofen,1  

E-Print Network [OSTI]

Disordered graphene and boron nitride in a microwave tight-binding analogue S. Barkhofen,1 M Sophia-Antipolis, 06108 Nice, France (Dated: December 20, 2012) Experiments on hexagonal graphene of the high flexibility of the discs positions, consequences of the disorder introduced in the graphene

Paris-Sud XI, Université de

319

Influenza Virus Neuraminidases with Reduced Enzymatic Activity That Avidly Bind Sialic Acid Receptors  

Science Journals Connector (OSTI)

...reaction, the catalytic efficiency (k cat/Km ) is...enhancement of the catalytic efficiency of avian NAs by binding...the governments of Egypt and the United States...S. Department of Energy (DOE) Office of Basic Energy Sciences. The Stanford...

Xueyong Zhu; Ryan McBride; Corwin M. Nycholat; Wenli Yu; James C. Paulson; Ian A. Wilson

2012-09-26T23:59:59.000Z

320

Pax-2 is a DNA-binding protein expressed in embryonic kidney and Wilms tumor  

Science Journals Connector (OSTI)

...ingly, the Zn finger-containing gene WTI (34, 35) is expressed during kidney development...capsule (38). In the mouse expression of WTI peaks at about 3 days postpartum and decreases...tectable levels in the adult (39). The WTI gene can bind DNA specifically, indicative...

G R Dressler; E C Douglass

1992-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

Poly(C)-binding proteins as transcriptional regulators of gene expression  

SciTech Connect (OSTI)

Poly(C)-binding proteins (PCBPs) are generally known as RNA-binding proteins that interact in a sequence-specific fashion with single-stranded poly(C). They can be divided into two groups: hnRNP K and PCBP1-4. These proteins are involved mainly in various posttranscriptional regulations (e.g., mRNA stabilization or translational activation/silencing). In this review, we summarize and discuss how PCBPs act as transcriptional regulators by binding to specific elements in gene promoters that interact with the RNA polymerase II transcription machinery. Transcriptional regulation of PCBPs might itself be regulated by their localization within the cell. For example, activation by p21-activated kinase 1 induces increased nuclear retention of PCBP1, as well as increased promoter activity. PCBPs can function as a signal-dependent and coordinated regulator of transcription in eukaryotic cells. We address the molecular mechanisms by which PCBPs binding to single- and double-stranded DNA mediates gene expression.

Choi, Hack Sun [Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455 (United States)], E-mail: choix074@umn.edu; Hwang, Cheol Kyu; Song, Kyu Young; Law, P.-Y.; Wei, L.-N.; Loh, Horace H. [Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455 (United States)

2009-03-13T23:59:59.000Z

322

Nuclear Physics A 611 ( 1996) 484-513 Mesonic and binding contributions to the EMC  

E-Print Network [OSTI]

NUCLEAR PHYSICS A Nuclear Physics A 611 ( 1996) 484-513 Mesonic and binding contributions November 1995; revised 30 July 1996 Abstract We revise the conventional nuclear effects of Fermi motion for an interacting Fermi sea and the local density approximation to translate results from nuclear matter to finite

Fernández de Córdoba, Pedro

323

The Structural Basis for the Ligand Specificity of Family 2 Carbohydrate-binding Modules*  

E-Print Network [OSTI]

of proteins with polysaccharides play a key role in the microbial hydrolysis of cellulose and xylan, the most family, CBM2, contains members that bind cellu- lose (CBM2a) and xylan (CBM2b), respectively. A possi- ble explanation for the different ligand specificity of CBM2b is that one of the surface tryptophans

Williamson, Mike P.

324

Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis  

Science Journals Connector (OSTI)

...desorption, despite high xylan solubilization, which...inactive enzymes from the surface of cellulose is competitive...the increased fibril surface hydrophilicity as confirmed...enzyme binding, cellulose surface chain extraction, and...substrates and chemical treatment methods used are provided in SI...

Dahai Gao; Shishir P. S. Chundawat; Anurag Sethi; Venkatesh Balan; S. Gnanakaran; Bruce E. Dale

2013-01-01T23:59:59.000Z

325

Comparison between the many-body perturbative and Green's-function approaches for calculating electron binding  

E-Print Network [OSTI]

electron binding energies and affinities: Brueckner and Dyson orbitals Ingvar Lindgren November 30, 2003 exact. The former approach leads to Brueckner orbitals and the latter to Dyson orbitals, and it is shown's-function technique, Brueckner orbital, Dyson equation, Dyson orbital, self energy, electron affinity Table

Lindgren, Ingvar

326

Epigallocatechin gallate, the main polyphenol in green tea, binds to the T-cell receptor,  

E-Print Network [OSTI]

Epigallocatechin gallate, the main polyphenol in green tea, binds to the T-cell receptor, CD4D,b and William T. Shearer, MD, PhDb Sheffield, United Kingdom, and Houston, Tex Background: The green tea that is one of the main active components of green tea. Among the properties ascribed to EGCG

Williamson, Mike P.

327

ATP-binding cassette transporters are required for efficient RNA interference in Caenorhabditis elegans  

E-Print Network [OSTI]

that facilitate RNAi have been identified, current descriptions of RNAi and interrelated mechanisms are far from complete. Here, we report that the Caenorhabditis elegans gene haf-6 is required for efficient RNAi. HAF-6 is a member of the ATP-binding cassette (ABC...

Timmons, Lisa; Hull, Dawn; Han, Wang; Echalier, B.; Sundaram, P.

2006-08-01T23:59:59.000Z

328

A blue-light-activated GTP-binding protein in the plasma membranes of etiolated peas.  

Science Journals Connector (OSTI)

...GTP-binding protein in the plasma membranes of etiolated peas KATHERINE M. F. WARPEHA*, HEIDI E. HAMMt, MARK M. RASENICKt...Acad. Sci. USA 85, 3066-3070. 20. Rasenick, M. M., Wheeler, G. L., Bitensky, M. W., Kosack, C. & Stein, P...

K M Warpeha; H E Hamm; M M Rasenick; L S Kaufman

1991-01-01T23:59:59.000Z

329

Using electrospray ionization FTICR mass spectrometry to study competitive binding of inhibitors to carbonic anhydrase  

SciTech Connect (OSTI)

We report a method based on mass spectrometry for the characterization of noncovalent complexes of proteins with mixtures of ligands; this method is relevant to the study of drug leads and may be useful in screening libraries for tight-binding compounds. This study describes the competitive binding of inhibitors derived from para-substituted benzenesulfonamides to bovine carbonic anhydrase II (BCAII, EC 4.2.1.1) using this technique. Relative binding constants and structural information for a mixture of inhibitors can be obtained in a single experiment using ESI-FTICR-MS. The work demonstrates that ESI-MS has significant potential for measuring relative binding affinities and characterizing the structures of ligands associated noncovalently to proteins. We have detected noncovalent complexes in the gas phase for ligands having values of K{sub b} as low as 1.7 x 10{sup 6} M{sup -1} in solution. The technique also allowed identification of tightbinding ligands from small libraries. The structures of inhibitors having similar masses can be identified by the high-resolution and multistep dissociation mass spectrometry of which FTICR is uniquely capable. This range of capabilities for ESI-FTICR-MS should be widely useful in medicinal chemistry. 22 refs., 2 figs.

Cheng, X.; Chen, R.; Bruce, J.E.; Schwartz, B.L.; Anderson, G.A.; Hofstadler, S.A.; Gale, D.C.; Smith, R.D. [Pacific Northwest Lab., Richland, WA (United States); Gao, J.; Sigal, G.B.; Mammen, M.; Whitesides, G.M. [Harvard Univ., Cambridge, MA (United States)

1995-08-30T23:59:59.000Z

330

Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel  

E-Print Network [OSTI]

We obtained unanticipated synthetic byproducts from alkylation of the ?[superscript 1] nitrogen (N3) of the histidine imidazole ring of the polo-like kinase-1 (Plk1) polo-box domain (PBD)-binding peptide PLHSpT. For the ...

Lim, Dan

331

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea  

Science Journals Connector (OSTI)

We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some ... Keywords: Genome size, Helix-turn-helix DNA-binding motif, Protein families, Transcription factors

Ernesto Prez-Rueda; Julio Collado-Vides; Lorenzo Segovia

2004-12-01T23:59:59.000Z

332

Monoclonal antibodies to the human insulin receptor block insulin binding and inhibit insulin action  

Science Journals Connector (OSTI)

...This 10-fold difference in the relative affinitv ; c 60 A God of the antibody for the receptors from different tissues may...IGF-I binding to its receptor in both IM-9 cells and placenta particles. However, 500-fold higher antibody concen- , ;, E 40 1...

R A Roth; D J Cassell; K Y Wong; B A Maddux; I D Goldfine

1982-01-01T23:59:59.000Z

333

Membrane Binding of Ribosomes Occurs at SecYE-based Sites in the Archaea Haloferax volcanii  

E-Print Network [OSTI]

by the signal recognition particle (SRP).10 SRP binding subsequently slows or pre- vents the continuation of further protein synthe- sis.11 The ternary complex of ribosome­nascent polypeptide chain­SRP then interacts with the ER membrane via the affinities of SRP for the mem- brane-associated SRP receptor,12

Eichler, Jerry

334

Structural Basis for Simultaneous Binding of Two Carboxy-terminal Peptides of Plant Glutamate  

E-Print Network [OSTI]

of glutamate decarboxylase (GAD) by calcium-bound calmodulin (CaM) is required for normal plant growth through- otic cell-cycle rely on fine-tuned intracellular calcium (Ca2þ ) regulation for normal operation. Proteins containing the Ca2þ -binding EF-hand (helix-loop-helix) motif are known to be involved

Ikura, Mitsuhiko

335

MODELING OF CAPILLARY FORCES AND BINDING SITES FOR FLUIDIC SELF-ASSEMBLY  

E-Print Network [OSTI]

MODELING OF CAPILLARY FORCES AND BINDING SITES FOR FLUIDIC SELF-ASSEMBLY Karl F. Böhringer 1-1774 ABSTRACT Massively parallel self-assembly is emerging as an efficient, low-cost alternative to conventional pick-and-place assembly of microfabricated components. The fluidic self-assembly technique we have

336

Strip, Bind, and Search: A Method for Identifying Abnormal Energy Consumption in Buildings  

E-Print Network [OSTI]

Strip, Bind, and Search: A Method for Identifying Abnormal Energy Consumption in Buildings Romain usage that leads to energy waste. The av- erage waste uncovered is as high as 2500 kWh per device; Energy Consumption; Anomaly Detection 1. INTRODUCTION Buildings are one of the prime targets to reduce

California at Berkeley, University of

337

Hydrogen-impurity binding energy in vanadium and niobium A. Mokrani and C. Demangeat  

E-Print Network [OSTI]

2243 Hydrogen-impurity binding energy in vanadium and niobium A. Mokrani and C. Demangeat IPCMS, UM by the hydrogen) contribution, ii) the band structure contribution, iii) the electron-electron interaction without. Strong H-H repulsion is observed when the hydrogen atoms are at first nearest neighbouring positions

Boyer, Edmond

338

A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate  

E-Print Network [OSTI]

A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate of determining and evaluating protein folding conditions, we have designed a new fractional factorial protein folding screen. The screen includes 12 factors shown by previous experiments to enhance protein folding

Lebendiker, Mario

339

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability  

E-Print Network [OSTI]

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

Weston, Ken

340

Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors  

E-Print Network [OSTI]

different cellular functions: steroidogenic acute regulatory protein (StAR), hepatocyte nuclear factor-4a (HNF-4a) and acyl-CoA binding protein (ACBP). First, StAR mediates delivery of cholesterol to inner mitochondrial membrane in steroidogenesis by a...

Petrescu, Anca Daniela

2004-09-30T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

RESEARCH Open Access HIV-1 Tat protein binds to TLR4-MD2 and signals  

E-Print Network [OSTI]

RESEARCH Open Access HIV-1 Tat protein binds to TLR4-MD2 and signals to induce TNF- and IL-10 Nawal in a TLR4 dependent manner. Conclusions: Collectively, our data showed for the first time that, HIV-1 Tat progression. Keywords: HIV-1, TLR4, Tat, IL-10, TNF- Background HIV-1 infects numerous cells of the immune

Boyer, Edmond

342

Characterization of network morphology in anion binding hydrogels used for wastewater remediation  

E-Print Network [OSTI]

Characterization of network morphology in anion binding hydrogels used for wastewater remediation wastewater effluents. The sorbent used was crosslinked polyamine (PAA$HCl) polymeric hydrogels. The surface of crosslinking. q 2005 Elsevier Ltd. All rights reserved. Keywords: Hydrogel; Atomic force microscopy; Wastewater

Rubloff, Gary W.

343

Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study  

SciTech Connect (OSTI)

The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented.

Ramrez-Morales, A.; Martnez-Orozco, J. C.; Rodrguez-Vargas, I. [Unidad Acadmica de Fsica, Universidad Autnoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, Zac. (Mexico)

2014-05-15T23:59:59.000Z

344

Single-molecule binding experiments on long time scales Mark P. Elenko,1  

E-Print Network [OSTI]

Single-molecule binding experiments on long time scales Mark P. Elenko,1 Jack W. Szostak,2; accepted 11 July 2010; published online 27 August 2010 We describe an approach for performing single-molecule than have been previously investigated by single-molecule techniques. Total internal reflection

Heller, Eric

345

Ammonium PerchlorateBinding Poly(allylamine hydrochloride) Hydrogels for Wastewater Remediation  

E-Print Network [OSTI]

(allylamine hydrochloride) (PAA HCl) polymeric hydrogel. The pH-sensitive PAA HCl hydrogels were synthesized by chemically crosslinking a solu- tion of linear PAA HCl chains with epichlorohydrin (EPI). The perchlorate-binding capacity opportunities to recover and reuse the hydrogel over multiple regeneration cycles. The PAA HCl hydrogels

Kofinas, Peter

346

Methanobactin: a copper binding compound having antibiotic and antioxidant activity isolated from methanotrophic bacteria  

DOE Patents [OSTI]

A means and method for treating bacterial infection, providing antioxidant activity, and chelating copper using a copper binding compound produced by methanotrophic bacteria is described. The compound, known as methanobactin, is the first of a new class of antibiotics having gram-positive activity. Methanobactin has been sequenced, and its structural formula determined.

DiSpirito, Alan A. (Ames, IA); Zahn, James A. (Harbor Beach, MI); Graham, David W. (Lawrence, KS); Kim, Hyung J. (St. Paul, MN); Alterman, Michail (Lawrence, KS); Larive, Cynthia (Lawrence, KS)

2007-04-03T23:59:59.000Z

347

Structural and Functional Analysis of Coxsackievirus A9 Integrin ?v?6 Binding and Uncoating  

Science Journals Connector (OSTI)

...which binds to the bent alpha2beta1 integrin...D Stuart. 1999. The crystal structure of coxsackievirus...integrins by conversion from bent to extended conformations...and MA Arnaout. 2002. Crystal structure of the extracellular...method for identifying spherical particles in electron...

Shabih Shakeel; Jani J. T. Seitsonen; Tommi Kajander; Pasi Laurinmki; Timo Hyypi; Petri Susi; Sarah J. Butcher

2013-01-30T23:59:59.000Z

348

JOURNAL OF CELLULAR PHYSIOLOGY 198:188196 (2004) Geldanamycin, a Heat Shock Protein 90-Binding Agent,  

E-Print Network [OSTI]

JOURNAL OF CELLULAR PHYSIOLOGY 198:188­196 (2004) Geldanamycin, a Heat Shock Protein 90-Binding and Feramisco, 1982). It has been reported that Hsp90 plays a critical role in regulating signal transduc- tion of proteins including nuclear hormone receptors, protein kinases, and transcription factors (Pratt, 1998

Tian, Weidong

349

Distribution of binding energies of a water molecule in the water liquid-vapor interface  

SciTech Connect (OSTI)

Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

2008-01-01T23:59:59.000Z

350

Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds  

SciTech Connect (OSTI)

Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah; Kaminsky, Werner; Malmquist, Nicholas A.; Goldsmith, Elizabeth J.; Rathod, Pradipsinh K.; Phillips, Margaret A.; (UWASH); (UTSMC)

2010-01-20T23:59:59.000Z

351

Original article Increase of plasma eCG binding rate after  

E-Print Network [OSTI]

Original article Increase of plasma eCG binding rate after administration of repeated high dose of eCG to cows Pierre V. DRIONa*, Rudy DE ROOVERb, Jean-Yves HOUTAINc, Edmond M. MCNAMARAd, Benoît chorionic gonadotrophin (eCG) is still used to promote follicular growth in cat- tle and, more recently

Paris-Sud XI, Université de

352

Effect of pH on the Binding of -Lactoglobulin to Sodium Polystyrenesulfonate R. K. Hallberg and P. L. Dubin*  

E-Print Network [OSTI]

or for pentalysine/DNA data. The current results suggest that the free energy of binding of a protein to a synthetic, Indianapolis, Indiana 46202-3274 ReceiVed: June 23, 1998 The binding of -lactoglobulin to the synthetic. Introduction Proteins interact strongly with both natural polyelectrolytes and synthetic polyelectrolytes

Dubin, Paul D.

353

Binding energies and electronic structures of adsorbed titanium chains on carbon nanotubes Chih-Kai Yang,1  

E-Print Network [OSTI]

Binding energies and electronic structures of adsorbed titanium chains on carbon nanotubes Chih studied the binding energies and electronic structures of metal Ti, Al, Au chains adsorbed on single in nanoscale materials and devices. A nanotube with adsorbed materials may also significantly changes its physi

354

ATP Utilization by Yeast Replication Factor C II. MULTIPLE STEPWISE ATP BINDING EVENTS ARE REQUIRED TO LOAD PROLIFERATING CELL  

E-Print Network [OSTI]

ATP Utilization by Yeast Replication Factor C II. MULTIPLE STEPWISE ATP BINDING EVENTS ARE REQUIRED of adenosine (3-thiotriphosphate) (ATP S), a nonhydrolyzable analog of ATP, to replication factor C with a N-terminal truncation ( 2­273) of the Rfc1 sub- unit (RFC) was studied by filter binding. RFC alone bound 1.8 ATP

Burgers, Peter M.

355

Biochem. J. (2000) 345, 5360 (Printed in Great Britain) 53 Carbohydrate-binding modules from a thermostable Rhodothermus marinus  

E-Print Network [OSTI]

binding to insoluble xylan and to phosphoric-acid- swollen cellulose but not to Avicel or crystalline occurred with different xylans and -glucan. CBM4-2 displayed a somewhat higher binding affinity than CBM4 in the effective enzyme concentration on the substrate surface that is caused by the attachment of the CBM [14

Williamson, Mike P.

356

A Secondary Xylan-binding Site Enhances the Catalytic Activity of a Single-domain Family 11  

E-Print Network [OSTI]

A Secondary Xylan-binding Site Enhances the Catalytic Activity of a Single-domain Family 11 surface region. Chemical shift perturbation mapping and affinity electrophoresis, combined with mutational studies, identified the xylan-specific secondary binding site (SBS) as a shallow groove lined by Asn, Ser

McIntosh, Lawrence P.

357

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures  

Science Journals Connector (OSTI)

......ligand-binding sites than inspection of sequence conservation alone. Indeed, binding sites with a...Press 2002 LigBase themselves; however, water molecules are not retained in the database...integration will also dramatically increase the pool of available structures for the study......

Ashley C. Stuart; Valentin A. Ilyin; Andrej Sali

2002-01-01T23:59:59.000Z

358

A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome  

E-Print Network [OSTI]

the human genome; 1,654 proteins are predicted to have DNA-binding function. Comparison with existing Gene) A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. PLo have been released, and about 5,000 active genome sequencing projects are on the way [6

Skolnick, Jeff

359

1997 Oxford University Press49945002 Nucleic Acids Research, 1997, Vol. 25, No. 24 Information analysis of Fis binding sites  

E-Print Network [OSTI]

analysis of Fis binding sites Paul N. Hengen1, Stacy L. Bartram1,2,+, Lisa E. Stewart1 and Thomas D 30, 1997 ABSTRACT Originally discovered in the bacteriophage Mu DNA inversion system gin, Fis (Factor for Fis to locate its binding sites, we collected a set of 60 experimentally defined wild-type Fis DNA

Schneider, Thomas D.

360

Measurement of the Binding Energy for Di-C2H4/Pt{111}: Does a Radical Intermediate Form  

E-Print Network [OSTI]

Measurement of the Binding Energy for Di- C2H4/Pt{111}: Does a Radical Intermediate Form During energy surface. This well depth, or binding energy, is determined by measuring the threshold that temperature-programmed desorption involves a nonequilibrium measurement; thus, the activation energy

Levis, Robert J.

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361

Dirac Point and Edge States in a Microwave Realization of Tight-Binding Graphene-like Structures  

E-Print Network [OSTI]

Dirac Point and Edge States in a Microwave Realization of Tight-Binding Graphene-like Structures U-binding graphene-like structures. The structures are realized using disks with a high index of refraction properties, mechan- ically as electronically. Another realization is graphene, a one-atom-thick allotrope

Boyer, Edmond

362

Inhibition of Both HIV-1 Reverse Transcription and Gene Expression by a Cyclic Peptide that Binds the Tat-  

E-Print Network [OSTI]

Inhibition of Both HIV-1 Reverse Transcription and Gene Expression by a Cyclic Peptide that Binds the Tat- Transactivating Response Element (TAR) RNA Matthew S. Lalonde1" , Michael A. Lobritz2" , Annette The RNA response element TAR plays a critical role in HIV replication by providing a binding site

Levin, Judith G.

363

Identification of a putative calcium-binding protein as a dioxin-responsive gene in zebrafish and rainbow trout  

E-Print Network [OSTI]

Identification of a putative calcium-binding protein as a dioxin-responsive gene in zebrafish; accepted 16 October 2002 Abstract 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD, dioxin) is a widespread in zebrafish and rainbow trout that dioxin increases expression of this EF-hand calcium-binding protein gene

Tullos, Desiree

364

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0  

Science Journals Connector (OSTI)

......Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0 Xiaolei Zhu 1 Yi Xiong 1 Daisuke Kihara...Results: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for......

Xiaolei Zhu; Yi Xiong; Daisuke Kihara

2014-10-01T23:59:59.000Z

365

Vacancies and small vacancy clusters in BCC transition metals : calculation of binding energy, atomic relaxation and electronic  

E-Print Network [OSTI]

921 Vacancies and small vacancy clusters in BCC transition metals : calculation of binding energy(E) and gi(03C9), for vacancy-type lattice defects in BCC transition metals : The short-range repulsive energies between neighbouring atomic sites are simulated by a Born-Mayer potential. Binding energies of di-vacancies

Paris-Sud XI, Université de

366

Cable Pili and the 22-Kilodalton Adhesin Are Required for Burkholderia cenocepacia Binding to and Transmigration across the Squamous Epithelium  

Science Journals Connector (OSTI)

...PATHOGEN-HOST CELL MOLECULAR INTERACTIONS Cable Pili and the 22-Kilodalton Adhesin Are...Burkholderia cenocepacia strains expressing both cable (Cbl) pili and the 22-kDa adhesin bind...binding (0 to 8%). Mutants lacking either cable pili or the adhesin were compromised in...

Teresa A. Urban; Joanna B. Goldberg; Janet F. Forstner; Umadevi S. Sajjan

2005-09-01T23:59:59.000Z

367

Specific Fluorine Labeling of the HyHEL10 Antibody Affects Antigen Binding and Dynamics  

SciTech Connect (OSTI)

To more fully understand the molecular mechanisms responsible for variations in binding affinity with antibody maturation, we explored the use of site specific fluorine labeling and {sup 19}F nuclear magnetic resonance (NMR). Several single-chain (scFv) antibodies, derived from an affinity-matured series of anti-hen egg white lysozyme (HEL) mouse IgG1, were constructed with either complete or individual replacement of tryptophan residues with 5-fluorotryptophan ({sup 5F}W). An array of biophysical techniques was used to gain insight into the impact of fluorine substitution on the overall protein structure and antigen binding. SPR measurements indicated that {sup 5F}W incorporation lowered binding affinity for the HEL antigen. The degree of analogue impact was residue-dependent, and the greatest decrease in affinity was observed when {sup 5F}W was substituted for residues near the binding interface. In contrast, corresponding crystal structures in complex with HEL were essentially indistinguishable from the unsubstituted antibody. {sup 19}F NMR analysis showed severe overlap of signals in the free fluorinated protein that was resolved upon binding to antigen, suggesting very distinct chemical environments for each {sup 5F}W in the complex. Preliminary relaxation analysis suggested the presence of chemical exchange in the antibody-antigen complex that could not be observed by X-ray crystallography. These data demonstrate that fluorine NMR can be an extremely useful tool for discerning structural changes in scFv antibody-antigen complexes with altered function that may not be discernible by other biophysical techniques.

Acchione, Mauro; Lee, Yi-Chien; DeSantis, Morgan E.; Lipschultz, Claudia A.; Wlodawer, Alexander; Li, Mi; Shanmuganathan, Aranganathan; Walter, Richard L.; Smith-Gill, Sandra; Barchi, Jr., Joseph J. (SAIC); (NCI)

2012-10-16T23:59:59.000Z

368

Aldosterone binding in isolated tubules. IV. Autoradiography along the nephron of the spontaneously hypertensive rat  

SciTech Connect (OSTI)

The binding of aldosterone was studied in tubular segments isolated by microdissection from kidneys of spontaneously hypertensive (SHR, n = 8), Kyoto normotensive (KWR, n = 8), and normal Wistar (NWR, n = 6) rats with an autoradiographic technique on dry film. All animals had been previously adrenalectomized. Kidney pyramids were incubated in vitro before microdissection with collagenase and 2 X 10(-9) M (/sup 3/H)aldosterone in the presence or absence of an excess of unlabeled aldosterone. In addition, the displacement of the binding by 10 times excess dexamethasone or aldosterone was examined in the cortical and medullary collecting tubule of SHR and KWR to assess the specificity of binding sites. In the three groups, no specific nuclear labeling was detectable in the proximal tubule. The highest specific nuclear labeling was found in the distal portions of the nephron, and intermediate values were present along the loop of Henle. In the cortical collecting tubule, the most specific mineralocorticoid segment, the specific nuclear binding, expressed in silver grains per unit surface, was significantly elevated in SHR (16.1 +/- 1.5) and KWR (13.7 +/- 1.5) as compared with NWR (10.2 +/- 0.8, P less than 0.001 and less than 0.05, respectively). The difference between SHR and KWR did not reach statistical significance. In the medullary collecting tubule, binding was higher in SHR (14.3 +/- 1.6) than in both KWR (8.7 +/- 1.0, P less than 0.005) and NWR (10.1 +/- 0.9, P less than 0.025).

Farman, N.; Bonvalet, J.P.

1985-07-01T23:59:59.000Z

369

Calculation of the binding affinity of the anticancer drug daunomycin to DNA by a statistical mechanics approach  

Science Journals Connector (OSTI)

Equilibrium binding constants of the anticancer drug daunomycin, bound to several GC containing polymeric DNAs (G represent guanine and C cytosine), are calculated by means of a microscopic statistical mechanics approach and based on observed x-ray crystal structures. Our calculation shows base sequence specificity of daunomycin in agreement with the observations. We find the drug binding constant to be sensitive to the base composition of the host sequence. The binding stability decreases in the order of CGTACG, CGATCG, and CGGCCG, which is consistent with observations (T represents thymine and A adenine). This binding specificity arises from sequence specific hydrogen bond and nonbonded interactions between the drug and a host DNA. These interactions are affected by sequence specific structural features exhibited from x-ray crystallography. The agreement between our calculations and experiments shows that our method is of practical application in analyzing sequence specific binding stability of anticancer drugs.

Y. Z. Chen and Yong-Li Zhang

1997-06-01T23:59:59.000Z

370

A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors  

SciTech Connect (OSTI)

GspB is a serine-rich repeat (SRR) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIb{alpha}. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB{sub BR}), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB{sub BR} structure revealed that it is comprised of three independently folded subdomains or modules: (1) an Ig-fold resembling a CnaA domain from prokaryotic pathogens; (2) a second Ig-fold resembling the binding region of mammalian Siglecs; (3) a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIb{alpha}. Further examination of purified GspB{sub BR}-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspBBR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.

Pyburn, Tasia M.; Bensing, Barbara A.; Xiong, Yan Q.; Melancon, Bruce J.; Tomasiak, Thomas M.; Ward, Nicholas J.; Yankovskaya, Victoria; Oliver, Kevin M.; Cecchini, Gary; Sulikowski, Gary A.; Tyska, Matthew J.; Sullam, Paul M.; Iverson, T.M. (VA); (UCLA); (Vanderbilt); (UCSF)

2014-10-02T23:59:59.000Z

371

High-Affinity and Cooperative Binding of Oxidized Calmodulin by Methionine Sulfoxide Reductase  

SciTech Connect (OSTI)

Methionines play an important role in modulating protein-protein interactions associated with intracellular signaling, and their reversible oxidation to form methionine sulfoxides [Met(O)] in calmodulin (CaM) and other signaling proteins has been suggested to couple cellular redox changes to protein function changes through the action of methionine sulfoxide reductases (Msr). Prior measurements indicate the full recovery of target protein activation upon the stereospecific reduction of oxidized CaM by MsrA, where the formation of the S-stereoisomer of Met(O) selectively inhibits the CaM-dependent activation of the Ca-ATPase. However, the physiological substrates of MsrA remain unclear, as neither the binding specificities nor affinities of protein targets have been measured. To assess the specificity of binding and its possible importance in the maintenance of CaM function, we have measured the kinetics of repair and the binding affinity between oxidized CaM and MsrA. Reduction of Met(O) in fully oxidized CaM by MsrA is sensitive to protein folding, as repair of the intact protein is incomplete, with > 6 Met(O) remaining in each CaM following MsrA reduction. In contrast, following proteolytic digestion, MsrA is able to fully reduce one-half of the oxidized methionines, indicating that Met(O) within folded proteins are not substrates for MsrA repair. Further, in comparison to free Met(O), the turnover number and Km for oxidized CaM (CaMox) are substantially smaller, indicating that the binding interaction retards Msr recycling to reduce steady-state enzyme activity. Mutation of the active site (i.e., C72S) in MsrA permitted equilibrium-binding measurements using both ensemble and single-molecule measurements obtained by fluorescence correlation spectroscopy (FCS). Multiple MsrA bind tightly to CaMox (Kd = 70 +- 10 nM) with an affinity that is three orders of magnitude greater than the Michaelis constant (KM = 71 +- 8 micromolar). These results indicate that MsrA selectively reduces surface-exposed Met(O) within unstructured sequences and suggest that only a small subset of oxidized proteins are substrates for MsrA, which may selectively modulate the function of key signaling proteins as part of an adaptive response to oxidative stress.

Xiong, Yijia; Chen, Baowei; Smallwood, Heather S.; Urbauer, Ramona J.; Markillie, Lye Meng; Galeva, Nadezhda A.; Williams, Todd D.; Squier, Thomas C.

2006-12-12T23:59:59.000Z

372

Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli  

E-Print Network [OSTI]

Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for ...

Phillips, Christine M.

373

Promiscuous 8Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding  

E-Print Network [OSTI]

and Off-Pathway Protein Binding Uday Ghanty, Erik Fostvedt, Rachel Valenzuela, Peter A. Beal, and Cynthia

Beal, Peter A.

374

Mutually exclusive binding of two cellular factors within a critical promoter region of the gene for the IE110k protein of herpes simplex virus.  

Science Journals Connector (OSTI)

...between any of the constructs to endpoint - 89, and in fact pDRI exhibited activity very similar to that of the parent construct...construct pDR6 exhib- iting approximately 8% of the activity of pDRI. The deletion constructs pDR4 and pDR5, independent isolates...

D O'Rourke; P O'Hare

1993-12-01T23:59:59.000Z

375

Prediction of HLA-DRB1*0401 binding peptides using support vector machine  

Science Journals Connector (OSTI)

In recent years, many machine learning methods have been developed to predict HLA binding peptides. However, because only limited types of descriptors characterising the protein features are included in these approaches, these methods have poor prediction accuracy. In this study, we applied support vector machine methods to predict the peptides that bind to the major histocompatibility complexes Class II molecule HLA-DRB1*0401 using six sets of molecular descriptors characterising the primary structures of the peptides. We found that some feature groups provided good prediction accuracies and the overall accuracies were greater than 95% and some feature groups had poor accuracies of only 50%. The performance was improved significantly by additional feature selection and the overall accuracies from each group or combination of descriptors were greater than 90%. Of note, the inclusion of necessary informative and discriminative descriptors improved the prediction accuracies.

Wenli Huang; Guobing Yang; Xiaojun Zhao; Zerong Li

2014-01-01T23:59:59.000Z

376

Quenching methods for background reduction in luminescence-based probe-target binding assays  

DOE Patents [OSTI]

Background luminescence is reduced from a solution containing unbound luminescent probes, each having a first molecule that attaches to a target molecule and having an attached luminescent moiety, and luminescent probe/target adducts. Quenching capture reagent molecules are formed that are capable of forming an adduct with the unbound luminescent probes and having an attached quencher material effective to quench luminescence of the luminescent moiety. The quencher material of the capture reagent molecules is added to a solution of the luminescent probe/target adducts and binds in a proximity to the luminescent moiety of the unbound luminescent probes to quench luminescence from the luminescent moiety when the luminescent moiety is exposed to exciting illumination. The quencher capture reagent does not bind to probe molecules that are bound to target molecules and the probe/target adduct emission is not quenched.

Cai, Hong (Los Alamos, NM); Goodwin, Peter M (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Nolan, Rhiannon L. (Santa Fe, NM)

2007-04-10T23:59:59.000Z

377

Mutations in FMN Binding Pocket Diminish Chromate Reduction Rates for Gh-ChrR Isolated from Gluconacetobacter hansenii  

SciTech Connect (OSTI)

A putative chromate ion binding site was identified proximal to a rigidly bound FMN from electron densities in the crystal structure of the quinone reductase from Gluconacetobacter hansenii (Gh-ChrR) (3s2y.pdb). To clarify the location of the chromate binding site, and to understand the role of FMN in the NADPH-dependent reduction of chromate, we have expressed and purified four mutant enzymes involving the site-specific substitution of individual side chains within the FMN binding pocket that form non-covalent bonds with the ribityl phosphate (i.e., S15A and R17A in loop 1 between ?1 sheet and ?1 helix) or the isoalloxanzine ring (E83A or Y84A in loop 4 between the ?3 sheet and ?4 helix). Mutations that selectively disrupt hydrogen bonds between either the N3 nitrogen on the isoalloxanzine ring (i.e., E83) or the ribitylphos- phoate (i.e., S15) respectively result in 50% or 70% reductions in catalytic rates of chromate reduction. In comparison, mutations that disrupt ?-? ring stacking interactions with the isoal-loxanzine ring (i.e., Y84) or a salt bridge with the ribityl phosphate result in 87% and 97% inhibittion. In all cases there are minimal alterations in chromate binding affinities. Collectively, these results support the hypothesis that chromate binds proximal to FMN, and implicate a structural role for FMN positioning for optimal chromate reduction rates. As side chains proximal to the ?3/?4 FMN binding loop 4 contribute to both NADH and metal ion binding, we propose a model in which structural changes around the FMN binding pocket couples to both chromate and NADH binding sites.

Khaleel, Janin A.; Gong, Chunhong; Zhang, Yanfeng; Tan, Ruimin; Squier, Thomas C.; Jin, Hongjun

2013-06-01T23:59:59.000Z

378

Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition  

SciTech Connect (OSTI)

Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including {zeta}{sub cyt} and CD3{epsilon}{sub cyt} all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

Sigalov, Alexander B., E-mail: Alexander.sigalov@umassmed.edu [University of Massachusetts Medical School, Worcester, MA 01655 (United States); Hendricks, Gregory M. [University of Massachusetts Medical School, Worcester, MA 01655 (United States)] [University of Massachusetts Medical School, Worcester, MA 01655 (United States)

2009-11-13T23:59:59.000Z

379

Binding hotspots of BAZ2B bromodomain: histone interaction revealed by solution NMR driven docking  

E-Print Network [OSTI]

, Dow Street, Dundee, DD1 5EH, UK Corresponding Author * To whom correspondence should be addressed: Alessio Ciulli, Phone: +44 1382 386230, Fax: +44 1382 386373, Email: a.ciulli@dundee.ac.uk Funding Source Statement: This work was supported... spectroscopy and docking simulations. The resulting models were validated with site-directed mutagenesis and peptide binding studies using ITC. EXPERIMENTAL PROCEDURES Protein expression Escherichia coli Rosetta competent cells were transformed with a p...

Ferguson, Fleur M.; Dias, David M.; Rodrigues, Joao P. G. L. M.; Wienk, Hans; Bonvin, Alexandre M. J. J.; Abell, Chris; Ciulli, Alessio

2014-09-30T23:59:59.000Z

380

The use of binding arbitration for Arizona's public works disputes as viewed from the contractor's perspective  

E-Print Network [OSTI]

contract disputes in Arizona. The research was based upon a survey of Arizona contractors holding Class A ? General Engineering Contracting licenses. The research included an examination of the existing statutory requirements used in Arizona... for resolving public works contract disputes in addition to a comprehensive review of public works arbitration statutes in other states. Four conclusions were drawn from the research: 1) Most contractors prefer binding arbitration to litigation of public...

Bluff, Michael Robert

2012-06-07T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Biochem. J. (1987) 246, 227-232 (Printed in Great Britain) The binding of the cyclic AMP receptor protein to synthetic DNA  

E-Print Network [OSTI]

protein to synthetic DNA sites containing permutations in the consensus sequence TGTGA Claudia JANSEN synthetic DNA-binding sites was investigated with a gel-retardation assay. A set of ten different sequences of synthetic-DNA binding sites. First, we show that a completely symmetric site binds better to CRP than

Clore, G. Marius

382

Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATP on HfqRNA complexes  

E-Print Network [OSTI]

Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATP on Hfq­RNA complexes the first evidence indicating that Hfq is an ATP-binding protein. Using a combination of biochemical and genetic techniques, we have now determined a plausible ATP-binding site in Hfq and tested Hfq's ATP

Mura, Cameron

383

Biochemical and Domain Analyses of FSUAxe6B, a Modular Acetyl Xylan Esterase, Identify a Unique Carbohydrate Binding Module in Fibrobacter succinogenes S85  

Science Journals Connector (OSTI)

...insoluble b-1,4-xylan. The F. succinogenes...A CBMs are defined as surface binding, and they bind...FPm-1 preferred insoluble xylan, harboring heterogeneous...Lamed. 2008. Cell surface enzyme attachment is...modules and the presence of xylan-binding domains in...

Shosuke Yoshida; Roderick I. Mackie; Isaac K. O. Cann

2009-11-06T23:59:59.000Z

384

Calsensin: A Novel Calcium-binding Protein Expressed in a Subset of Peripheral Leech Neurons Fasciculating in a Single Axon Tract  

E-Print Network [OSTI]

helix-loop-helix domains. The calcium-binding domains are likely to be functional in vivo since a fusionCalsensin: A Novel Calcium-binding Protein Expressed in a Subset of Peripheral Leech Neurons. We have used this antibody to clone a novel EF-hand calcium-binding protein, calsensin, by screening

Johansen, Jorgen

385

T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service  

Broader source: Energy.gov (indexed) [DOE]

7: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of 7: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability T-677: F5 BIG-IP BIND Negative Caching RRSIG RRsets Denial of Service Vulnerability July 27, 2011 - 3:58pm Addthis PROBLEM: F5 has acknowledged a vulnerability in BIG-IP, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: The vulnerability is reported in the following products and versions: BIG-IP LTM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP GTM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP ASM versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2 BIG-IP Link Controller versions 9.0.0 through 9.4.8, 10.0.0 through 10.1.0, and 10.2.0 through 10.2.2

386

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids  

SciTech Connect (OSTI)

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2012-05-15T23:59:59.000Z

387

Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes  

SciTech Connect (OSTI)

The creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis.

C Simmons; C Magee; D Smith; L Lauman; J Chaput; J Allen

2011-12-31T23:59:59.000Z

388

Enhancing DNA binding rate using optical trapping of high-density gold nanodisks  

SciTech Connect (OSTI)

We present the dynamic study of optical trapping of fluorescent molecules using high-density gold nanodisk arrays. The gold nanodisks were fabricated by electron beam lithography with a diameter of 500 nm and a period of 1 ?m. Dark-field illumination showed ?15 times enhancement of fluorescence near edges of nanodisks. Such enhanced near-field generated an optical trapping force of ?10 fN under 3.58 10{sup 3} W/m{sup 2} illumination intensity as calculated from the Brownian motions of 590 nm polystyrene beads. Kinetic observation of thiolated DNA modified with Cy5 dye showed different binding rates of DNA under different illumination intensity. The binding rate increased from 2.14 10{sup 3} s{sup ?1} (I = 0.7 10{sup 3} W/m{sup 2}) to 1.15 10{sup 5} s{sup ?1} (I = 3.58 10{sup 3} W/m{sup 2}). Both enhanced fluorescence and binding rate indicate that gold nanodisks efficiently improve both detection limit and interaction time for microarrays.

Lin, En-Hung; Pan, Ming-Yang [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China) [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China); Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 11529 (China); Lee, Ming-Chang [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China)] [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan 30013 (China); Wei, Pei-Kuen, E-mail: pkwei@sinica.edu.tw [Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 11529 (China) [Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 11529 (China); Institute of Biophotonics, National Yang-Ming University, Taipei 11221, Taiwan (China)

2014-03-15T23:59:59.000Z

389

Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States) [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)] [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States)] [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand)] [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: daniel.sem@cuw.edu [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)

2013-01-04T23:59:59.000Z

390

Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin  

SciTech Connect (OSTI)

The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic {alpha}-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 {angstrom} resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 {alpha}-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.

Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T. (Globel Phasing); (Scripps)

2012-03-13T23:59:59.000Z

391

The nucleotide-binding domain of NLRC5 is critical for nuclear import and transactivation activity  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer NLRC5 requires an intact NLS for its function as MHC class I transactivator. Black-Right-Pointing-Pointer Nuclear presence of NLRC5 is required for MHC class I induction. Black-Right-Pointing-Pointer Nucleotide-binding controls nuclear import and transactivation activity of NLRC5. -- Abstract: Major histocompatibility complex (MHC) class I and class II are crucial for the function of the human adaptive immune system. A member of the NLR (nucleotide-binding domain, leucine-rich repeat) protein family, NLRC5, has recently been identified as a transcriptional regulator of MHC class I and related genes. While a 'master regulator' of MHC class II genes, CIITA, has long been known, NLRC5 specifically associates with and transactivates the proximal promoters of MHC class I genes. In this study, we analyzed the molecular requirements of NLRC5 nuclear import and transactivation activity. We show that NLRC5-mediated MHC class I gene induction requires an intact nuclear localization signal and nuclear distribution of NLRC5. In addition, we find that the nucleotide-binding domain (NBD) of NLRC5 is critical not only for nuclear translocation but also for the transactivation of MHC class I genes. Changing the cellular localization of NLRC5 is likely to immediately impact MHC class I expression as well as MHC class I-mediated antigen presentation. NLRC5 may thus provide a promising target for the modulation of MHC class I antigen presentation, especially in the setting of transplant medicine.

Meissner, Torsten B. [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States) [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215 (United States); Li, Amy; Liu, Yuen-Joyce [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States)] [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Gagnon, Etienne [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States) [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Institut de Recherche en Immunologie et Cancerologie, Departement de Microbiologie et Immunologie, Universite de Montreal, Montreal, Canada H3T1J4 (Canada); Kobayashi, Koichi S., E-mail: Koichi_Kobayashi@dfci.harvard.edu [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215 (United States); Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215 (United States)

2012-02-24T23:59:59.000Z

392

Precision Measurement of the 29Si, 33S, and 36Cl Binding Energies  

E-Print Network [OSTI]

The binding energies of 29Si, 33S, and 36Cl have been measured with a relative uncertainty $measurements are 1) nearly perfect crystals whose lattice spacing is known in meters, 2) a highly precise angle scale that is derived from first principles, and 3) a gamma-ray measurement facility that is coupled to a high flux reactor with near-core source capability. The binding energy is obtained by measuring all gamma-rays in a cascade scheme connecting the capture and ground states. The measurements require the extension of precision flat-crystal diffraction techniques to the 5 to 6 MeV energy region, a significant precision measurement challenge. The binding energies determined from these gamma-ray measurements are consistent with recent highly accurate atomic mass measurements within a relative uncertainty of $4.3 \\times 10^{-7}$. The gamma-ray measurement uncertainties are the dominant contributors to the uncertainty of this consistency test. The measured gamma-ray energies are in agreement with earlier precision gamma-ray measurements.

M. S. Dewey; E. G. Kessler Jr; R. D. Deslattes; H. G. Borner; M. Jentschel; C. Doll; P. Mutti

2005-07-06T23:59:59.000Z

393

Investigation of metal binding sites on soil fulvic acid using Eu(III) luminescence spectroscopy  

SciTech Connect (OSTI)

The [sup 7]F[sub 0] [yields] [sup 5]D[sub 0] excitation spectra of Eu(III) complexed with soil fulvic acid (FA) were acquired over a range of solution pH (2.9-7.8) and FA concentrations (800-3200 mg L[sup [minus]1]) using a pulsed tunable dye laser system. The broad asymmetric excitation spectra were well-fitted to a sum of two conventional Lorentzian-shaped curves, revealing the existence of two types of carboxylate moieties for the binding of metal ions on FA which formed 1:1 (EuL[sup 2+]; L = carboxylate) and 1:2 complexes (EuL[sub 2][sup +]). The weaker binding species, EuL[sup 2+], seemed to be quite abundant and showed a rapid increase as the pH was raised from 2.9 to 6.3, but it was susceptible to hydrolysis at pH higher than 7 while the stronger binding species, EuL[sub 2][sup +], showed only a modest growth with an increase in pH. By contrast, on a more flexible synthetic linear polymer, poly(acrylic acid) (PAA) and poly(vinylbenzoic acid) (PVBA) as model polymers, EuL[sub 2][sup +] was seen as the dominant species except in acidic media. 28 refs., 10 figs., 3 tabs.

Yoon, T.H.; Moon, H. (Korea Advanced Inst. of Science and Technology, Taejun (Korea, Democratic People's Republic of)); Park, Y.J.; Park, K.K. (Korea Atomic Energy Research Inst., Taejun (Korea, Democratic People's Republic of))

1994-11-01T23:59:59.000Z

394

Binding of Uridine 5-Diphosphate in the Basic Patch of the Zinc Deacetylase LpxC and Implications for Substrate Binding  

SciTech Connect (OSTI)

LpxC is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of lipid A, a vital component of the outer membrane of Gram-negative bacteria. Accordingly, the inhibition of LpxC is an attractive strategy for the treatment of Gram-negative bacterial infections. Here, we report the 2.7 {angstrom} resolution X-ray crystal structure of LpxC from Aquifex aeolicus complexed with uridine 5'-diphosphate (UDP), and the 3.1 {angstrom} resolution structure of LpxC complexed with pyrophosphate. The X-ray crystal structure of the LpxC-UDP complex provides the first view of interactions likely to be exploited by the substrate UDP group in the 'basic patch' of the active site. The diphosphate group of UDP makes hydrogen bond interactions with strictly conserved residue K239 as well as solvent molecules. The ribose moiety of UDP interacts with partially conserved residue E197. The UDP uracil group hydrogen bonds with both the backbone NH group and the backbone carbonyl group of E160, and with the backbone NH group of K162 through an intervening water molecule. Finally, the {alpha}-phosphate and uracil groups of UDP interact with R143 and R262 through intervening water molecules. The structure of LpxC complexed with pyrophosphate reveals generally similar intermolecular interactions in the basic patch. Unexpectedly, diphosphate binding in both complexes is accompanied by coordination to an additional zinc ion, resulting in the identification of a new metal-binding site termed the E-site. The structures of the LpxC-UDP and LpxC-pyrophosphate complexes provide new insights with regard to substrate recognition in the basic patch and metal ion coordination in the active site of LpxC.

Gennadios,H.; Christianson, D.

2006-01-01T23:59:59.000Z

395

Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Application to p53 and Low Dose Ionizing Radiation.  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Application to p53 and Low Dose Ionizing Radiation. Krassimira Botcheva, John J. Dunn and Carl W. Anderson Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA The effects of exposure to low doses of ionizing radiation on humans results largely from changes in gene expression mediated by the activation of sequence-specific DNA binding proteins (transcription factors) as well as changes to other chromosomal proteins and perhaps to DNA. To develop a molecular understanding of the consequences of exposures to low doses of ionizing radiation, it will be necessary to understanding where radiation-activated transcription factors bind in whole genomes and how

396

Natural and synthetic double-stranded DNA binding studies of macrocyclic tetraamine zinc(II) complexes appended with polyaromatic groups  

Science Journals Connector (OSTI)

...?The characteristic binding mode of zinc(II) complexes of macrocyclic tetraamines (1,4,7,10-tetraazacyclododecane, cyclen) appended with one or two arylmethyl group(s) [(4-quinolyl)methyl-, 1,7-bis(4-quinolyl)...

Emiko Kikuta; Naomi Katsube; E. Kimura

1999-08-01T23:59:59.000Z

397

Spatial and temporal coupling models for the discovery of binding events in ChIP-Seq data  

E-Print Network [OSTI]

In this thesis, we will present two methods for identifying binding events in ChIP-Seq data. The motivation of this venture is to propose a complete read generating process under a probabilistic graphical model framework ...

Papachristoudis, Georgios

2010-01-01T23:59:59.000Z

398

Purification, crystallization and preliminary X-ray diffraction analysis of water-soluble chlorophyll-binding protein from Chenopodium album  

Science Journals Connector (OSTI)

A water-soluble chlorophyll-binding protein with photoconvertibility from C. album was extracted, purified and crystallized in a darkroom. The crystal diffracted to around 2.0 resolution.

Ohtsuki, T.

2007-08-10T23:59:59.000Z

399

Dangling Bond Defects in a-Si,Ge Alloys: A Theoretical Study Using the Tight-Binding Method  

Science Journals Connector (OSTI)

This paper presents a theoretical study of Si and Ge atom dangling bond defects in a-Si,Ge alloys. We use a tight-binding Hamiltonian, and a structural model based on a cluster Bethe Lattice. The central clust...

S. Y. Lin; G. Lucovsky

1985-01-01T23:59:59.000Z

400

The HSV-1 ICP27 RGG box specifically binds flexible, GC-rich sequences but not G-quartet structures  

E-Print Network [OSTI]

recognition complex (ORC) proteins to the EBV episomal mini-the binding by EBNA1 to the ORC proteins was RNA dependentrich RNA may be a mechanism for ORC recruitment (41). It is

Corbin-Lickfett, Kara A.; Chen, I-Hsiung Brandon; Cocco, Melanie J.; Sandri-Goldin, Rozanne M.

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

Methyl p-Hydroxyphenyllactate and Nuclear Type II Binding Sites in Malignant Cells: Metabolic Fate and Mammary Tumor Growth  

Science Journals Connector (OSTI)

...Heterogeneity of estrogen-binding sites and the nuclear matrix. In: G. Maul (ed.). The Nuclear Matrix and the Nuclear Envelope, pp. 259-269. New York...inhibition on mitochondria! ATPase and energy-linked reactions in submitochondrial...

Barry M. Markaverich; Rebecca R. Gregory; MaryAnn Alejandro; Francis S. Kittrell; Daniel Medina; James H. Clark; Manju Varma; and Rajender S. Varma

1990-03-01T23:59:59.000Z

402

A Large-Scale Test of Free-Energy Simulation Estimates of ProteinLigand Binding Affinities  

Science Journals Connector (OSTI)

We have performed a large-scale test of alchemical perturbation calculations with the Bennett acceptance-ratio (BAR) approach to estimate relative affinities for the binding of 107 ligands to 10 different proteins. Employing 20- truncated spherical ...

Paulius Mikulskis; Samuel Genheden; Ulf Ryde

2014-09-29T23:59:59.000Z

403

Abstract 4495: Fisetin, a dietary flavonoid, binds to and disrupts microtubule dynamic instability in prostate cancer cells.  

Science Journals Connector (OSTI)

...2013; Washington, DC Abstract 4495: Fisetin, a dietary flavonoid, binds to and disrupts...urgently needed. We hypothesized that fisetin may offer PCa chemotherapeutic and/or...polymerization assay, we observed that fisetin enhanced tubulin polymerization whose...

Eiman Mukhtar; Vaqar M. Adhami; Deeba N. Syed; Hasan Mukhtar

2013-04-15T23:59:59.000Z

404

Interaction of monoclonal antibodies with the enzymatic domains of penicillin-binding protein 1b of Escherichia coli.  

Science Journals Connector (OSTI)

...transglycosylation reaction. Binding of penicillin by PBP lb. (i) Reaction results of in vitro murein synthesis by m( information about the amount of synthesized ever, the extent that transglycosylation or tr is involved could not be specified...

T den Blaauwen; M Aarsman; N Nanninga

1990-01-01T23:59:59.000Z

405

MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation  

Science Journals Connector (OSTI)

Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a ... in the natural state, they readily undergo disorder

Chun Fang; Tamotsu Noguchi; Daisuke Tominaga; Hayato Yamana

2013-10-01T23:59:59.000Z

406

Evolutionary substitution of two amino acids in chloroplast SRP54 of higher plants cause its inability to bind SRP RNA  

Science Journals Connector (OSTI)

The chloroplast signal recognition particle (cpSRP) consists of a conserved 54kDa subunit (cpSRP54) and a unique 43kDa subunit (cpSRP43) but lacks SRP-RNA, an essential and universally conserved component of cytosolic SRPs. High sequence similarity exists between cpSRP54 and bacterial SRP54 except for a plant-specific C-terminal extension containing the cpSRP43-binding motif. We found that cpSRP54 of higher plants lacks the ability to bind SRP-RNA because of two amino acid substitutions within a region corresponding to the RNA binding domain of cytosolic SRP54, whereas the C-terminal extension does not affect RNA binding. Phylogenetic analysis revealed that these mutations occur in the cpSRP54 homologues of higher plants but not in most algae.

Christine V. Richter; Chantal Trger; Danja Schnemann

2008-01-01T23:59:59.000Z

407

Basic residues of human group IIA phospholipase A2 are important for binding to factor Xa and prothrombinase inhibition  

E-Print Network [OSTI]

bridges, and a number of conserved amino acids located in the calcium-binding loop and the catalytic site (14±17 kDa), calcium-dependent catalytic activity, the pre- sence of between five and eight disulfide

Gelb, Michael

408

Characterization of IgG and IgE Binding to Parvalbumin Derived from Commercially Important Fish Species.  

E-Print Network [OSTI]

??Parvalbumin is a calcium-binding muscle protein that is present in all vertebrates. Despite being a pan-allergen in fish and frog, fish-specific IgE and antiparvalbumin IgG (more)

Lee, Poi-Wah

2012-01-01T23:59:59.000Z

409

On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence  

E-Print Network [OSTI]

METHODOLOGY ARTICLE Open Access On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence David S Huen1*, Steven Russell1,2 Abstract Background: In eukaryotes, most DNA-binding proteins exert their action... : Functional Anatomy of Polycomb and Trithorax chromatin landscapes in Drosophila embryos. Plos Biology 2009, 7:e1000013. 7. Solomon MJ, Larsen PL, Varshavsky A: Mapping protein-DNA interactions in vivo with formaldehyde - evidence that histone H4 is retained...

Huen, David S; Russell, Steven R

2010-06-30T23:59:59.000Z

410

On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine  

E-Print Network [OSTI]

that are highly correlated to binding constants. Most kinases with better binding affinities to staurosporine (dark red) have large gatekeeper residues, e.g. phenylalanine (F), methionine (M). A majority of kinases which are inhibited by ZD-6474 (blue) has... accessible region ................................................................. Figure 44. The MAHORI web-interface allows for various forms of ligand query, e.g. by providing a chemical structure, a SMILES string, a chemical name or a PDB three...

Tanramluk, Duangrudee

2010-02-09T23:59:59.000Z

411

Carcass characteristics and fatty acid-binding protein activity in tissues of porcine and bovine species fed elevated monounsaturated fats  

E-Print Network [OSTI]

CARCASS CHARACTERISTICS AND FATTY ACID ? BINDING PROTEIN ACTIVITY IN TISSUES OF PORCINE AND BOVINE SPECIES FED ELEVATED MONOUNSATURATED FATS A Thesis LORI CEANNE ST. JOHN Submitted to the Graduate College of Texas A g M University in partial... Thesis LORI CEANNE ST. JOHN Approved as to style and content by: S. B. ith (Chairman) H. R. Cross (Member) L. J. ' ger (Member) G. C. mit (Head of Department) May 1986 ABSTRACT Carcass Characteristics and Fatty Acid-Binding Protein Activity...

St. John, Lori Ceanne

2012-06-07T23:59:59.000Z

412

XENOBIOTIC REGULATION OF THE ATP BINDING CASSETTE TRANSPORTER ABCB6 AND ITS SIGNIFICANCE TO HEPATIC HEME HOMEOSTASIS  

E-Print Network [OSTI]

.2. Pathologies associated with disruption of heme homeostasis 3 1.3. Cellular heme homeostasis 5 1.4. The human ATP binding cassette transporter subfamily 23 1.5. Mitochondrial ATP binding cassette transporter Abcb6 38 Chapter 2: STATEMENT... OF ABCB6 SUBSTRATES 178 Chapter 8: CONCLUSIONS AND FUTURE DIRECTIONS 207 8.1. Summary and conclusions 208 8.2. Future directions 212 REFERENCES 217 XI LIST OF ABBREVIATIONS Abbreviation Full name 3-AT 3...

Chavan, Hemantkumar Dilip

2013-12-31T23:59:59.000Z

413

Particle trap to sheath non-binding contact for a gas-insulated transmission line having a corrugated outer conductor  

DOE Patents [OSTI]

A non-binding particle trap to outer sheath contact for use in gas insulated transmission lines having a corrugated outer conductor. The non-binding feature of the contact according to the teachings of the invention is accomplished by having a lever arm rotatably attached to a particle trap by a pivot support axis disposed parallel to the direction of travel of the inner conductor/insulator/particle trap assembly.

Fischer, William H. (Pittsburgh, PA)

1984-04-24T23:59:59.000Z

414

DNA Duplications and Deletions Help Determine Health  

Science Journals Connector (OSTI)

...with a microscope can break off, attach in...missing, it can shut down production altogether...brain of the protein {alpha}-synuclein. But unraveling...gene that codes an amylase, an enzyme that breaks down starch. CREDIT: CHARLES...

Jon Cohen

2007-09-07T23:59:59.000Z

415

What Wikipedia deletes: characterizing dangerous collaborative content  

Science Journals Connector (OSTI)

Collaborative environments, such as Wikipedia, often have low barriers-to-entry in order to encourage participation. This accessibility is frequently abused (e.g., vandalism and spam). However, certain inappropriate behaviors are more threatening ... Keywords: Wikipedia, collaboration, content removal, copyright, information security, redaction, user generated content

Andrew G. West; Insup Lee

2011-10-01T23:59:59.000Z

416

Structure of an Arrestin2-clathrin Complex Reveals a Novel Clathrin Binding Domain that Modulates Receptor Trafficking  

SciTech Connect (OSTI)

Non-visual arrestins play a pivotal role as adaptor proteins in regulating the signaling and trafficking of multiple classes of receptors. Although arrestin interaction with clathrin, AP-2, and phosphoinositides contributes to receptor trafficking, little is known about the configuration and dynamics of these interactions. Here, we identify a novel interface between arrestin2 and clathrin through x-ray diffraction analysis. The intrinsically disordered clathrin binding box of arrestin2 interacts with a groove between blades 1 and 2 in the clathrin {beta}-propeller domain, whereas an 8-amino acid splice loop found solely in the long isoform of arrestin2 (arrestin2L) interacts with a binding pocket formed by blades 4 and 5 in clathrin. The apposition of the two binding sites in arrestin2L suggests that they are exclusive and may function in higher order macromolecular structures. Biochemical analysis demonstrates direct binding of clathrin to the splice loop in arrestin2L, whereas functional analysis reveals that both binding domains contribute to the receptor-dependent redistribution of arrestin2L to clathrin-coated pits. Mutagenesis studies reveal that the clathrin binding motif in the splice loop is (L/I){sub 2}GXL. Taken together, these data provide a framework for understanding the dynamic interactions between arrestin2 and clathrin and reveal an essential role for this interaction in arrestin-mediated endocytosis.

Kang, D.; Kern, R; Puthenveedu, M; von Zastrow, M; Williams, J; Benovic, J

2009-01-01T23:59:59.000Z

417

Immunological properties of prolactin and studies on a gonadotropin binding inhibitor  

SciTech Connect (OSTI)

The physiological role of prolactin in horses has not yet been well defined. With the availability of highly purified ePRL for inducing antibody formation in rabbits and for radiolabeling with Na/sup 125/I, a very sensitive (0.4-0.6 ng/ml) and highly specific homologous RIA for ePRL was developed. A heterologous RIA using /sup 125/I-labeled ovine PRL and anti-ePRL antiserum was also developed and compared to the homologous RIA for ePRL. Of the two systems, it is concluded that this homologous RIA system is more suitable and more reliable for measuring prolactin concentration in horse serum samples. Until now, biochemical information on PRL has not been available for reptilian species. Sea turtle (Chelonia mydas) prolactin was purified from pituitary extracts by selective precipitation, DEAE-cellulose chromatography and gel filtration. Similar to other species of PRL, sea turtle PRL is a 22,000-24,000 daltons protein and contains a high content of glutamic acid, aspartic acid, serine and leucine, the N-terminal amino acid residue. Gonadotropin (FSH) binding inhibitor was partially purified from sheep testes by ammonium sulfate fractionation and ion exchange chromatography. The FSH-BI (molecular weight: 50,000 daltons, estimated by gel filtration) contains a protein moiety necessary for binding inhibitory activity. The inhibition of the binding of /sup 125/I-labeled ovine FSH to its receptor by the FSH-BI is not competitive. Both in vivo and in vitro biological studies of FSH-BI preparations in rats indicated various effects on FSH and LH activities at the gonadal level. These findings suggest a physiological role for FSH-BI in the regulation of reproduction.

Chang, Y.S.

1985-01-01T23:59:59.000Z

418

Effect of quark antisymmetrization on the binding energy of nuclear matter  

Science Journals Connector (OSTI)

We estimate, to leading order in the nuclear matter density, the effect of antisymmetrizing quarks belonging to different nucleons upon the binding energy per nucleon in nuclear matter. A simple Gaussian model for the nucleon quark wave function, together with a one-gluon-exchange potential between quarks, is assumed. Using a linked cluster expansion developed earlier for nuclear matter, we calculate separately the effect of quark interchanges upon the kinetic, hyperfine, Coulomb, and contact terms in the Hamiltonian. A strong net repulsion is found which grows rapidly with the dimensionless parameter ?=r0kF, where kF is the nuclear Fermi momentum and r0 the nucleon size.

Mohammad Nzar and Pervez Hoodbhoy

1990-10-01T23:59:59.000Z

419

Site-specific measurement of adatom binding energy differences by atom extraction with the STM  

Science Journals Connector (OSTI)

Using a scanning tunneling microscope, single adatoms can be extracted from a Si(111)77 surface by field evaporation, when the sample voltage is pulsed at 4 V or more in either polarity. Statistically, adatoms at the center of the 77 unit cell are more frequently removed than those near the corner holes, by a ratio of 1.6:1. This difference can be explained by assuming that the binding energy of center adatoms is approximately 0.01 eV less than for corner adatoms. The relationship of this result to previous observations of greater chemical reactivity at center adatom sites is discussed.

Hironaga Uchida; Dehuan Huang; Franois Grey; Masakazu Aono

1993-03-29T23:59:59.000Z

420

Glucose oxidation in heart-type fatty acid binding protein null mice  

E-Print Network [OSTI]

of Genetics Faculty, James R. Wild August 2006 Major Subject: Genetics iii ABSTRACT Glucose Oxidation in Heart-Type Fatty Acid Binding Protein Null Mice. (August 2006) Sean Adhikari, B.S., University of Washington Chair of Advisory... was incubated in media solely containing the above reagents, and the other muscle was incubated in media containing the above reagents supplemented with either 1 mM palmitic acid, 2 mU/mL insulin (Humulin R), 2 mM AICAR, 0.5 mM 2,4- dinitrophenol (DNP), or a...

Adhikari, Sean

2006-10-30T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
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421

Identification and functional characterization of lipid binding proteins in liver and adipose tissues of Gallus domesticus  

E-Print Network [OSTI]

; whereas the second hepatic lipid transport protein is most likely liver-FABP (L-FABP). An FABP from chicken adipose cytosol (A-FABP) was purified by membrane ultrafiltration and molecular sieve chromatography. Purification was verified by SDS... via ion exchange chromatography, pH 7. 73. Purification was verified by ligand binding assays and SDS-PAGE. The first protein eluted (designated ns-LTP) had a molecular weight of approximately 14. 5 kDa and the second protein (designated L...

Sams, Gretchen Hubler

1990-01-01T23:59:59.000Z

422

JC3 High Impact Assessment Bulletins | Department of Energy  

Broader source: Energy.gov (indexed) [DOE]

August 1, 2012 August 1, 2012 U-225: Citrix Access Gateway Plug-in for Windows nsepacom ActiveX Control Vulnerabilities Two vulnerabilities in Citrix Access Gateway Plug-in for Windows can be exploited by malicious people to compromise a user's system. July 30, 2012 U-223: Bugzilla May Disclose Confidential Information to Remote Users Two vulnerabilities were reported in Bugzilla. July 27, 2012 U-222: Apple Safari Bugs Let Remote Users Execute Arbitrary Code, Spoof the URL Address Bar, Conduct Cross-Site Scripting Attacks, and Obtain Potentially Sensitive Information Multiple vulnerabilities were reported in Apple Safari. July 26, 2012 U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability ISC BIND is prone to a denial-of-service vulnerability. July 24, 2012

423

JC3 Medium Impact Assessment Bulletins | Department of Energy  

Broader source: Energy.gov (indexed) [DOE]

3, 2012 3, 2012 U-227: bind-dyndb-ldap DN Escaping Flaw Lets Remote Users Deny Service A vulnerability has been reported in bind-dyndb-ldap, which can be exploited by malicious people to cause a DoS (Denial of Service). August 2, 2012 U-226: Linux Kernel SFC Driver TCP MSS Option Handling Denial of Service Vulnerability The Linux kernel is prone to a remote denial-of-service vulnerability. July 31, 2012 U-224: ISC DHCP Multiple Denial of Service Vulnerabilities ISC DHCP is prone to multiple denial-of-service vulnerabilities. July 25, 2012 U-220: Google Android DNS Resolver Randomization Flaw Lets Remote Users Poison the DNS Cache A remote user can poison the DNS cache. July 23, 2012 U-218: Cisco Linksys WMB54G TFTP Command Injection Vulnerability System access from local network

424

Sm and DNA Binding by dual reactive B cells requires distinct V{sub H}, V{sub {kappa}}, and V{sub H} CDR3 structures  

SciTech Connect (OSTI)

We have previously demonstrated an overlap of the anti-Sm and anti-DNA responses in MRL/Mp-Ipr/Ipr mice. The Ab produced by many anti-Sm hybridomas bind DNA and are encoded by Ig V genes used by anti-DNA hybridomas. In addition, some anti-Sm Ab that bind DNA have acquired mutations that improve DNA binding, indicating that DNA is a selecting Ag in the anti-Sm response. To gain insight into the basis for the dual binding ability of these Ab, we coexpressed the H chain from the anti-Sm hybridoma 2-12 with nine different L chains. Hybridoma 2-12 binds Sm but not DNA, yet expresses the same J558 V{sub H} gene as three anti-Sm hybridomas that bind ssDNA and at least one anti-DNA hybridoma that does not bind Sm. We found that most of the transfectoma Ab bind Sm, but their avidities vary over more than 3 orders of magnitude. Five of the nine transfectoma Ab bind ssDNA, and none bind dsDNA. In general, the ability to bind each Ag follows the binding ability of the hybridoma from which the L chain is derived. H Chain swapping experiments indicate that the H chain, V{sub H} CDR3 in particular contributes to the binding of both Sm and DNA. We conclude that Sm and DNA select for distinct features of V{sub H}, V{sub {kappa}}, and V{sub H} CDR3, suggesting selection by both Ag in the anti-Sm response.

Retter, M.W.; Eisenberg, R.A.; Cohen, P.L. [Univ. of North Carolina, Chapel Hill, NC (United States)] [and others

1995-08-15T23:59:59.000Z

425

Autoradiographic evidence of nuclear binding of spironolactone in rabbit cortical collecting tubule  

SciTech Connect (OSTI)

Previous biochemical studies indicated that the spirolactone-mineralocorticoid receptor complexes are unable to translocate into the nucleus. The present study was designed to reinvestigate the intracellular distribution of spirolactone-binding sites, using autoradiography. For this purpose, rabbit kidney pyramids were incubated at 30 C with tritiated SC9420 or aldosterone. Thereafter, aldosterone-sensitive cortical collecting tubules were microdissected and processed for dry film autoradiography. The concentration was 2 nM for both steroids. Non-specific labeling was determined by incubations with tritiated steroids plus a 100-fold excess of unlabeled steroids. Results show the presence of specific nuclear labeling for both ({sup 3}H) aldosterone and ({sup 3}H)SC9420. Specific cytoplasmic labeling was very low for both ({sup 3}H)aldosterone and ({sup 3}H)SC9420. The nuclear labeling by ({sup 3}H)SC9420 was equally and almost completely displaced by a 100-fold excess of unlabeled aldosterone or SC9420 (91% and 87%, respectively). We conclude that spironolactone-receptor complexes migrate into the nucleus. The difference between these results and those of previous studies with biochemical techniques, which failed to detect specific nuclear binding of spirolactone, may be due to methodological reasons.

Bonvalet, J.P.; Blot-Chabaud, M.; Farman, N. (CEN Saclay, Gif-Yvette (France))

1991-01-01T23:59:59.000Z

426

A single domain thermophilic xylanase can bind insoluble xylan: evidence for surface aromatic clusters  

Science Journals Connector (OSTI)

A clone expressing xylanase activity in Escherichia coli has been selected from a genomic plasmid library of the thermophilic Bacillus strain D3. Subcloning from the 9-kb insert located the xylanase activity to a 2.7-kb HindII/BamHI fragment. The DNA sequence of this clone revealed an ORF of 367 codons encoding a single domain type-F or family 10 enzyme, which was designated as XynA. Purification of the enzyme following over-expression in E. coli produced an enzyme of 42 kDa with a temperature optimum of 75C which can efficiently bind and hydrolyse insoluble xylan. The pH optimum of the enzyme is 6.5, but it is active over a broad pH range. A homology model of the xylanase has been constructed which reveals a series of surface aromatic residues which form hydrophobic clusters. This unusual structural feature is strikingly similar to the situation observed in the structure determined for the type-G xylanase from the Bacillus D3 strain and may constitute a common evolutionary mechanism imposed on different structural frameworks by which these xylanases may bind potential substrates and exhibit thermostability.

Ian Connerton; Nicola Cummings; Gillian W. Harris; Philippe Debeire; Christelle Breton

1999-01-01T23:59:59.000Z

427

Tight-binding study of the electronic structure of amorphous silicon  

Science Journals Connector (OSTI)

We have performed tight-binding calculations on a model of an amorphous silicon sample generated previously by a molecular-dynamics simulation employing the Stillinger-Weber potential. The sample consists of 588 atoms and contains a high density of floating-bond defects. Two tight-binding calculations are presented, one using the widely accepted Chadi parameters, which include only nearest-neighbor interactions, and the other using the parameters recently proposed by Allen, Broughton, and McMahan (ABM) [Phys. Rev. B 34, 859 (1986)] for a nonorthogonal basis set. Comparison of the densities of states shows similar behavior in the valence band, but the electron density near a defect is less localized with the ABM parameters. It is also found that the projected density of states on the fivefold-coordinated atoms is very close to that on the fourfold-coordinated atoms, while the projected density of states on the threefold-coordinated atoms is distinctly different and has more states in the gap.

James L. Mercer; Jr. and M. Y. Chou

1991-03-15T23:59:59.000Z

428

Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1  

SciTech Connect (OSTI)

CUG-binding protein 1 (CUGBP1) regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of myotonic dystrophy. CUGBP1 harbors three RRM domains and preferentially targets UGU-rich mRNA elements. We describe crystal structures of CUGBP1 RRM1 and tandem RRM1/2 domains bound to RNAs containing tandem UGU(U/G) elements. Both RRM1 in RRM1-RNA and RRM2 in RRM1/2-RNA complexes use similar principles to target UGU(U/G) elements, with recognition mediated by face-to-edge stacking and water-mediated hydrogen-bonding networks. The UG step adopts a left-handed Z-RNA conformation, with the syn guanine recognized through Hoogsteen edge-protein backbone hydrogen-bonding interactions. NMR studies on the RRM1/2-RNA complex establish that both RRM domains target tandem UGUU motifs in solution, whereas filter-binding assays identify a preference for recognition of GU over AU or GC steps. We discuss the implications of CUGBP1-mediated targeting and sequestration of UGU(U/G) elements on pre-mRNA alternative-splicing regulation, translational regulation, and mRNA decay.

M Teplova; J Song; H Gaw; A Teplov; D Patel

2011-12-31T23:59:59.000Z

429

Ab initio study of dihydrogen binding in metal-decorated polyacetylene for hydrogen storage  

Science Journals Connector (OSTI)

Using first-principles calculations based on the density-functional theory, we perform a detailed study of the dihydrogen (H2) binding in cis- and trans-polyacetylene decorated with transition metal atoms. First, we investigate the origin of metal-dihydrogen bonding and observe the hybridization of eg (t2g) orbitals of the Ti atom with the ? (?*) orbitals of the H2 molecules in octahedral geometries, which is consistent with the Kubas model. Second, using a statistical model parametrized by the results of ab initio calculations and experimental data, the adsorption and desorption of molecular hydrogens are calculated at ambient temperature and pressure. We find that the usable capacity at ambient conditions is dramatically reduced from the maximum capacity, the zero-point energy affects the storage capacity significantly, and the optimal binding energy of H2 molecules under practical conditions is ?0.3eV?H2. Third, we examine the effects of the aggregation and intercalation of the Ti atoms on H2 adsorption.

Hoonkyung Lee; Woon Ih Choi; Manh Cuong Nguyen; Moon-Hyun Cha; Eungook Moon; Jisoon Ihm

2007-11-09T23:59:59.000Z

430

Crystal structure of Plasmodium falciparum phosphoglycerate kinase: Evidence for anion binding in the basic patch  

SciTech Connect (OSTI)

3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the open conformation is presented in two different groups, namely I222 and P6{sub 1}22. The structure in I222 space group is solved using MAD and refined at 3 {angstrom} whereas that in P6{sub 1}22A is solved using MR and refined at 2.7 {angstrom}. I222 form has three monomers in asymmetric unit whereas P6{sub 1}22 form has two monomers in the asymmetric unit. In both crystal forms a sulphate ion is located at the active site where ATP binds, but no Mg{sup 2+} ion is observed. For the first time another sulphate ion is found at the basic patch where the 3-phosphate of 1,3-biphosphoglycerate normally binds. This was found in both chains of P6{sub 1}22 form but only in chain A of I222 form.

Smith, Craig D.; Chattopadhyay, Debasish; Pal, Biswajit (UAB)

2012-11-09T23:59:59.000Z

431

NMr studies of the AMP binding site and mechanism of adenylate kinase  

SciTech Connect (OSTI)

The authors recently located by NMR the MgATP binding site on adenylate kinase correcting the proposed location for this site based on X-ray studies of the binding of salicylate. To determine the conformation and location of the other substrate, they have determined distances from Cr/sup 3 +/ AMPPCP to 6 protons and to the phosphorus atom of AMP on adenylate kinase using the paramagnetic-probe-T/sub 1/ method. They have also used time-dependent NOEs to measure five interproton distances on AMP, permitting evaluation of the conformation of enzyme-bound AMP and its position with respect to metal-ATP. Enzyme-bound AMP exhibits a high-anti glycosyl torsional angle (X = 110/sup 0/), a 3'-endo sugar pucker (delta = 105/sup 0/), and a gauche-trans orientation about the C/sub 4/'-C/sub 5/' bond (..gamma.. = 180/sup 0/). The distance from Cr/sup 3 +/ to the phosphorus of AMP is 6.4 +/- 0.3 A, indicating a reaction coordinate distance of greater than or equal to A which is consistent with an associative SN2 mechanism for the phosphoryl transfer. Ten intermolecular NOEs, from protons of the enzyme to those of AMP were detected. These constraints, together with the conformation of AMP and the X-ray structure of the enzyme, suggest proximity (less than or equal to A) of AMP to leu 116, arg 171, val 173, gln 185, thr 188, and asp 191.

Kuby, S.A.; Fry, D.C.; Mildvan, A.S.

1986-05-01T23:59:59.000Z

432

Binding motifs in bacterial gene promoters modulate transcriptional effects of global regulators CRP and ArcA  

SciTech Connect (OSTI)

Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.

Leuze, Mike; Karpinets, Tatiana V.; Syed, Mustafa H.; Beliaev, Alex S.; Uberbacher, Edward

2012-05-30T23:59:59.000Z

433

One-step synthesis of efficient binding-inhibitor for influenza virus through multiple addition of sialyloligosaccharides on chitosan  

Science Journals Connector (OSTI)

We have succeeded in one-step synthesis of an efficient binding-inhibitor for influenza virus, which is composed of only sugar chains. This binding-inhibitor utilizes the carbohydrate recognition of influenza virus, thus it can prevent the virus from infection. We modified chitosan with multiple sialyl saccharides, ?2,6-sialyllactose or free sialyl glycan, using reductive amination reaction. The resulting inhibitors showed sufficient inhibitory activity against influenza virus infection in MDCK cells compared to that of ?2,6-sialyllactose or free sialyl glycan. Unlike the other binding-inhibitors of influenza virus, this virus inhibitor of sugar chains requires only one step in its synthesis. Therefore this inhibitor is suitable for use in products such as filters and masks.

Myco Umemura; Yutaka Makimura; Masae Itoh; Takeshi Yamamoto; Toshiki Mine; Seiji Mitani; Ichiro Simizu; Hisashi Ashida; Kenji Yamamoto

2010-01-01T23:59:59.000Z

434

A van der Waals density functional study of adenine on graphene: Single molecular adsorption and overlayer binding  

SciTech Connect (OSTI)

The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional (vdW-DF) [Dion et al., Phys. Rev. Lett. 92, 246401 (2004)]. The cohesive energy of an ordered adenine overlayer is also estimated. For the adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similar-sized naphthalene. Based on the single molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.

Berland, Kristian [Chalmers University of Technology, Sweden; Cooper, Valentino R [ORNL; Langreth, David C. [Rutgers University; Schroder, Prof. Elsebeth [Chalmers University of Technology, Sweden; Chakarova-Kack, Svetla [Chalmers University of Technology, Sweden

2011-01-01T23:59:59.000Z

435

IQGAP Proteins Reveal an Atypical Phosphoinositide (aPI) Binding Domain with a Pseudo C2 Domain Fold  

SciTech Connect (OSTI)

Class I phosphoinositide (PI) 3-kinases act through effector proteins whose 3-PI selectivity is mediated by a limited repertoire of structurally defined, lipid recognition domains. We describe here the lipid preferences and crystal structure of a new class of PI binding modules exemplified by select IQGAPs (IQ motif containing GTPase-activating proteins) known to coordinate cellular signaling events and cytoskeletal dynamics. This module is defined by a C-terminal 105-107 amino acid region of which IQGAP1 and -2, but not IQGAP3, binds preferentially to phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3). The binding affinity for PtdInsP3, together with other, secondary target-recognition characteristics, are comparable with those of the pleckstrin homology domain of cytohesin-3 (general receptor for phosphoinositides 1), an established PtdInsP3 effector protein. Importantly, the IQGAP1 C-terminal domain and the cytohesin-3 pleckstrin homology domain, each tagged with enhanced green fluorescent protein, were both re-localized from the cytosol to the cell periphery following the activation of PI 3-kinase in Swiss 3T3 fibroblasts, consistent with their common, selective recognition of endogenous 3-PI(s). The crystal structure of the C-terminal IQGAP2 PI binding module reveals unexpected topological similarity to an integral fold of C2 domains, including a putative basic binding pocket. We propose that this module integrates select IQGAP proteins with PI 3-kinase signaling and constitutes a novel, atypical phosphoinositide binding domain that may represent the first of a larger group, each perhaps structurally unique but collectively dissimilar from the known PI recognition modules.

Dixon, Miles J.; Gray, Alexander; Schenning, Martijn; Agacan, Mark; Tempel, Wolfram; Tong, Yufeng; Nedyalkova, Lyudmila; Park, Hee-Won; Leslie, Nicholas R.; van Aalten, Daan M.F.; Downes, C. Peter; Batty, Ian H. (Toronto); (Dundee)

2012-10-16T23:59:59.000Z

436

Interaction of Salivary alpha-Amylase and Amylase-Binding-Protein A (AbpA) ofStreptococcus gordoniiwith Glucosyltransferase ofS. gordoniiandStreptococcus mutans  

Science Journals Connector (OSTI)

Glucosyltransferases (Gtfs), enzymes that produce extracellular glucans from dietary sucrose, contribute to dental plaque formation byStreptococcus gordoniiandStreptococcus mutans. The alpha-amylase-binding prote...

Biswendu Chaudhuri; Jennifer Rojek; M Margaret Vickerman

2007-06-01T23:59:59.000Z

437

Fluorescence-detected assembly of the signal recognition particle: binding of the two SRP protein heterodimers to SRP RNA is noncooperative  

Science Journals Connector (OSTI)

Fluorescence-detected assembly of the signal recognition particle: binding of the two SRP protein heterodimers to SRP RNA is noncooperative ...

Fabiola Janiak; Peter Walter; Arthur E. Johnson

1992-06-01T23:59:59.000Z

438

Crystal structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains  

E-Print Network [OSTI]

binding site. Using atomic absorption spectroscopy and TrpElmer AAnalyst 400 atomic absorption spectrometer (AAS) withthe metal, we employed atomic absorption spectroscopy on the

Zheng, Meiying

2009-01-01T23:59:59.000Z

439

Structure of the second RRM domain of Nrd1, a fission yeast MAPK target RNA binding protein, and implication for its RNA recognition and regulation  

SciTech Connect (OSTI)

Highlights: Solution structure of the second RRM of Nrd1 was determined. RNA binding site of the second RRM was estimated. Regulatory mechanism of RNA binding by phosphorylation is discussed. -- Abstract: Negative regulator of differentiation 1 (Nrd1) is known as a negative regulator of sexual differentiation in fission yeast. Recently, it has been revealed that Nrd1 also regulates cytokinesis, in which physical separation of the cell is achieved by a contractile ring comprising many proteins including actin and myosin. Cdc4, a myosin II light chain, is known to be required for cytokinesis. Nrd1 binds and stabilizes Cdc4 mRNA, and thereby suppressing the cytokinesis defects of the cdc4 mutants. Interestingly, Pmk1 MAPK phosphorylates Nrd1, resulting in markedly reduced RNA binding activity. Furthermore, Nrd1 localizes to stress granules in response to various stresses, and Pmk1 phosphorylation enhances the localization. Nrd1 consists of four RRM domains, although the mechanism by which Pmk1 regulates the RNA binding activity of Nrd1 is unknown. In an effort to delineate the relationship between Nrd1 structure and function, we prepared each RNA binding domain of Nrd1 and examined RNA binding to chemically synthesized oligo RNA using NMR. The structure of the second RRM domain of Nrd1 was determined and the RNA binding site on the second RRM domain was mapped by NMR. A plausible mechanism pertaining to the regulation of RNA binding activity by phosphorylation is also discussed.

Kobayashi, Ayaho; Kanaba, Teppei [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)] [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan); Satoh, Ryosuke [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan)] [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan); Fujiwara, Toshinobu [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan) [Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo (Japan); Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,Nagoya 467-8603 (Japan); Ito, Yutaka [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)] [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan); Sugiura, Reiko [Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka 577-8502 (Japan)] [Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka 577-8502 (Japan); Mishima, Masaki, E-mail: mishima-masaki@tmu.ac.jp [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)] [Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji 192-0397 (Japan)

2013-07-19T23:59:59.000Z

440

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 765363 I-INGEGNERIA NUCLEARE MI BV 110 05/07/1988  

E-Print Network [OSTI]

765363 I-INGEGNERIA NUCLEARE MI BV 110 05/07/1988 2 766599 I-INGEGNERIA NUCLEARE MI 110 21/03/1988 3 764813 I-INGEGNERIA ELETTRICA MI 110 29/04/1987 4 765411 I-INGEGNERIA CHIMICA MI 110 23/05/1988 5 781546 NANOTECHNOLOGY MI 110 19/08/1989 6 778979 NANOTECHNOLOGY MI 110 21/05/1990 7 764495 I-INGEGNERIA NUCLEARE MI 110

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


441

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 781330 I-GESTIONE DEL COSTRUITO MI 110 11/08/1988  

E-Print Network [OSTI]

781330 I-GESTIONE DEL COSTRUITO MI 110 11/08/1988 2 783933 I-GESTIONE DEL COSTRUITO MI BV 110 03/09/1987 3 766434 I-INGEGNERIA DEI SISTEMI EDILIZI MI 110 30/08/1988 4 761490 I-INGEGNERIA DEI SISTEMI EDILIZI MI 108 17/08/1989 5 776698 I-GESTIONE DEL COSTRUITO MI MI 106 02/05/1989 6 784798 I-INGEGNERIA DEI

442

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 764721 I-INGEGNERIA MATEMATICA MI 110 05/11/1988  

E-Print Network [OSTI]

764721 I-INGEGNERIA MATEMATICA MI 110 05/11/1988 2 771099 I-INGEGNERIA BIOMEDICA MI 110 19/10/1987 3 783806 I-INGEGNERIA BIOMEDICA MI MI 110 19/05/1989 4 783463 I-INGEGNERIA BIOMEDICA MI MI 110 19/05/1989 5 769961 I-INGEGNERIA BIOMEDICA MI MI 110 10/01/1989 6 764825 I-INGEGNERIA MATEMATICA MI LC 110 22

443

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 782252 A-ARCHITETTURA MI BV 110 07/05/1989  

E-Print Network [OSTI]

782252 A-ARCHITETTURA MI BV 110 07/05/1989 2 766298 A-PIANIFICAZIONE URBANA E POLITICHE TERRITORIALI MI BV 110 20/04/1989 3 770229 A-PIANIFICAZIONE URBANA E POLITICHE TERRITORIALI MI 110 27/06/1988 4 767317 A-ARCHITETTURA MI 110 13/06/1988 5 765987 A-PIANIFICAZIONE URBANA E POLITICHE TERRITORIALI MI 110

444

Posizione Matricola Corso di Luarea magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 783525 I-INGEGNERIA INFORMATICA MI 110 10/04/1989  

E-Print Network [OSTI]

783525 I-INGEGNERIA INFORMATICA MI 110 10/04/1989 2 766724 I-INGEGNERIA ELETTRONICA MI 110 11/01/1989 3 752109 I-INGEGNERIA INFORMATICA MI 110 03/12/1984 4 783081 I-INGEGNERIA INFORMATICA MI BV 110 09/03/1989 5 783397 I-INGEGNERIA DELLE TELECOMUNICAZIONI MI 110 16/02/1988 6 750317 I-INGEGNERIA INFORMATICA MI

445

Posizione Matricola Corso di Laurea Magistrale Sede isc. Sede alt. Voto laurea Data nascita 1 783078 I-INGEGNERIA CIVILE MI CO 110 26/09/1989  

E-Print Network [OSTI]

783078 I-INGEGNERIA CIVILE MI CO 110 26/09/1989 2 783301 I-INGEGNERIA CIVILE MI 110 31/10/1989 3 767166 I-INGEGNERIA PER L'AMBIENTE E IL TERRITORIO MI 110 06/08/1988 4 784194 I-INGEGNERIA PER L'AMBIENTE E IL TERRITORIO MI 110 28/04/1989 5 783920 I-INGEGNERIA CIVILE MI MI 110 31/12/1989 6 782721 I-INGEGNERIA PER L

446

Repertoire Selection of Variant Single-Chain Cro:? Toward Directed DNA-Binding Specificity of Helix?Turn?Helix Proteins  

Science Journals Connector (OSTI)

Utilizing phage display-afforded affinity selection, scCro variants have been isolated for binding to synthetic DNA ligands. ... Variant proteins with altered DNA-sequence specificity were identified, which favored binding of targeted synthetic DNA sequences over a consensus operator sequence, bound with high affinity by wild-type Cro. ... The specificities were relatively modest (2?3-fold, as calculated from KD values), which can be attributed to the inherent properties in the design of the selection system; one half-site of the synthetic DNA sequences maintains the consensus operator sequence, and one subunit of the variant single-chain Cro dimers was conserved as wild-type sequence. ...

Mikael T. I. Nilsson; Mikael Widersten

2004-08-28T23:59:59.000Z

447

Dependence of Nuclear Binding Energies on the Cutoff Momentum of Low-Momentum Nucleon-Nucleon Interaction  

E-Print Network [OSTI]

Binding energies of ^{3}H, ^{4}He, and ^{16}O are calculated, using low-momentum nucleon-nucleon interactions (V_{low-k}) for a wide range of the cutoff momentum \\Lambda. In addition, single-particle energies in nuclei around ^{16}O are computed. The dependence of the binding energies and the single-particle energies in these nuclei on the cutoff momentum \\Lambda of the V_{low-k} is examined. Furthermore, the availability of the V_{low-k} in nuclear structure calculations is discussed.

S. Fujii; H. Kamada; R. Okamoto; K. Suzuki

2004-06-30T23:59:59.000Z

448

Structure of Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain  

Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

Human Toll-like Receptor Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain Jungwoo Choe1, Matthew S. Kelker1, and Ian A. Wilson1 1Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 Figure 1. Overall structure of human TLR3 ECD. The N-terminal region is colored blue, the 23 canonical LRRs are in yellow and the C-terminal region is in pink. N-linked sugars that are observed in the electron density maps are shown in ball-and-stick. (From Choe et al. 2005). Innate immunity is the front line host defense that acts within minutes of infection to counter invasion by microorganisms. Members of the Toll-like receptor (TLR) family recognize conserved pathogen-associated molecular

449

DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding  

SciTech Connect (OSTI)

DNA nanotechnology allows the design and construction of nanoscale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect.

Nangreave, Jeanette; Yan, Hao; Liu, Yan

2011-01-01T23:59:59.000Z

450

Tight-Binding Modeling and Low-Energy Behavior of the Semi-Dirac Point  

Science Journals Connector (OSTI)

We develop a tight-binding model description of semi-Dirac electronic spectra, with highly anisotropic dispersion around point Fermi surfaces, recently discovered in electronic structure calculations of VO2-TiO2 nanoheterostructures. We contrast their spectral properties with the well-known Dirac points on the honeycomb lattice relevant to graphene layers and the spectra of bands touching each other in zero-gap semiconductors. We also consider the lowest order dispersion around one of the semi-Dirac points and calculate the resulting electronic energy levels in an external magnetic field. In spite of apparently similar electronic structures, Dirac and semi-Dirac systems support diverse low-energy physics.

S. Banerjee; R. R. P. Singh; V. Pardo; W. E. Pickett

2009-07-01T23:59:59.000Z

451

CO2-Binding Organic Liquids, an Integrated Acid Gas Capture System  

SciTech Connect (OSTI)

Amine systems are effective for CO2 capture, but they are still inefficient because the solvent regeneration energy is largely defined by the amount of water in the process. Most amines form heat-stable salts with SO2 and COS resulting in parasitic solvent loss and degradation. Stripping the CO2-rich solvent is energy intensive it requires temperatures above 100 ?C due to the high specific heat and heat of vaporization of water. CO2-capture processes could be much more energy efficient in a water free amine process. In addition, if the capture-material is chemically compatible with other acid gases, less solvent would be lost to heat-stable salts and the process economics would be further improved. One such system that can address these concerns is Binding Organic Liquids (BOLs), a class of switchable ionic liquids.

Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

2011-04-01T23:59:59.000Z

452

Visualization of Iron-Binding Micelles in Acidic Recombinant Biomineralization Protein, MamC  

SciTech Connect (OSTI)

Biological macromolecules are utilized in low-temperature synthetic methods to exert precise control over nanoparticle nucleation and placement. They enable low-temperature formation of a variety of functional nanostructured materials with properties often not achieved via conventional synthetic techniques. Here we report on the in situ visualization of a novel acidic bacterial recombinant protein, MamC, commonly present in the magnetosome membrane of several magnetotactic bacteria, including Magnetococcus marinus, strain MC-1. Our findings provide an insight into the self-assembly of MamC and point to formation of the extended protein surface, which is assumed to play an important role in the formation of biotemplated inorganic nanoparticles. The self-organization of MamC is compared to the behavior of another acidic recombinant iron-binding protein, Mms6.

Kashyap, Sanjay [Ames Laboratory; Woehl, Taylor [Ames Laboratory; Valverde-Tercedor, Carmen [University of Granada; Sanchez-Quesada, Miguel [University of Granada; Lopez, Concepcion Jimenez [University of Granada; Prozorov, Tanya [Ames Laboratory

2014-03-07T23:59:59.000Z

453

3D calculation of Tucson-Melbourne 3NF effect in triton binding energy  

E-Print Network [OSTI]

As an application of the new realistic three-dimensional (3D) formalism reported recently for three-nucleon (3N) bound states, an attempt is made to study the effect of three-nucleon forces (3NFs) in triton binding energy in a non partial wave (PW) approach. The spin-isospin dependent 3N Faddeev integral equations with the inclusion of 3NFs, which are formulated as function of vector Jacobi momenta, specifically the magnitudes of the momenta and the angle between them, are solved with Bonn-B and Tucson-Melbourne NN and 3N forces in operator forms which can be incorporated in our 3D formalism. The comparison with numerical results in both, novel 3D and standard PW schemes, shows that non PW calculations avoid the very involved angular momentum algebra occurring for the permutations and transformations and it is more efficient and less cumbersome for considering the 3NF.

M. R. Hadizadeh; L. Tomio; S. Bayegan

2010-03-24T23:59:59.000Z

454

Tight-binding theory of spin-orbit coupling in graphynes  

Science Journals Connector (OSTI)

We investigate the effects of Rashba and intrinsic spin-orbit couplings (SOC) in graphynes. First, we develop a general method to address spin-orbit couplings within the tight-binding theory. Then, we apply this method to ?-, ?-, and ?-graphyne, and determine the SOC parameters in terms of the microscopic hopping and onsite energies. We find that for ?-graphyne, as in graphene, the intrinsic SOC opens a nontrivial gap, whereas the Rashba SOC splits each Dirac cone into four. In ?- and ?-graphyne, the Rashba SOC can lead to a Lifshitz phase transition, thus transforming the zero-gap semiconductor into a gapped system or vice versa, when pairs of Dirac cones annihilate or emerge. The existence of internal (within the benzene ring) and external SOC in these compounds allows us to explore a myriad of phases not available in graphene.

Guido van Miert; Vladimir Juri?i?; Cristiane Morais Smith

2014-11-11T23:59:59.000Z

455

Atmospheric Oxygen Binding and Hole Doping in Deformed Graphene on a SiO2 Substrate  

E-Print Network [OSTI]

Using micro-Raman spectroscopy and scanning tunneling microscopy, we study the relationship between structural distortion and electrical hole doping of graphene on a silicon dioxide substrate. The observed upshift of the Raman G band represents charge doping and not compressive strain. Two independent factors control the doping: (1) the degree of graphene coupling to the substrate, and (2) exposure to oxygen and moisture. Thermal annealing induces a pronounced structural distortion due to close coupling to SiO2 and activates the ability of diatomic oxygen to accept charge from graphene. Gas flow experiments show that dry oxygen reversibly dopes graphene; doping becomes stronger and more irreversible in the presence of moisture and over long periods of time. We propose that oxygen molecular anions are stabilized by water solvation and electrostatic binding to the silicon dioxide surface.

Sunmin Ryu; Li Liu; Stephane Berciaud; Young-Jun Yu; Haitao Liu; Philip Kim; George W. Flynn; Louis E. Brus

2010-11-13T23:59:59.000Z

456

Trp22, Trp24, and Tyr8 Play a Pivotal Role in the Binding of the Family 10 Cellulose-Binding Module from Pseudomonas Xylanase A to Insoluble Ligands+  

E-Print Network [OSTI]

-bromosuccinimide indicated that Trp22 and Trp24 were on the surface of the protein, while Trp7 was buried. Collectively of five CBMs that bind cellulose and one that interacts with xylan, from five different families, have been solved (3-8). Each protein contains several surface aromatic residues, which site

Williamson, Mike P.

457

Precisely Defined ProteinPolymer Conjugates: Construction of Synthetic DNA Binding Domains on Proteins by Using Multivalent Dendrons  

Science Journals Connector (OSTI)

Precisely Defined ProteinPolymer Conjugates: Construction of Synthetic DNA Binding Domains on Proteins by Using Multivalent Dendrons ... The authors describe the parallel synthesis of a library comprising 146 nanoparticles decorated with different synthetic small mols. ... (a) Newkome, G. R.; Moorefield, C. N.; Vgtle, F. Dendrimers and Dendrons:Concepts, Syntheses, Applications; Wiley-VCH: Weinheim, 2001. ...

Mauri A. Kostiainen; Gza R. Szilvay; Julia Lehtinen; David K. Smith; Markus B. Linder; Arto Urtti; Olli Ikkala

2007-08-25T23:59:59.000Z

458

Highly Sensitive in Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding Affinity and Specificity  

E-Print Network [OSTI]

Highly Sensitive in Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding oligonucleotides to corresponding synthetic molecules, either as a consequence of DNA-templated organic synthesis3 or as a result of conjugating DNA to synthetic molecules, in theory enables synthetic molecules to satisfy

Liu, David R.

459

Single-Molecule Detection of Transcription Factor Binding to DNA in Real Time:? Specificity, Equilibrium, and Kinetic Parameters  

Science Journals Connector (OSTI)

Preparation of Synthetic DNA Duplexes. ... DNA targets for the proteins consisted of short synthetic DNA duplexes formed from oligonucleotides purchased from Integrated DNA Technologies. ... Binding of synthetic DNA duplexes was tested by measuring the ability of duplexes labeled with the quencher dabcyl to quench GFP or BFL emission, because the excitation spectrum of dabcyl overlaps with the emission spectrum of these fluorophores. ...

Eric A. Nalefski; Eugene Nebelitsky; Janice A. Lloyd; Steven R. Gullans

2006-10-31T23:59:59.000Z

460

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs  

Science Journals Connector (OSTI)

...orange squares, exp, Yun et al.; green diamonds, calculation. Table-1. Binding...Black line, WT; red line, G719S; green line, L858R; navy blue line, T790M...Kollman, and D. A. Case 1998 Continuum solvent studies of the stability of DNA, RNA...

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

The Bacteroides fragilis BtgA Mobilization Protein Binds to the oriT Region of pBFTM10  

Science Journals Connector (OSTI)

...conformational change of the nick site. TraK is not required...It binds downstream of the nick site over an approximate 180-nucleotide...inverted repeats, and possible nick site, raises the possibility...Administration Medical Research Service Merit Review grant 001. We thank...

Leonid A. Sitailo; Alexander M. Zagariya; Patrick J. Arnold; Gayatri Vedantam; David W. Hecht

1998-09-01T23:59:59.000Z

462

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data  

Science Journals Connector (OSTI)

......size to the original dataset, selected at random...using TRANSFAC data for nuclear hormone receptor proteins...3 Similarity of the nuclear hormone receptor DNA-binding...of HNF4alpha and each nuclear hormone receptor protein...cross-validation error for each dataset were corrupted with varying......

Kenzie D. MacIsaac; D. Benjamin Gordon; Lena Nekludova; Duncan T. Odom; Joerg Schreiber; David K. Gifford; Richard A. Young; Ernest Fraenkel

2006-02-15T23:59:59.000Z

463

Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein  

Science Journals Connector (OSTI)

A neutron crystallographic study of perdeuterated transthyretin reveals important aspects of the structure relating to its stability and its propensity to form fibrils, as well as evidence of a single water molecule that affects the symmetry of the two binding pockets.

Haupt, M.

2014-10-21T23:59:59.000Z

464

The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding  

Science Journals Connector (OSTI)

The crystal structure of Human cytomegalovirus immune modulator UL141 was solved at 3.25 ? resolution. Here, a detailed analysis of its intimate dimerization interface and the biophysical properties of its receptor (TRAIL-R2 and CD155) binding interactions are presented.

Nemcovicov?, I.

2014-02-22T23:59:59.000Z

465

Effect of Polyethylene Glycol, Alkyl, and Oligonucleotide Spacers on the Binding, Secondary Structure, and Self-Assembly of Fractalkine  

E-Print Network [OSTI]

Effect of Polyethylene Glycol, Alkyl, and Oligonucleotide Spacers on the Binding, Secondary-amphiphiles with no spacer (NoSPR), polyethylene glycol (PEG4, PEG8, PEG24), alkyl (C12 and C24), or oligonucleotide (T10 a polyethylene glycol (PEG) or an oligo-T (thymine) spacer is added to the aptamer, especially when attaching

Kokkoli, Efie

466

Cellulose Binding Protein from the Parasitic Nematode Heterodera schachtii Interacts with Arabidopsis Pectin Methylesterase: Cooperative Cell Wall Modification during Parasitism  

Science Journals Connector (OSTI)

...Two-week-old seedlings were inoculated with 250 surface-sterilized J2 Heterodera schachtii or...d, each plant was inoculated with 150 surface-sterilized J2 of H. schachtii, and...recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules...

Tarek Hewezi; Peter Howe; Tom R. Maier; Richard S. Hussey; Melissa Goellner Mitchum; Eric L. Davis; Thomas J. Baum

2008-11-11T23:59:59.000Z

467

Cellulose Binding Protein from the Parasitic Nematode Heterodera schachtii Interacts with Arabidopsis Pectin Methylesterase: Cooperative Cell Wall Modification during Parasitism  

Science Journals Connector (OSTI)

...seedlings were inoculated with 250 surface-sterilized J2 Heterodera...plant was inoculated with 150 surface-sterilized J2 of H. schachtii...manufacturers instructions. DNase treatment of total RNA was performed...plant cell walls by microbial xylan-specific carbohydrate-binding...

Tarek Hewezi; Peter Howe; Tom R. Maier; Richard S. Hussey; Melissa Goellner Mitchum; Eric L. Davis; Thomas J. Baum

2008-11-11T23:59:59.000Z

468

Mapping of the SecA Signal Peptide Binding Site and Dimeric Interface by Using the Substituted Cysteine Accessibility Method  

Science Journals Connector (OSTI)

...binding induces changes in the oligomeric state and conformation of Sec A in a lipid environment: a small-angle neutron-scattering study. J. Mol. Biol. 332 :23-30. 13. Or E , A Navon, and T Rapoport. 2002. Dissociation of the dimeric...

Meera K. Bhanu; Ping Zhao; Debra A. Kendall

2013-08-09T23:59:59.000Z

469

Heparan Sulfate Glycosaminoglycans Are Receptors Sufficient To Mediate the Initial Binding of Adenovirus Types 2 and 5  

Science Journals Connector (OSTI)

...Therefore, the experiments in CAR-defective CHO K1 il cells grown at low...experiments performed. Ad binding to CAR-defective recombinant CHO cells as a function...density. Ad2 is able to infect CAR-defective CHO K1 il cells in a time-dependent...

M. C. Dechecchi; P. Melotti; A. Bonizzato; M. Santacatterina; M. Chilosi; G. Cabrini

2001-09-01T23:59:59.000Z

470

Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX  

SciTech Connect (OSTI)

We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

Poulin, Kathy L. [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Tong, Grace; Vorobyova, Olga [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Pool, Madeline [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Kothary, Rashmi [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Parks, Robin J., E-mail: rparks@ohri.ca [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario (Canada)

2011-11-25T23:59:59.000Z

471

Identification of small-molecule binding pockets in the soluble monomeric form of the A?42 peptide  

Science Journals Connector (OSTI)

The aggregation of intrinsically disordered peptides and proteins is associated with a wide range of highly debilitating neurological and systemic disorders. In this work we explored the potential of a structure-based drug discovery procedure to target one such system the soluble monomeric form of the A?42 peptide. We utilised for this purpose a set of structures of the A?42 peptide selected from clusters of conformations within an ensemble generated by molecular dynamics simulations. Using these structures we carried out fragment mapping calculations to identify binding hot spots on the monomeric form of the A?42 peptide. This procedure provided a set of hot spots with ligand efficiencies comparable to those observed for structured proteins and clustered into binding pockets. Such binding pockets exhibited a propensity to bind small molecules known to interact with the A?42 peptide. Taken together these results provide an initial indication that fragment-based drug discovery may represent a potential therapeutic strategy for diseases associated with the aggregation of intrinsically disordered proteins.

Michele Vendruscolo

2013-01-01T23:59:59.000Z

472

A New Trick for an Old Dog: TraY Binding to a Homopurine-homopyrimidine Run Attenuates  

E-Print Network [OSTI]

progression in E. coli strains carrying FH episomes. The potency of replica- tion stalling increased, or transcription through the repeat. Treatment of E. coli cells with the protein synthesis inhibitor. Overexpression of an individual TraY protein in the F ? E. coli strain con- veyed d(GA)n Ád(TC)n-binding activity

Mirkin, Sergei

473

CELL REGULATION, Vol. 2, 851-859, October 1991 An ATP-binding membrane protein is required for  

E-Print Network [OSTI]

steps: signal sequence recognition by signal recognition particle (SRP), targeting to the ER via the SRP chain (Rapoport, 1990). Both SRP and SRP re- ceptor bind GTP (Connolly and Gilmore, 1989; Miller, GTP hydrolysis by SRP and SRP receptor probably does not contribute to the vectorial movement

Walter, Peter

474

Cell, Vol. 94, 181191, July 24, 1998, Copyright 1998 by Cell Press Crystal Structure of the Signal Sequence Binding  

E-Print Network [OSTI]

with their eukary- otic counterparts, SRP54, SRP RNA, and the SRP re- ceptor. Ffh is essential for viability of the SRP- dependent cotranslational targeting pathway blocks theSchool of Medicine University of California; Valent et al., 1995) and substitutes for the signal se- quence binding activity of SRP54 when

Walter, Peter

475

RNA Interference of Signal Peptide-binding Protein SRP54 Elicits Deleterious Effects and Protein Sorting Defects in Trypanosomes*  

E-Print Network [OSTI]

RNA Interference of Signal Peptide-binding Protein SRP54 Elicits Deleterious Effects and Protein recognition particle (SRP) has a unique composition compared with all known SRP complexes, because it contains the essentiality of the SRP pathway and its role in protein translocation in Trypanosoma brucei. The production

Unger, Ron

476

Translocation of Proteins Across the Endoplasmic Reticulum I . Signal Recognition Protein (SRP) Binds to In-Vitro-  

E-Print Network [OSTI]

Translocation of Proteins Across the Endoplasmic Reticulum I . Signal Recognition Protein (SRP protein, termed signal recognition protein (SRP), has been shown here (a) to inhibit translation-affinity binding as wel l as the selective translation- inhibitory effect were abol ished after modification of SRP

Walter, Peter

477

A Distal Arginine in Oxygen-Sensing Heme-PAS Domains Is Essential to Ligand Binding, Signal Transduction, and Structure  

E-Print Network [OSTI]

loop (the FG loop) with the helix of heme attachment was weakened. Binding of carbon monoxide was nevertheless preserved. Carbon monoxide and nitric oxide regulation, although weak in BjFixL, were abolished basic helix-loop-helix (bHLH) transcription factor and two different groups of microbial enzymes (3, 4

Scott, William

478

Mapping the Phospholipid-binding Surface and Translocation Determinants of the C2 Domain from Cytosolic Phospholipase A2*  

E-Print Network [OSTI]

in living cells. We have identified sets of exposed hydro- phobic residues in loops known as calcium C2 domain, we show that two of the calcium-binding loops, CBR1 and CBR3, penetrate in a calcium to translocate in a calcium-dependent manner from the cytosol to the nuclear envelope and endoplasmic retic- ulum

Williams, Roger L.

479

Effect of lactose feeding on cell renewal, disaccharidase activity and calcium-binding protein content in the intestinal  

E-Print Network [OSTI]

is injected into the lumen of the intestinal ligated loop, the absorption of calcium increases onlyEffect of lactose feeding on cell renewal, disaccharidase activity and calcium-binding protein Edouard Herriot, 69374 Lyon Cedex 2, France. Summary. To determine how lactose increases calcium

Paris-Sud XI, Université de

480

Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action  

E-Print Network [OSTI]

Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action-box proteins, EBF1 and -2, that work coordinately in SCF complexes to repress ethylene action. Mutations in either gene cause hypersensitivity to exogenous ethylene and its precursor 1-aminocyclopropane-1

Sheen, Jen

Note: This page contains sample records for the topic "isc bind deleted" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

Electron microprobe and X-ray microfluorescence analyses of copper binding to active and inactivated cells of Mucor rouxii  

SciTech Connect (OSTI)

Electron microprobe and x-ray microfluorescence spectroscopies have been used to study copper binding to active and inactivated Mucor rouxii copper-sensitive and copper-tolerant cells. A better understanding of metal resistance may help in the application of fungal biomass for the treatment of metal-contaminated water, and also in enrichment or recycling of valuable metals. After repeated culturing in progressively higher concentrations of copper sulfate, a copper-tolerant Mucor rouxii strain was obtained. The copper-tolerant strain differed from the sensitive parental strain in both shape and size. Copper binding studies using a laboratory batch technique revealed that the copper-tolerant strain cultured at higher copper levels bound large amounts of this metal. Electron microprobe and x-ray microfluorescence analyses showed that the copper characteristic x-ray signal on the cell surface of the copper-tolerant strain after copper binding was higher than the copper signal in sensitive cells. The copper signal in cross sections of the copper-tolerant cells also showed a statistically significant correlation with the sulfur signal but no correlation with the phosphorus signal. These results suggest that there are several mechanisms for metal detoxification inside and outside of the Mucor rouxii cells and that copper may be binding to sulfur-containing groups.

Cano-Aguilera, I.; Gardea-Torresdey, J.L.; Pingitore, N.E. Jr.; Webb, R. [Univ. of Texas, El Paso, TX (United States)

1997-12-31T23:59:59.000Z

482

Discovery of New Small Molecules Targeting the Vitronectin-Binding Site of the Urokinase Receptor That Block Cancer Cell Invasion  

Science Journals Connector (OSTI)

...364 compounds) were extracted by the website (31) and prepared using LigPrep software...Protein Data Bank). Before starting the search, the binding site for vitronectin was...Biochem J 2001;358:673-9. 38. Bodary SC , McLean JW.The integrin beta 1 subunit...

Vincenza Elena Anna Rea; Antonio Lavecchia; Carmen Di Giovanni; Francesca Wanda Rossi; Anna Gorrasi; Ada Pesapane; Amato de Paulis; Pia Ragno; and Nunzia Montuori

2013-08-01T23:59:59.000Z

483

THE JOURNAL OF CHEMICAL PHYSICS 134, 134701 (2011) Binding of hydrogen on benzene, coronene, and graphene from quantum  

E-Print Network [OSTI]

, and graphene from quantum Monte Carlo calculations Jie Ma,1,2,3 Angelos Michaelides,2,3,4 and Dario Alfè3 the binding energy curves of hydrogen on benzene, coronene, and graphene. The DMC results on benzene agree well with MP2, giving an adsorption energy of 40 meV. For physisorbed hydrogen on graphene, DMC

Alfè, Dario

484

Hydrogen Bonds Involved in Binding the Qi-site Semiquinone in the bc1 Complex, Identified through Deuterium Exchange  

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Hydrogen Bonds Involved in Binding the Qi-site Semiquinone in the bc1 Complex, Identified through them. The strength of interactions indicates that the protons are involved in hydrogen bonds with SQ. The hyperfine cou- plings differ from values typical for in-plane hydrogen bonds previously observed in model

Crofts, Antony R.

485

The integrity of a cholesterol-binding pocket in NiemannPick C2 protein is necessary to  

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cholesterol accumulation in cells. We find that purified NPC2, a secreted soluble protein, binds cholesterol as important, including one required for efficient secretion. point mutants secretion protein evolution Niemann. At the cellular level, mutant cells accumulate cholesterol and other lipids in aberrant compartments with features

Quake, Stephen R.

486

Ensemble Modeling of Substrate Binding to Cytochromes P450: Analysis of Catalytic Differences between CYP1A Orthologs,  

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Ensemble Modeling of Substrate Binding to Cytochromes P450: Analysis of Catalytic Differences substrates (TCB and B[a]P) as well as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) were docked to multiple observed closer to the heme in ensembles of rat or human CYP1A1 than of killifish CYP1A. Analysis

Vajda, Sandor

487

Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding to  

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Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding by single molecule force spectroscopy. T7 gp2.5- 26C, lacking 26 acidic C-terminal residues, also reduces of single DNA molecules by stretch- ing the molecules and measuring the required force for a given extension

Richardson, Charles C.

488

Anion Binding Properties of Reduced and Oxidized Iron-Containing Superoxide Dismutase Reveal No Requirement for Tyrosine 34  

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nuclear magnetic relaxation dispersion (NMRD) results. Thus, we propose that two F- ions can bind magnetic resonance; NMRD, nuclear magnetic relaxation dispersion; OCN- , cyanate; PIPES, piperazine circular dichroism; MES, 2-(N-morpholino) ethane sulfonic acid; MnSOD, Mn-containing SOD; NMR, nuclear

Miller, Anne-Frances

489

Modeling Binding Kinetics at the QA Site in Bacterial Reaction Centers Jennifer Madeo and M. R. Gunner*  

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. Gunner* Physics Department J-419 City College of New York 138th Street and ConVent AVenue, New York, New quinones with similar Kd values take minutes to bind or dissociate. These slow rates are independent). The primary electron donor P, a bacte- riochlorophyll dimer, absorbs a photon obtaining the energy to reduce

Gunner, Marilyn

490

Different adsorbate binding mechanisms of hydrocarbons: Theoretical studies for Cu(111)C2H2 and Cu(111)C2H4  

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Different adsorbate binding mechanisms of hydrocarbons: Theoretical studies for Cu(111)±C2H2 and Cu qualitatively different adsorbate binding mechanisms, depending on the adsorbate and substrate material. Experiments on Cu(111)±C2H2 identify a strongly distorted adsorbate while the adsorption energy is small

491

ATP Utilization by Yeast Replication Factor C III. THE ATP-BINDING DOMAINS OF Rfc2, Rfc3, AND Rfc4 ARE ESSENTIAL FOR DNA RECOGNITION AND  

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ATP Utilization by Yeast Replication Factor C III. THE ATP-BINDING DOMAINS OF Rfc2, Rfc3, AND Rfc4 lysine in the Walker A motif of the ATP- binding domain encoded by the yeast RFC1, RFC2, RFC3, and RFC4 loading activity. In addition to their defects in ATP hydrolysis, these complexes were defective for DNA

Burgers, Peter M.

492

Involvement of ATP synthase residues aArg-376, bArg-182, and bLys-155 in Pi binding  

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Involvement of ATP synthase residues aArg-376, bArg-182, and bLys-155 in Pi binding Zulfiqar AhmadArg-182 are catalytically important ATP synthase residues that were proposed to be in- volved in substrate Pi binding and subsequent steps of ATP syn- thesis [Senior, A.E., Nadanaciva, S. and Weber, J. (2002

Zulfiqar Ahmad

493

Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins  

Science Journals Connector (OSTI)

Membrane-embedded voltage-activated potassium channels (Kv) bind intracellular scaffold proteins, such as the Post Synaptic Density 95 (PSD-95) protein, using a conserved PDZ-binding motif located at the channels' C-terminal tip. This interaction underlies ...

Elhanan Magidovich; Sarel J. Fleishman; Ofer Yifrach

2006-07-01T23:59:59.000Z

494

Isolation and characterization of a cDNA clone encoding the 19 kDa protein of signal recognition particle (SRP): expression and binding to 7SL RNA  

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particle (SRP): expression and binding to 7SL RNA K.Lingelbach, C.Zwieb+, J.R.Webb, C.Marshallsay, P Signal recognition particle (SRP) consists of a 7SL RNA molecule and 6 protein subunits. We have isolated and characterized cDNA clones from human liver which encode the 19kDa protein subunit (SRP19). This subunit binds

Walter, Peter

495

A New Arabidopsis Gene, FLK, Encodes an RNA Binding Protein with K Homology Motifs and Regulates Flowering Time via FLOWERING LOCUS C  

Science Journals Connector (OSTI)

...It is now evident that a battery of different RNA binding proteins...Motifs A high-throughput thermal asymmetric interlaced PCR method...T-DNA insert junctions by thermal asymmetric interlaced PCR...It is now evident that a battery of different RNA binding proteins...

Mi-Hye Lim; Joonki Kim; Youn-Sung Kim; Kyung-Sook Chung; Yeon-Hee Seo; Ilha Lee; Jungmook Kim; Choo Bong Hong; Hie-Joon Kim; Chung-Mo Park

2004-02-18T23:59:59.000Z

496

Letters to the Editor Resonance assignments of 30 kDa complexes of TFIID subunit TAF1 with TATA-binding protein  

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occupies TATA binding concave surface of TBP thereby inhibiting the DNA-binding activity of TBP. In yeast y- mined. We report backbone 1 H, 13 C and 15 N chemical shifts of TBP-yTAND1-2 and TBP-dTAND1 complexes Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA; e Division

Ikura, Mitsuhiko

497

Selective collision-induced desorption: Measurement of the -bonded C2H4 binding energy on Pt^111 precovered with atomic oxygen  

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Selective collision-induced desorption: Measurement of the -bonded C2H4 binding energy on Pt^111 CID is used to selectively probe the well depth of one particular adsorbate­surface potential energy K x-ray photoelectron XP spectra suggests that C(1s) XP binding energy is 283.1 eV for -C2H4

Levis, Robert J.

498

Quantum Monte Carlo calculation of the electronic binding energy in a C60 molecule Fei Lin, Jurij Smakov, Erik S. Srensen, Catherine Kallin, and A. John Berlinsky  

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Quantum Monte Carlo calculation of the electronic binding energy in a C60 molecule Fei Lin, Jurij electrons4­11 and lattice-level calculations based on an effec- tive Hamiltonian in which the intramolecular,5,15­17 This argument was supported by perturbative calculations of the electronic binding energies of the conven

Sørensen, Erik S.

499

A tight-binding potential for atomistic simulations of carbon interacting with transition metals: Application to the Ni-C system  

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for transition metals, carbon, and transition metal carbides, which has been optimized through a systematicA tight-binding potential for atomistic simulations of carbon interacting with transition metals of the transition metal, is used to obtain a transferable tight-binding model of the carbon-carbon, metal-metal

Paris-Sud XI, Université de

500

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