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Sample records for folds grabens horst

  1. Horst and Graben | Open Energy Information

    Open Energy Info (EERE)

    W 49,500,000,000 mW 0.0495 GW 4.95e-5 TW 470.15 K197 C 386.6 F 846.27 R Brady Hot Springs Geothermal Area Northwest Basin and Range Geothermal Region Extensional...

  2. John Horst | Department of Energy

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

    Horst About Us John Horst - Public Affairs Specialist with the Office of Energy Efficiency and Renewable Energy John Horst is a Public Affairs Specialist with the Office of Energy Efficiency and Renewable Energy. Most Recent Super Bowl City Leads on Energy Efficient Forefront February 2 Ultra Energy Efficient Data Center Saves NREL $200,000 November 14

  3. Anastomosing grabens, low-angle faults, and Tertiary thrust( ) faults, western Markagunt Plateau, southwestern Utah

    SciTech Connect (OSTI)

    Maldonado, F.; Sable, E.G. )

    1993-04-01

    A structurally complex terrane composed of grabens and horsts, low-angle faults, Tertiary thrust( ) faults, gravity-slide blocks, and debris deposits has been mapped along the western Markagunt Plateau, east of Parowan and Summit, southwestern Utah. This terrane, structurally situated within the transition between the Basin and Range and Colorado Plateau provinces, contains Tertiary volcanic and sedimentary and Cretaceous sedimentary rocks. The structures are mostly Miocene to Oligocene but some are Pleistocene. The oldest structure is the Red Hills low-angle shear zone, interpreted as a shallow structure that decoupled an upper plate composed of a Miocene-Oligocene volcanic ash-flow tuff and volcaniclastic succession from a lower plate of Tertiary sedimentary rocks. The period of deformation on the shear zone is bracketed from field relationships between 22.5 and 20 Ma. The graben-horst system trends northeast and formed after about 20 Ma (and probably much later) based on displacement of dated dikes and a laccolith. The central part of the system contains many grabens that merge toward its southerly end to become a single graben. Within these grabens, (1) older structures are preserved, (2) debris eroded from horst walls forms lobe-shaped deposits, (3) Pleistocene basaltic cinder cones have localized along graben-bounding faults, and (4) rock units are locally folded suggesting some component of lateral translation along graben-bounding faults. Megabreccia deposits and landslide debris are common. Megabreccia deposits are interpreted as gravity-slide blocks of Miocene-Oligocene( ) age resulting from formation of the Red Hills shear zone, although some may be related to volcanism, and still others to later deformation. The debris deposits are landslides of Pleistocene-Pliocene( ) age possibly caused by continued uplift of the Markagunt Plateau.

  4. Growth faulting and syntectonic casting of the Dawson Creek Graben Complex: A North American craton-marginal trough; Carboniferous-Permian Peace River Embayment, western Canada

    SciTech Connect (OSTI)

    Barclay, J.E.; Utting, J. ); Krause, F.F.; Campbell, R.I. )

    1991-06-01

    The Dawson Creek Graben Complex was a 150 {times} 300 km, craton-perpendicular trough near the western North American craton margin. Sedimentary infill spanned 100 million years, and this tectonically controlled basin provides a comparison with other craton-marginal troughs or aulacogens, such as the Big Snowy, Uinta, Delaware, and Southern Oklahoma. The authors suspect that the graben complex was controlled by outboard, Antler-like orogeny and perhaps some strike-slip control. This syntectonic graben infill model provides a basis for developing new structural-stratigraphic plays in this mature basin. This extensional trough rests on a former basement arch and is centered in the broadly downwarped Peace River embayment. Sediment infill records several graben casting stages beginning with westernmost down-dropping, which then extended eastward and was accompanied by an increase in growth-type block faulting. Subsidence and faulting decay was followed by a retreat to western areas and tectonic stabilization. The complex was an arcuate half-graben, steep to the north, that widened asymmetrically and increased in depth to the west through time. The complex contained a principal half-graben with neighboring satellite grabens; throughout the complex are numerous kilometer-scale horst and graben blocks. The horsts subsided slower than neighboring grabens. This differential subsidence along block-bounding syn- and postdepositional growth-type normal faults controlled formation and bed thickness, as did inter- and intraformational unconformities.

  5. Microsoft PowerPoint - Horst Simon.BitstoBuidings2

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

    Efficient Computing: From Bits to Energy Efficient Computing: From Bits to Buildings Horst D. Simon Lawrence Berkeley National Laboratory Lawrence Berkeley National Laboratory and EECS Dept., UC Berkeley hdsimon@lbl.gov The Salishan Conference on High-Speed Computing April 29, 2009 Acknowledgements A l b f i di id l h t ib t d t A large number of individuals have contributed to energy efficiency in computing at Berkeley Lab, UC Berkeley, and to this presentation: David Bailey (CRD), Michael

  6. Property:TopoFeatures | Open Energy Information

    Open Energy Info (EERE)

    Geothermal Area + Horst and Graben + Blue Mountain Geothermal Area + Horst and Graben + Brady Hot Springs Geothermal Area + Horst and Graben + C Coso Geothermal Area + Horst and...

  7. Folded waveguide coupler

    DOE Patents [OSTI]

    Owens, Thomas L.

    1988-03-01

    A resonant cavity waveguide coupler for ICRH of a magnetically confined plasma. The coupler consists of a series of inter-leaved metallic vanes disposed withn an enclosure analogous to a very wide, simple rectangular waveguide that has been "folded" several times. At the mouth of the coupler, a polarizing plate is provided which has coupling apertures aligned with selected folds of the waveguide through which rf waves are launched with magnetic fields of the waves aligned in parallel with the magnetic fields confining the plasma being heated to provide coupling to the fast magnetosonic wave within the plasma in the frequency usage of from about 50-200 mHz. A shorting plate terminates the back of the cavity at a distance approximately equal to one-half the guide wavelength from the mouth of the coupler to ensure that the electric field of the waves launched through the polarizing plate apertures are small while the magnetic field is near a maximum. Power is fed into the coupler folded cavity by means of an input coaxial line feed arrangement at a point which provides an impedance match between the cavity and the coaxial input line.

  8. Shongaloo field: A recent smackover (Jurassic) discovery in the Arkansas-Louisiana state-line graben

    SciTech Connect (OSTI)

    DeMis, W.D.; Milliken, J.V. )

    1993-09-01

    The new North Shongaloo/Red Rock/Haynesville/East Haynesville (herein called Shongaloo) field is a recent discovery (1988) with reserves of 20-30 MMBOE. The field has over 50 wells producing from the Smackover Formation at about 11,000 ft depth, and is the largest field discovered in the very mature Arkansas-Louisiana state-line Smackover play in the past 20 yr. More significantly, the field is locate within the state-line graben, an area considered by industry as barren of Smackover potential because Smackover reservoir rocks were assumed absent. Shongaloo field pay is from the Smackover. The [open quotes]C[close quotes] sand has average porosity of 5-7% and average permeability of less than 1 md (average initial flow rate is 1500 MCFGD with 430 BCPD). The [open quotes]B[close quotes] carbonate reservoirs consist of ooid grainstones with average porosity of 14% and average permeability of 60 md, ranging up to 1800 md (average initial flow rate is 550 BOPD and 950 MCFGD). Shongaloo field is an upthrown fault trap within the overall downthrown central graben. Shongaloo field was found by overcoming two technical hurdles. First, reservoir rock distribution was shown to follow paleoshorelines through the graben. Porous ooid grainstones facies within a mappable cycle of the Smackover [open quotes]B[close quotes] are parallel to, and immediately downdip (<1.5 mi) of paleoshorelines. Paleoshorelines are documented by the updip pinchout of [open quotes]B[close quotes] cycles into time-equivalent Buckner red beds. Second, the critical trapping fault was resolved by shooting and interpreting modern proprietary seismic data. The discovery of Shongaloo field proves that significant reserves can be found in mature domestic plays by applying new technology and stratigraphic concepts.

  9. Interpretation of recent seismic data from a frontier hydrocarbon province: western Rough Creek graben, southern Illinois and western Kentucky

    SciTech Connect (OSTI)

    Bertagne, A.J.; Pisasale, E.T.; Leising, T.C.

    1986-05-01

    The northern basement fault of the Rough Creek graben is seismically discernible and has surface expression in the Rough Creek fault zone. The southern basement fault is not clearly defined seismically, but can be inferred from shallow faulting and gravity data. This fault is roughly coincident with the Pennyrile fault zone. Extensional faults that formed the rift boundaries were the sites of late-stage compressional and extensional tectonics. Flower structures observed along the graben boundaries probably indicate post-Pennsylvanian wrench faulting. The basement within the graben plunges north-northwest, with the lowest point occurring south of the Rough Creek fault zone. Pre-Knox sediments thicken to approximately 12,000 in this area. The Knox Megagroup thickens toward the Mississippi Embayment, ranging from 4800 ft (southeastern graben area) to more than 7000 ft (west end of graben). Upper Ordovician to Devonian units also display westward thickening. The top of the Meramecian, New Albany, Maquoketa, and the base of the Knox generate continuous, high-amplitude seismic reflections due to large impedance contrasts between clastic and carbonate units. Shallow oil and gas production (Mississippian and Pennsylvanian) is present in this area. However, deep horizons (Knox, Lower Cambrian) remain relatively untested. Potential hydrocarbon traps in the pre-Knox sequence observed on seismic include fault blocks and updip pinch-outs.

  10. Protein folding in the ER.

    SciTech Connect (OSTI)

    Stevens, F. J.; Argon, Y.; Biosciences Division; Univ. of Chicago

    1999-10-01

    The endoplasmic reticulum (ER) is a major protein folding compartment for secreted, plasma membrane and organelle proteins. Each of these newly-synthesized polypeptides folds in a deterministic process, affected by the unique conditions that exist in the ER. An understanding of protein folding in the ER is a fundamental biomolecular challenge at two levels. The first level addresses how the amino acid sequence programs that polypeptide to efficiently arrive at a particular fold out of a multitude of alternatives, and how different sequences obtain similar folds. At the second level are the issues introduced by folding not in the cytosol, but in the ER, including the risk of aggregation in a molecularly crowded environment, accommodation of post-translational modifications and the compatibility with subsequent intracellular trafficking. This review discusses both the physicochemical and cell biological constraints of folding, which are the challenges that the ER molecular chaperones help overcome.

  11. Laboratory modeling of graben inversion with application to broad fourteens basin, Netherlands offshore

    SciTech Connect (OSTI)

    Nalpas, T.; Brun, J.P. ); Le Douaran, S. ); Richert, J.P. )

    1993-09-01

    The southern North Sea presents spectacular examples of basin inversion, which have been documented by numerous projects of the oil industry. Some basic inversion patterns identified through wells and seismic data were used to prepare a laboratory modeling investigation. Models are built with sand and silicone putty, respectively, which represent the frictional behavior of Mesozoic cover and Paleozoic basement and the viscous behavior of the decollement layer, mainly Permian salt, between them. They are scaled to fit natural configurations observed in the Broad Fourteens basin. All experiments are done in two steps: (1) graben formation with synkinematic sedimentation and (2) compression oblique to the graben. The experiments show that structures generated by or reactivated during inversion are strongly dependent on the strength of the decollement layer at the base of the sedimentary cover, which is itself dependent on the silicone viscosity, the layer thickness, and the displacement velocity applied at model boundaries; and the strength of the sedimentary cover, which is solely dependent on its thickness. This work is in progress. Preliminary results will be compared with examples from the Broad Fourteens basin on the basis of both seismic data and structural maps.

  12. Graphene folding on flat substrates

    SciTech Connect (OSTI)

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong; Zhang, Liuyang; Wang, Xianqiao

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57?eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  13. Compact intermediates in RNA folding

    SciTech Connect (OSTI)

    Woodson, S.A. (JHU)

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  14. Fast events in protein folding

    SciTech Connect (OSTI)

    Woodruff, W.; Callender, R.; Causgrove, T.; Dyer, R.; Williams, S.

    1996-04-01

    The primary objective of this work was to develop a molecular understanding of how proteins achieve their native three-dimensional (folded) structures. This requires the identification and characterization of intermediates in the protein folding process on all relevant timescales, from picoseconds to seconds. The short timescale events in protein folding have been entirely unknown. Prior to this work, state-of-the-art experimental approaches were limited to milliseconds or longer, when much of the folding process is already over. The gap between theory and experiment is enormous: current theoretical and computational methods cannot realistically model folding processes with lifetimes longer than one nanosecond. This unique approach to employ laser pump-probe techniques that combine novel methods of laser flash photolysis with time-resolved vibrational spectroscopic probes of protein transients. In this scheme, a short (picosecond to nanosecond) laser photolysis pulse was used to produce an instantaneous pH or temperature jump, thereby initiating a protein folding or unfolding reaction. Structure-specific, time-resolved vibrational probes were then used to identify and characterize protein folding intermediates.

  15. Controlling Structures | Open Energy Information

    Open Energy Info (EERE)

    fault terminations or tip-lines with multiple closely-spaced faults that enhance permeability. Mountainous, Horst and Graben Extensional Tectonics, Rift Zone Stepover or Relay...

  16. Mountainous | Open Energy Information

    Open Energy Info (EERE)

    Horst and Graben Shield Volcano Flat Lava Dome Stratovolcano Cinder Cone Caldera Depression Resurgent Dome Complex The interior of Iceland holds a vast expanse of mountainous...

  17. Lava Dome | Open Energy Information

    Open Energy Info (EERE)

    Horst and Graben Shield Volcano Flat Lava Dome Stratovolcano Cinder Cone Caldera Depression Resurgent Dome Complex "Volcanic or lava domes are formed by relatively small,...

  18. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01

    The three-dimensional structure of a protein is encoded in its linear sequence of amino acids. Studies of protein folding are aimed at understanding the nature of this code which translates one-dimensional information to three-dimensions. It is now well-established that protein folding intermediates exist and can be populated significantly under some conditions. A method to characterize kinetic folding intermediates is described. The method takes advantage of the decrease in exchange rates between amide protons (i.e., peptide backbone NH) and solvent water protons, when the amide proton is involved in structure. The feasibility of using amide proton exchange to pulse-label proteins during folding has been demonstrated using (/sup 3/H)-H/sub 2/O. The results with ribonuclease A (RNase A) support a framework model for folding, in which the secondary structure of a protein is formed before tertiary structure changes are complete. Extension of these studies using NMR should permit characterization of early secondary structure folding frameworks.

  19. SciTech Connect: "protein folding"

    Office of Scientific and Technical Information (OSTI)

    protein folding" Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: "protein folding" Semantic Semantic Term Title: Full Text: Bibliographic Data:...

  20. Structural styles of subandean fold and thrust belt of Peru and Southern Ecuador

    SciTech Connect (OSTI)

    Aleman, A.M.

    1988-01-01

    Along-strike variations in structural styles of the east-verging Subandean fold and thrust belt (SAFTB) in Peru and southern Ecuador are controlled by the presence or absence of thick Late Permian to Jurassic evaporite sequences rather than changes in subducting plate geometries as has been suggested previously for the Andes. Salt distribution and thickness have not only controlled the styles and segmentation along the SAFTB but also have been important factors in strike variations across the belt. The southern Ecuador SAFTB lacks significant evaporite units and is characterized by thick-skinned deformation that encompasses high-angle reverse faults, and broad, low-amplitude folds. The style changes to thin-skinned deformation near 2S lat. and it is well illustrated in the Santiago and Huallaga basins where thick evaporite units are present. This segment is characterized by a major decollement on the salt, grabens formed by salt withdrawal from reactivation of thrust faults as listric normal faults, salt piercement at or near synclinal axes, and periclines and asymmetric folds. The frontal thrust of this thin-skinned segment consists of box, overturned and upright folds above shallow salt domes, and by a major backthrust at the mountain front. This segment extends to 1030'S lat., near Oxapampa, Peru, where the thin-skinned SAFTB is narrow and changes across strike to a thick-skinned deformation as the evaporite units thin and disappear eastward. South of 1030'S lat., a new thick-skinned deformation segment is present in southern Peru and characterizes most of the deformation in the SAFTB of the Ucayali and Madre De Dios basins.

  1. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

    Zheng, Zhongzhou; Sosnick, Tobin R. (UC)

    2010-05-25

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  2. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect (OSTI)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A.

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  3. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  4. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, R.R.; Cowan, T.E.

    1996-06-11

    Disclosed are fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figs.

  5. Mechanical Models of Fault-Related Folding

    SciTech Connect (OSTI)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  6. Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles, for Large-Scale Geologic Storage of CO₂

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-12-08

    Geomechanics Technologies has completed a detailed characterization study of the Wilmington Graben offshore Southern California area for large-scale CO₂ storage. This effort has included: an evaluation of existing wells in both State and Federal waters, field acquisition of about 175 km (109 mi) of new seismic data, new well drilling, development of integrated 3D geologic, geomechanics, and fluid flow models for the area. The geologic analysis indicates that more than 796 MMt of storage capacity is available within the Pliocene and Miocene formations in the Graben for midrange geologic estimates (P50). Geomechanical analyses indicate that injection can be conducted without significant risk for surface deformation, induced stresses or fault activation. Numerical analysis of fluid migration indicates that injection into the Pliocene Formation at depths of 1525 m (5000 ft) would lead to undesirable vertical migration of the CO₂ plume. Recent well drilling however, indicates that deeper sand is present at depths exceeding 2135 m (7000 ft), which could be viable for large volume storage. For vertical containment, injection would need to be limited to about 250,000 metric tons per year per well, would need to be placed at depths greater than 7000ft, and would need to be placed in new wells located at least 1 mile from any existing offset wells. As a practical matter, this would likely limit storage operations in the Wilmington Graben to about 1 million tons per year or less. A quantitative risk analysis for the Wilmington Graben indicate that such large scale CO₂ storage in the area would represent higher risk than other similar size projects in the US and overseas.

  7. Tectonic and eustatic controls on facies distribution in the middle of upper Jurassic, Viking Graben, Norwegian North Sea

    SciTech Connect (OSTI)

    Sneider, J.S.; Vail, P.R. ); De Clarens, P. )

    1993-09-01

    The Middle of Upper Jurassic in the Viking Graben area was deposited during an overall transgression. From the lower Toarcian to the base of the cretaceous, there are seven 2nd-order (3-5 m.y.) transgressive-regressive (T/R) facies cycles that are related to regional tectonic events. These cycles dominate facies distribution, appear synchronous, and can be correlated throughout the study area. Local tectonics and sediment supply can modify these cycles. Local tectonics, sediment supply, and position in the T/R facies cycles control development of 3rd-order (0.5-3 m.y.) cycles. Where sediment supply is low, 3rd-order sequences are poorly developed. During a 2nd-order regression, shelfal areas and local highs are often eroded. Third-order sequences have well developed lowstands system-Y tracts (LST) and poorly developed transgressive systems tracts (TST). During 2nd-order transgressions, 3rd-order sequences have enhanced TST, starved HST, and poorly developed LST. Thick, stacked, shoreface sandstones may develop in the TST on terraces or on gently dipping slopes if sediment supply is high. The base of these sequences often shows an abrupt basinward shift in facies followed by backstepping facies. turbidites develop during 3rd-order lowstands when there is a steeply dipping slope and high sediment supply, but their distribution is more limited.

  8. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2008-06-24

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  9. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  10. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  11. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-14

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  12. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

    Carangelo, R.M.; Wright, D.D.

    1995-08-08

    A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal foci coincidence and thereby to increase the radiation energy throughput characteristic of the cell. 10 figs.

  13. Self-folding graphene-polymer bilayers

    SciTech Connect (OSTI)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  14. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

    Carangelo, Robert M. (Glastonbury, CT); Wright, David D. (Vershire, VT)

    1995-01-01

    A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal focii coincidence and thereby to increase the radiation energy throughput characteristic of the cell.

  15. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

    Ben-Naim, A. (Hebrew Univ., Jerusalem (Israel))

    1990-08-23

    The solvent-induced forces between various groups on the protein are examined. It is found that the intramolecular hydrophilic forces are likely to be the strongest forces mediated through the solvent. It is argued that these are probably the most important solvent-induced driving forces in the process of protein folding.

  16. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Title: Simplified Protein Models: Predicting Folding Pathways and Structure Using ...

  17. Category:Topographic Features | Open Energy Information

    Open Energy Info (EERE)

    Features" The following 9 pages are in this category, out of 9 total. C Caldera Depression Cinder Cone F Flat H Horst and Graben L Lava Dome M Mountainous R Resurgent Dome...

  18. Geometry of Cenozoic extensional faulting: Dixie Valley, Nevada...

    Open Energy Info (EERE)

    was also 15 km instead of the previously reported 40 km. Local microearthquakes cluster around 10-15 km. The geometrical block models indicate that crustal horst-graben...

  19. Folded membrane dialyzer with mechanically sealed edges

    DOE Patents [OSTI]

    Markley, Finley W.

    1976-01-01

    A semipermeable membrane is folded in accordion fashion to form a stack of pleats and the edges are sealed so as to isolate the opposite surfaces of the membrane. The stack is contained within a case that provides ports for flow of blood in contact with one surface of the membrane through channels formed by the pleats and also provides ports for flow of a dialysate through channels formed by the pleats in contact with the other surface of the membrane. The serpentine side edges of the membrane are sealed by a solidified plastic material, whereas effective mechanical means are provided to seal the end edges of the folded membrane. The mechanical means include a clamping strip which biases case sealing flanges into a sealed relationship with end portions of the membrane near the end edges, which portions extend from the stack and between the sealing flanges.

  20. Manipulating and Visualizing Proteins Simon, Horst D. 59 BASIC...

    Office of Scientific and Technical Information (OSTI)

    ACIDS; CALIFORNIA; CHAINS; CHEMISTRY; DISEASES; FIBROSIS; FORECASTING; GENETICS; OPTIMIZATION; PROTEIN STRUCTURE; PROTEINS; QUEUES; SHAPE; SIMULATION PROTEIN STRUCTURE...

  1. Microsoft Word - RNA_folding_Herschlag.doc

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

    March 2003 Exploring the Folding Landscape of a Structured RNA by SAXS Rick Russell, Ian S. Millett, Sebastian Doniach and Daniel Herschlag Stanford University One goal of genome projects is to systematically identify genes (1,2). The best current knowledge indicates that humans carry approximately 35000 genes. This number is an estimate that varies from expert to expert and range up to 100,000 (3-5). To anyone who has taken an elementary biology class, this ambiguity must seem strange. How hard

  2. Folding and association of a homotetrameric protein complex in...

    Office of Scientific and Technical Information (OSTI)

    Folding and association of a homotetrameric protein complex in an all-atom Go model Title: Folding and association of a homotetrameric protein complex in an all-atom Go model ...

  3. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a

  4. Accordian-folded boot shield for flexible swivel connection

    DOE Patents [OSTI]

    Hoh, Joseph C.

    1986-01-01

    A flexible swivel boot connector for connecting a first boot shield section to a second boot shield section, both first and second boot sections having openings therethrough, the second boot section having at least two adjacent accordian folds at the end having the opening, the second boot section being positioned through the opening of the first boot section such that a first of the accordian folds is within the first boot section and a second of the accordian folds is outside of the first boot, includes first and second annular discs, the first disc being positioned within and across the first accordian fold, the second disc being positioned within and across the second accordian fold, such that the first boot section is moveably and rigidly connected between the first and second accordian folds of the second boot section.

  5. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  6. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  7. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  8. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  9. Microsecond Microfluidic Mixing for Investigation of Protein Folding

    Office of Scientific and Technical Information (OSTI)

    Kinetics (Conference) | SciTech Connect Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics Citation Details In-Document Search Title: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first demonstrated

  10. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN ...

  11. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these...

  12. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE...

  13. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley,...

  14. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1994-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  15. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, R.R.; Cowan, T.E.

    1994-12-27

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figures.

  16. Folding associated with extensional faulting: Sheep Range detachment, southern Nevada

    SciTech Connect (OSTI)

    Guth, P.L.

    1985-01-01

    The Sheep Range detachment is a major Miocene extensional fault system of the Great Basin. Its major faults have a scoop shape, with straight, N-S traces extending 15-30 km and then abruptly turning to strike E-W. Tertiary deformation involved simultaneous normal faulting, sedimentation, landsliding, and strike-slip faulting. Folds occur in two settings: landslide blocks and drag along major faults. Folds occur in landslide blocks and beneath them. Most folds within landslide blocks are tight anticlines, with limbs dipping 40-60 degrees. Brecciation of the folds and landslide blocks suggests brittle deformation. Near Quijinump Canyon in the Sheep Range, at least three landslide blocks (up to 500 by 1500 m) slid into a small Tertiary basin. Tertiary limestone beneath the Paleozoic blocks was isoclinally folded. Westward dips reveal drag folds along major normal faults, as regional dips are consistently to the east. The Chowderhead anticline is the largest drag fold, along an extensional fault that offsets Ordovician units 8 km. East-dipping Ordovician and Silurian rocks in the Desert Range form the hanging wall. East-dipping Cambrian and Ordovician units in the East Desert Range form the foot wall and east limb of the anticline. Caught along the fault plane, the anticline's west-dipping west limb contains mostly Cambrian units.

  17. Water dynamics clue to key residues in protein folding

    SciTech Connect (OSTI)

    Gao, Meng [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Zhu, Huaiqiu, E-mail: hqzhu@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Yao, Xin-Qiu [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China) [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Department of Biophysics, Kyoto University, Sakyo Kyoto 606-8502 (Japan); She, Zhen-Su, E-mail: she@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)

    2010-01-29

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  18. Office of Small and Disadvantaged Business Utilization Tri-Fold

    Broader source: Energy.gov [DOE]

    OSDBU has created a downloadable, print-on-demand tri-fold PDF that introduces the office, its role in the Department of Energy and its goals for supporting small business nationwide.

  19. UFO (UnFold Operator) computer program abstract

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F.

    1982-11-01

    UFO (UnFold Operator) is an interactive user-oriented computer program designed to solve a wide range of problems commonly encountered in physical measurements. This document provides a summary of the capabilities of version 3A of UFO.

  20. Nonlinear vs. linear biasing in Trp-cage folding simulations

    SciTech Connect (OSTI)

    Spiwok, Vojt?ch Oborsk, Pavel; Krlov, Blanka; Pazrikov, Jana

    2015-03-21

    Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200?ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

  1. Determining the role of hydration forces in protein folding

    SciTech Connect (OSTI)

    Sorenson, J.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry] [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Hura, G. [Univ. of California, Berkeley, CA (United States)] [Univ. of California, Berkeley, CA (United States); [Lawrence Berkeley National Lab., CA (United States). Life Sciences Div.; Soper, A.K. [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility] [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility; Pertsemlidis, A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry] [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Head-Gordon, T. [Lawrence Berkeley National Lab., CA (United States)] [Lawrence Berkeley National Lab., CA (United States)

    1999-07-01

    One of the primary issues in protein folding is determining what forces drive folding and eventually stabilize the native state. A delicate balance exists between electrostatic forces such as hydrogen bonding and salt bridges, and the hydrophobic effect, which are present for both intramolecular protein interactions and intermolecular contributions with the surrounding aqueous environment. This article describes a combined experimental, theoretical, and computational effort to show how the complexity of aqueous hydration can influence the structure, folding and aggregation, and stability of model protein systems. The unification of the theoretical and experimental work is the development or discovery of effective amino acid interactions that implicitly include the effects of aqueous solvent. The authors show that consideration of the full range of complexity of aqueous hydration forces such as many-body effects, long-ranged character of aqueous solvation, and the assumptions made about the degree of protein hydrophobicity can directly impact the observed structure, folding, and stability of model protein systems.

  2. In the OSTI Collections: Determining How Proteins Fold | OSTI...

    Office of Scientific and Technical Information (OSTI)

    ... Some of the research into how proteins fold has been funded by the Department of Energy ... in terms of how the object's energy would change if a force acted to change the shape. ...

  3. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING

    Office of Scientific and Technical Information (OSTI)

    SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY (Conference) | SciTech Connect MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein

  4. Solitons and protein folding: An In Silico experiment

    SciTech Connect (OSTI)

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  5. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  6. Collective aspects of protein folding illustrated by a toy model

    SciTech Connect (OSTI)

    Stillinger, F.H. [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States)] [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States); Head-Gordon, T. [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)] [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)

    1995-09-01

    A simple toy model for polypeptides serves as a testbed to illuminate some nonlocal, or collective, aspects of protein folding phenomena. The model is two dimensional and has only two amino acids, but involves a continuous range of backbone bend angles. Global potential energy minima and their folding structures have been determined for leading members of two special and contrasting polypeptide sequences, center doped and Fibonacci, named descriptively for their primary structures. The results display the presence of spontaneous symmetry breaking, elastic strain, and substantial conformational variation for specific embedded amino acid strings. We conclude that collective variables generated by the primary amino acid structure may be required for fully effective protein folding predictors, including those based on neural networks.

  7. Heteropolymer freezing and design: Towards physical models of protein folding

    SciTech Connect (OSTI)

    Pande, Vijay S. [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States)] [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States); Grosberg, Alexander Yu. [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States)] [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Tanaka, Toyoichi [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2000-01-01

    Protein folding has become one of the most actively studied problems in modern molecular biophysics. Approaches to the problem combine ideas from the physics of disordered systems, polymer physics, and molecular biology. Much can be learned from the statistical properties of model heteropolymers, the chain molecules having different monomers in irregular sequences. Even in highly evolved proteins, there is a strong random element in the sequences, which gives rise to a statistical ensemble of sequences for a given folded shape. Simple analytic models give rise to phase transitions between random, glassy, and folded states, depending on the temperature T and the design temperature T{sup des} of the ensemble of sequences. Besides considering the analytic results obtainable in a random-energy model and in the Flory mean-field model of polymers, the article reports on confirming numerical simulations. (c) 2000 The American Physical Society.

  8. Folding model description of reactions with exotic nuclei

    SciTech Connect (OSTI)

    Ibraheem, Awad A.; Hassanain, M. A.; Mokhtar, S. R.; Zaki, M. A.; Mahmoud, Zakaria M. M.; Farid, M. El-Azab

    2012-08-15

    Microscopic folding calculations based upon the effective M3Y nucleon-nucleon interaction and the nuclearmatter densities of the interacting nuclei have been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering cross section at four different laboratory energies near the Coulomb barrier. The extracted reaction cross sections are also considered.

  9. New approach to folding with the Coulomb wave function

    SciTech Connect (OSTI)

    Blokhintsev, L. D.; Savin, D. A.; Kadyrov, A. S.; Mukhamedzhanov, A. M.

    2015-05-15

    Due to the long-range character of the Coulomb interaction theoretical description of low-energy nuclear reactions with charged particles still remains a formidable task. One way of dealing with the problem in an integral-equation approach is to employ a screened Coulomb potential. A general approach without screening requires folding of kernels of the integral equations with the Coulomb wave. A new method of folding a function with the Coulomb partial waves is presented. The partial-wave Coulomb function both in the configuration and momentum representations is written in the form of separable series. Each term of the series is represented as a product of a factor depending only on the Coulomb parameter and a function depending on the spatial variable in the configuration space and the momentum variable if the momentum representation is used. Using a trial function, the method is demonstrated to be efficient and reliable.

  10. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.

  11. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist ``invariants`` across lattices that define fundamental properties of protein folding process; an invariant defines a property that transcends particular lattice formulations. This paper identifies two classes of invariants, defined in terms of sublattices that are related to the design of algorithms for the structure prediction problem. The first class of invariants is, used to define a master approximation algorithm for which provable performance guarantees exist. This algorithm can be applied to generalizations of the hydrophobic-hydrophilic model that have lattices other than the cubic lattice, including most of the crystal lattices commonly used in protein folding lattice models. The second class of invariants applies to a related lattice model. Using these invariants, we show that for this model the structure prediction problem is intractable across a variety of three-dimensional lattices. It`` turns out that these two classes of invariants are respectively sublattices of the two- and three-dimensional square lattice. As the square lattices are the standard lattices used in empirical protein folding` studies, our results provide a rigorous confirmation of the ability of these lattices to provide insight into biological phenomenon. Our results are the first in the literature that identify algorithmic paradigms for the protein structure prediction problem which transcend particular lattice formulations.

  12. Combined approach to the inverse protein folding problem. Final report

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01

    The main scientific contribution of the project ''Combined approach to the inverse protein folding problem'' submitted in 1996 and funded by the Department of Energy in 1997 is the formulation and development of the idea of the multilink recognition method for identification of functional and structural homologues of newly discovered genes. This idea became very popular after they first announced it and used it in prediction of the threading targets for the CASP2 competition (Critical Assessment of Structure Prediction).

  13. Folding and insertion thermodynamics of the transmembrane WALP peptide

    SciTech Connect (OSTI)

    Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-12-28

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

  14. Directed evolution methods for improving polypeptide folding and solubility and superfolder fluorescent proteins generated thereby

    DOE Patents [OSTI]

    Waldo, Geoffrey S.

    2007-09-18

    The current invention provides methods of improving folding of polypeptides using a poorly folding domain as a component of a fusion protein comprising the poorly folding domain and a polypeptide of interest to be improved. The invention also provides novel green fluorescent proteins (GFPs) and red fluorescent proteins that have enhanced folding properties.

  15. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Protein-Folding Landscapes in Multi-Chain Systems Citation Details In-Document Search Title: Protein-Folding Landscapes in Multi-Chain Systems Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the

  16. A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry

    SciTech Connect (OSTI)

    Kato, Koji; Tanaka, Hideaki; Sumizawa, Tomoyuki; Yoshimura, Masato; Yamashita, Eiki; Iwasaki, Kenji; Tsukihara, Tomitake

    2008-05-01

    A vault from rat liver was crystallized in space group C2. Rotational symmetry searches indicated that the particle has 39-fold dihedral symmetry. Vault is a 12.9 MDa ribonucleoprotein particle with a barrel-like shape, two protruding caps and an invaginated waist structure that is highly conserved in a wide variety of eukaryotes. Multimerization of the major vault protein (MVP) is sufficient to assemble the entire exterior shell of the barrel-shaped vault particle. Multiple copies of two additional proteins, vault poly(ADP-ribose) polymerase (VPARP) and telomerase-associated protein 1 (TEP1), as well as a small vault RNA (vRNA), are also associated with vault. Here, the crystallization of vault particles is reported. The crystals belong to space group C2, with unit-cell parameters a = 708.0, b = 385.0, c = 602.9 Å, β = 124.8°. Rotational symmetry searches based on the R factor and correlation coefficient from noncrystallographic symmetry (NCS) averaging indicated that the particle has 39-fold dihedral symmetry.

  17. Folding and Function of Proteorhodopsins in Photoenergy Transducing Membranes

    SciTech Connect (OSTI)

    Spudich, John L

    2012-08-10

    The overall research objectives are to develop proteorhodopsin (PR) proteins as a model system for {alpha}?-helical membrane protein insertion and folding, and to advance understanding of the diversity and mechanisms of PRs, a large family of photoenergy transducers (~4000 identified) abundant in the worlds oceans. Specific aims are: (1) To develop a highefficiency genetic selection procedure for light-driven proton-pumping in E. coli cells. Such a procedure would provide a positive selection method for proper folding and function of PRs in the E. coli membrane. (2) Characterize flash-induced absorption changes and photocurrents in PR variants in organisms from various environments, and their expression level and function when expressed in E. coli. Subaims are to: (a) elucidate the relationship of the transport mechanism to mechanisms of other microbial rhodopsins, some of which like PRs function as ion transporters and some of which use light energy to activate signaling pathways (sensory rhodopsins); and (b) identify important residues and chemical events in light-driven proton transport by PRs. In addition to their importance to the energy of the biosphere PRs have attracted interest for their potential for use in making photoenergy-transducing membranes for bioengineering applications.

  18. Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding

    SciTech Connect (OSTI)

    Garde, S.; Hummer, G.; Garcia, A.E.; Paulaitis, M.E.; Pratt, L.R. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); [Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716 (United States); [Department of Chemical Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    1996-12-01

    An information theory model of hydrophobic effects is used to construct a molecular explanation why hydrophobic solvation entropies of protein unfolding measured by high sensitivity calorimetry converge to zero at a common convergence temperature. The entropy convergence follows directly from the weak temperature dependence of occupancy fluctuations {l_angle}{delta}{ital n}{sup 2}{r_angle} for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior of water relative to common organic solvents is the {ital relative} temperature insensitivity of the water isothermal compressibility compared to hydrocarbon liquids. The information theory model used provides a quantitative description of small molecule hydration and, in addition, predicts that the value of the entropy at convergence is slightly {ital negative}. Interpretations of entropic contributions to protein folding should account for this result. {copyright} {ital 1996 The American Physical Society.}

  19. Discovering The Folding Rules That Proteins Obey FY08 LDRD Final...

    Office of Scientific and Technical Information (OSTI)

    Discovering The Folding Rules That Proteins Obey FY08 LDRD Final Report Citation Details In-Document Search Title: Discovering The Folding Rules That Proteins Obey FY08 LDRD Final ...

  20. New N-Acetyltransferase Fold in the Structure and Mechanism of...

    Office of Scientific and Technical Information (OSTI)

    New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF Citation Details In-Document Search Title: New N-Acetyltransferase Fold in ...

  1. Protein-Folding Landscapes in Multi-Chain Systems Cellmer, Troy...

    Office of Scientific and Technical Information (OSTI)

    37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; FREE ENERGY; MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein...

  2. Development of a Fast Microfluidic Mixer for Studies of Protein Folding

    Office of Scientific and Technical Information (OSTI)

    KineticsFinal Report Cover Page (Technical Report) | SciTech Connect Technical Report: Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page Citation Details In-Document Search Title: Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page We designed and fabricated mixing devices that will help us elucidate the mechanisms of protein folding through measurements of folding reaction rates. These

  3. Chemical relationship between discharging fluids in the Siena-Radicofani Graben and the deep fluids produced by the geothermal fields of Mt Amiata, torre Afina and Latera (Central Italy)

    SciTech Connect (OSTI)

    Duchi, V.; Paolieri, M.; Prati, F ); Minissale, A. Centro di Studio per Mineralogia e la Geochimica dei Sedimenti, Via La Pira 4, 50121 Firenze ); Valori, A )

    1992-06-01

    This paper reports that the thermal springs discharging in the Siena-Radicofani basin and the deep fluids within the geothermal systems of Piancastagnaio (Mt Amiata), Torre Alfina and Latera (Vulsini Mts) have a common origin. The chemical composition and evolution towards the low enthalpy of the springs as compared to the high enthalpy of the geothermal fluids are affected by both the structural setting of the region and the deep hydraulic conditions. Recharge of both the shallow thermal aquifer and the deep geothermal systems takes place in the outcrop areas of Mesozoic carbonate rocks, which constitute the main potential geothermal reservoir in central Italy. The waters of meteoric origin are heated at depth, as a consequence of anomalous heat flow in the region; these waters acquire a CO[sub 2]-rich rising gas phase, equilibrate with the reservoir rocks and, finally, assume their Ca--HCO[sub 3]--SO[sub 4] composition. If these waters discharge rapidly from the border fault systems of the Siena-Radicofani basin they maintain their original composition. If, instead, they emerge from the inner faults of the graben, their temperature and dissolved solids increase so that they become Na--Cl with a high content of NH[sub 4], and H[sub 3]BO[sub 3].

  4. Contact order revisited: Influence of protein size on the folding rate

    SciTech Connect (OSTI)

    Ivankov, Dmitry N.; Garbuzynskiy, Sergiy O.; Alm, Eric; Plaxco, Kevin W.; Baker, David; Finkelstein, Alexei V.

    2003-05-28

    Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical model of protein folding that predicts that logarithm of the folding rate decreases with the protein chain length L as L2/3, and by the finding that the folding rates of multistate folding proteins strongly correlate with their sizes and have very bad correlation with CO, we reexamined the dependence of folding rate on CO and L in attempt to find a structural parameter that determines folding rates for the totality of proteins. We show that the Abs{sub CO} = CO x L, is able to predict rather accurately folding rates for both two-state and multistate folding proteins, as well as short peptides, and that this Abs{sub CO} scales with the protein chain length as L0.70 {+-} 0.07 for the totality of studied single-domain proteins and peptides.

  5. Energy barriers, cooperativity, and hidden intermediates in the folding of small proteins

    SciTech Connect (OSTI)

    Bai Yawen [Laboratory of Biochemistry, National Cancer Institute, NIH, Building 37, Room 6114E, Bethesda, MD 20892 (United States)]. E-mail: yawen@helix.nih.gov

    2006-02-17

    Current theoretical views of the folding process of small proteins (<{approx}100 amino acids) postulate that the landscape of potential mean force (PMF) for the formation of the native state has a funnel shape and that the free energy barrier to folding arises from the chain configurational entropy only. However, recent theoretical studies on the formation of hydrophobic clusters with explicit water suggest that a barrier should exist on the PMF of folding, consistent with the fact that protein folding generally involves a large positive activation enthalpy at room temperature. In addition, high-resolution structural studies of the hidden partially unfolded intermediates have revealed the existence of non-native interactions, suggesting that the correction of the non-native interactions during folding should also lead to barriers on PMF. To explore the effect of a PMF barrier on the folding behavior of proteins, we modified Zwanzig's model for protein folding with an uphill landscape of PMF for the formation of transition states. We found that the modified model for short peptide segments can satisfy the thermodynamic and kinetic criteria for an apparently two-state folding. Since the Levinthal paradox can be solved by a stepwise folding of short peptide segments, a landscape of PMF with a locally uphill search for the transition state and cooperative stabilization of folding intermediates/native state is able to explain the available experimental results for small proteins. We speculate that the existence of cooperative hidden folding intermediates in small proteins could be the consequence of the highly specific structures of the native state, which are selected by evolution to perform specific functions and fold in a biologically meaningful time scale.

  6. Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

    SciTech Connect (OSTI)

    Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G.; Kevrekidis, Ioannis G.

    2015-02-28

    Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories in a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.

  7. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article...

    Office of Scientific and Technical Information (OSTI)

    contacts, suggesting that native topology plays a role in early stages of aggregation. ... MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein aggregation ...

  8. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

    SciTech Connect (OSTI)

    Agarwala, R. [National Institutes of Health, Bethesda, MD (United States); Batzoglou, S. [MIT, Cambridge, MA (United States); Dancik, V. [Univ. of Southern California, Los Angeles, CA (United States)] [and others

    1997-06-01

    We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill, which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail gave approximation algorithms for folding proteins on the cubic lattice under HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio which they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.

  9. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect (OSTI)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  10. A Survey of lamba Repressor Fragments from Two-State to to Downhill Folding

    SciTech Connect (OSTI)

    Liu, F.; Gao, Y; Gruebele, M

    2010-01-01

    We survey the two-state to downhill folding transition by examining 20 {lambda}{sub 6-85}* mutants that cover a wide range of stabilities and folding rates. We investigated four new {lambda}{sub 6-85}* mutants designed to fold especially rapidly. Two were engineered using the core remodeling of Lim and Sauer, and two were engineered using Ferreiro et al.'s frustratometer. These proteins have probe-dependent melting temperatures as high as 80 C and exhibit a fast molecular phase with the characteristic temperature dependence of the amplitude expected for downhill folding. The survey reveals a correlation between melting temperature and downhill folding previously observed for the {beta}-sheet protein WW domain. A simple model explains this correlation and predicts the melting temperature at which downhill folding becomes possible. An X-ray crystal structure with a 1.64-{angstrom} resolution of a fast-folding mutant fragment shows regions of enhanced rigidity compared to the full wild-type protein.

  11. Time Resolved Collapse of a Folding Protein Observed with Small Angle X-Ray Scattering

    SciTech Connect (OSTI)

    Pollack, L.; Tate, M. W.; Finnefrock, A. C.; Kalidas, C.; Trotter, S.; Darnton, N. C.; Lurio, L.; Austin, R. H.; Batt, C. A.; Gruner, S. M. (and others)

    2001-05-21

    High-intensity, ''pink'' beam from an undulator was used in conjunction with microfabricated rapid-fluid mixing devices to monitor the early events in protein folding with time resolved small angle x-ray scattering. This Letter describes recent work on the protein bovine {beta} -lactoglobulin where collapse from an expanded to a compact set of states was directly observed on the millisecond time scale. The role of chain collapse, one of the initial stages of protein folding, is not currently understood. The characterization of transient, compact states is vital in assessing the validity of theories and models of the folding process.

  12. A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples

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

    Chemie International Edition Year: 2010 Volume: 49 Pages: 1414-1417 ABSTRACT: A new strategy is presented to scale up DNA origami using multi-helical DNA tiles as folding...

  13. Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits...

    Office of Scientific and Technical Information (OSTI)

    Title: Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-...

  14. Crystallographic Structure of SurA, a Molecular Chaperone that Facilitates Folding of Outer Membrane Porins

    SciTech Connect (OSTI)

    Bitto, E.

    2002-01-01

    The SurA protein facilitates correct folding of outer membrane proteins in gram-negative bacteria. The sequence of Escherichia coli SurA presents four segments, two of which are peptidyl-prolyl isomerases (PPIases); the crystal structure reveals an asymmetric dumbbell, in which the amino-terminal, carboxy-terminal, and first PPIase segments of the sequence form a core structural module, and the second PPIase segment is a satellite domain tethered approximately 30 A from this module. The core module, which is implicated in membrane protein folding, has a novel fold that includes an extended crevice. Crystal contacts show that peptides bind within the crevice, suggesting a model for chaperone activity whereby segments of polypeptide may be repetitively sequestered and released during the membrane protein-folding process.

  15. Tri-fold - Agencies Assisting with EEOICPA and the Former worker Program |

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

    Department of Energy Tri-fold - Agencies Assisting with EEOICPA and the Former worker Program Tri-fold - Agencies Assisting with EEOICPA and the Former worker Program March 2015 Agencies Assisting with EEOICPA and the Former Worker Program The Joint Outreach Task Group (JOTG) includes representatives from DOE, Department of Labor (DOL), the National Institute for Occupational Safety and Health (NIOSH), the Offices of the Ombudsman for DOL and NIOSH, and the DOE-funded FWP projects. The JOTG

  16. DOE Science Showcase - Protein Folding | OSTI, US Dept of Energy Office of

    Office of Scientific and Technical Information (OSTI)

    Scientific and Technical Information Protein Folding Proteins are the main constitute of our bones, muscles, hair, skin and blood vessels, performing a vast array of functions such as catalyzing metabolic reactions, replicating DNA, response to stimuli, moving muscles, and protecting the immune system. These proteins consist of long chains of molecules called amino acids that interact with each other to produce a well-defined three-dimensional structure - the folded protein. The correct

  17. Heavy oil reservoirs in the Tulare Fold Belt, Cymric-McKittrick fields, Kern County, California

    SciTech Connect (OSTI)

    Farley, T. )

    1990-05-01

    The Tulare fold belt is a series of asymmetric, generally northeast-verging anticlines and synclines in the Pliocene-Pleistocene Tulare Formation that trend northwestward through the Cymric-McKittrick fields. Anticlines within the deformed belt generally originated as fault propagation folds above decollements, the most important of which is the regional decollement on top of the Amnicola sand, the basal Tulare unit. The Amnicola decollement is the northeast subsurface extension of the McKittrick thrust, a low-angle fault that has displaced the Miocene Antelope shale over the Pliocene San Joaquin Formation and locally over the Tulare Formation. The Amnicola decollement is itself deformed by folding related to a younger, deeper decollement near the base of the San Joaquin Formation that merges westward with the Amnicola decollement and defines a zone of faulting associated with the McKittrick thrust Heavy oil reservoirs in the Tulare Formation are currently undergoing active development by thermal recovery techniques. In general, the geometry of heavy oil reservoirs is determined by location within the Tulare fold belt combined with the position of a subhorizontal fluid level trap that forms the updip limit of fluid-saturated rock Reservoir geometry is complicated by complex local structure, discontinuous stratigraphy, and partial depletion of heavy oil reservoirs by fluid withdrawal due to gravity drainage. Proper resolution of fold geometry, fault geometry, and position of the fluid level trap is crucial to the design and monitoring of thermal recovery projects within the Tulare fold belt.

  18. Folding chair

    DOE Patents [OSTI]

    Cornell, Howell N.

    1985-08-20

    A foldable chair of the lawn chair type has ground-engaging front and rear legs, attached to and carrying a back frame and seat frame, the back frame and seat frame being pivotally attached to a spreader rod which extends beyond the back and seat frames to bear against one of the leg members when the chair is unfolded. A contact pad mounted on the extending portion of the spreader rod is formed as an externally-contoured bushing fit over the spreader rod and adapted to engage the leg member to restrict side-to-side movement of the spreader rod, with respect to the leg member, when the chair is unfolded.

  19. RNA Folding

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

    3 Rick Russell, Ian S. Millett, Sebastian Doniach and Daniel Herschlag Stanford University One goal of genome projects is to systematically identify genes (1,2). The best current knowledge indicates that humans carry approximately 35000 genes. This number is an estimate that varies from expert to expert and range up to 100,000 (3-5). To anyone who has taken an elementary biology class, this ambiguity must seem strange. How hard can it be to count genes? After all, don't cells translate genes

  20. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    SciTech Connect (OSTI)

    Hsu, P. J.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320 Taiwan (China); Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Cheong, S. A. [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)

    2014-05-28

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with ? helix and ? hairpin, but also the important role played by weaker correlations in such protein

  1. Characterization of fold defects in AZ91D and AE42 magnesium alloy permanent mold castings

    SciTech Connect (OSTI)

    Bichler, L. [Centre for Near-net-shape Processing of Materials, Ryerson University, 101 Gerrard St. E., Toronto, M5B 2K3 (Canada); Ravindran, C., E-mail: rravindr@ryerson.ca [Centre for Near-net-shape Processing of Materials, Ryerson University, 101 Gerrard St. E., Toronto, M5B 2K3 (Canada)

    2010-03-15

    Casting premium-quality magnesium alloy components for aerospace and automotive applications poses unique challenges. Magnesium alloys are known to freeze rapidly prior to filling a casting cavity, resulting in misruns and cold shuts. In addition, melt oxidation, solute segregation and turbulent metal flow during casting contribute to the formation of fold defects. In this research, formation of fold defects in AZ91D and AE42 magnesium alloys cast via the permanent mold casting process was investigated. Computer simulations of the casting process predicted the development of a turbulent metal flow in a critical casting region with abrupt geometrical transitions. SEM and light optical microscopy examinations revealed the presence of folds in this region for both alloys. However, each alloy exhibited a unique mechanism responsible for fold formation. In the AZ91D alloy, melt oxidation and velocity gradients in the critical casting region prevented fusion of merging metal front streams. In the AE42 alloy, limited solubility of rare-earth intermetallic compounds in the {alpha}-Mg phase resulted in segregation of Al{sub 2}RE particles at the leading edge of a metal front and created microstructural inhomogeneity across the fold.

  2. Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

    SciTech Connect (OSTI)

    Wu, Ying; Kondrashkina, Elena; Kayatekin, Can; Matthews, C. Robert; Bilsel, Osman (NWU); (UMASS, Amherst)

    2008-09-29

    The earliest kinetic folding events for ({beta}{alpha}){sub 8} barrels reflect the appearance of off-pathway intermediates. Continuous-flow microchannel mixing methods interfaced to small-angle x-ray scattering (SAXS), circular dichroism (CD), time-resolved Foerster resonant energy transfer (trFRET), and time-resolved fluorescence anisotropy (trFLAN) have been used to directly monitor global and specific dimensional properties of the partially folded state in the microsecond time range for a representative ({beta}{alpha}){sub 8} barrel protein. Within 150 {micro}s, the {alpha}-subunit of Trp synthase ({alpha}TS) experiences a global collapse and the partial formation of secondary structure. The time resolution of the folding reaction was enhanced with trFRET and trFLAN to show that, within 30 {micro}s, a distinct and autonomous partially collapsed structure has already formed in the N-terminal and central regions but not in the C-terminal region. A distance distribution analysis of the trFRET data confirmed the presence of a heterogeneous ensemble that persists for several hundreds of microseconds. Ready access to locally folded, stable substructures may be a hallmark of repeat-module proteins and the source of early kinetic traps in these very common motifs. Their folding free-energy landscapes should be elaborated to capture this source of frustration.

  3. Geometry of wrapped M5-branes in Calabi-Yau 2-folds

    SciTech Connect (OSTI)

    Fayyazuddin, Ansar; Husain, Tasneem Zehra; Pappa, Ioanna

    2006-06-15

    We study the geometry of M5-branes wrapping a 2-cycle which is special Lagrangian with respect to a specific complex structure in a Calabi-Yau 2-fold. Using methods recently applied to the 3-fold case, we are again able to find a characterization of the geometry, in terms of a nonintegrable almost complex structure and a (2,0) form. This time, however, due to the hyper-Kaehler nature of the underlying 2-fold, we also have the freedom of choosing a different almost complex structure with respect to which the wrapped 2-cycle is holomorphic. We show that this latter almost complex structure is integrable. We then relate our geometry to previously found geometries of M5-branes wrapping holomorphic cycles and go further to prove some previously unknown results for M5-branes on holomorphic cycles.

  4. Parallel continuation-based global optimization for molecular conformation and protein folding

    SciTech Connect (OSTI)

    Coleman, T.F.; Wu, Z. [Cornell Univ., Ithaca, NY (United States)

    1994-12-31

    This paper presents the authors` recent work on developing parallel algorithms and software for solving the global minimization problem for molecular conformation, especially protein folding. Global minimization problems are difficult to solve when the objective functions have many local minimizers, such as the energy functions for protein folding. In their approach, to avoid directly minimizing a ``difficult`` function, a special integral transformation is introduced to transform the function into a class of gradually deformed, but ``smoother`` or ``easier`` functions. An optimization procedure is then applied to the new functions successively, to trace their solutions back to the original function. The method can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation and protein folding. Mathematical theory for the method, as a special continuation approach to global optimization, is established. Algorithms with different solution tracing strategies are developed. Different levels of parallelism are exploited for the implementation of the algorithms on massively parallel architectures.

  5. Femtosecond spectroscopy probes the folding quality of antibody fragments expressed as GFP fusions in the cytoplasm

    SciTech Connect (OSTI)

    Didier, P. [Faculte de Pharmacie, UMR 7175, 74, route du Rhin, 67412 Illkirch (France); Weiss, E.; Sibler, A.-P. [Ecole Superieure de Biotechnologie de Strasbourg, UMR 7175, Boulevard Sebastien Brant, F-67412 Illkirch (France); Philibert, P.; Martineau, P. [Centre de recherche en cancerologie de Montpellier, UMR 5160, Val d'Aurelle-Paul Lamarque, 34298 Montpellier cedex 5 (France); Bigot, J.-Y. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Guidoni, L. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Laboratoire Materiaux et Phenomenes Quantiques, UMR 7162, Batiment Condorcet, 10 rue Alice Domon et Leonie Duquet, 75205 Paris cedex 13 (France)], E-mail: luca.guidoni@univ-paris-diderot.fr

    2008-02-22

    Time-resolved femtosecond spectroscopy can improve the application of green fluorescent proteins (GFPs) as protein-folding reporters. The study of ultrafast excited-state dynamics (ESD) of GFP fused to single chain variable fragment (scFv) antibody fragments, allowed us to define and measure an empirical parameter that only depends on the folding quality (FQ) of the fusion. This method has been applied to the analysis of genetic fusions expressed in the bacterial cytoplasm and allowed us to distinguish folded and thus functional antibody fragments (high FQ) with respect to misfolded antibody fragments. Moreover, these findings were strongly correlated to the behavior of the same scFvs expressed in animal cells. This method is based on the sensitivity of the ESD to the modifications in the tertiary structure of the GFP induced by the aggregation state of the fusion partner. This approach may be applicable to the study of the FQ of polypeptides over-expressed under reducing conditions.

  6. The evolution and hydrocarbon habitat of the Papuan fold belt, PNG

    SciTech Connect (OSTI)

    Dalton, D.G.; Smith, R.I.; Cawley, S.J. )

    1990-05-01

    After over 70 years of hydrocarbon exploration in the Papuan fold belt of PNG (Papua New Guinea) there have been a number of hydrocarbon discoveries over recent years that have confirmed its potential as a significant producing province. The Papuan basin developed during the early Mesozoic as part of the northeast corner of the Australian passive margin. The basin's tertiary evolution and the development of the Papuan fold belt within the Papuan basin has evolved in response to oblique convergence between the northerly moving Australian plate and westerly moving Pacific plate. Restacking of the Mesozoic passive margin sequence within the Papuan Basin was initiated in the early miocene by southward abduction of the Solomon Sea plate and the subsequent collision, in the late Miocene, of the Melanesian Island arc along the northeastern margin of PNG. This later collision provided the driving mechanism for the development of the papuan thrust belt. To date, all the significant hydrocarbon discoveries made within the Papuan fold belt have been located within the frontal zone of the fold belt, which is characterized by relatively simple ramp anticlines and thick-skinned inversion structures. The primary proven reservoir fairway is the Jurassic Toro formation, which is a sequence of stacked submarine bars prograding out across a shallow-marine low-gradient shelf. Geochemical analysis of produced hydrocarbons and samples collected from the many surface seeps found in the fold belt indicate two main families of oil. A model explains the distribution of hydrocarbons discovered to date, which involves Jurassic and Cretaceous source intervals and a complex history of secondary migration and entrapment. The unique technical problems associated with exploration of the Papuan fold belt leave many elements of the proven play systems uncertain, but in so doing, they present many challenges and opportunities for the future.

  7. The earliest events in protein folding: Helix dynamics in proteins and model peptides

    SciTech Connect (OSTI)

    Dyer, R.B.; Williams, S.; Woodruff, W.H. [Los Alamos National Lab., NM (United States)] [and others

    1996-12-31

    The earliest events in protein folding are critically important in determining the folding pathway, but have proved difficult to study by conventional approaches. We have developed new rapid initiation methods and structure-specific probes to interrogate the earliest events of protein folding. Our focus is the pathways. Folding or unfolding reactions are initiated on a fast timescale (10 ns) using a laser induced temperature jump (15 C) and probed with time-resolved infrared spectroscopy. We obtained the kinetics of the helix-coil transition for a model 21-residue peptide. The observed rate constant k{sub obs} = k{sub f} + k{sub u} for reversible kinetics; from the observed rate (6 x 10{sup 6} s{sup -1}) and the equilibrium constant favoring folding of 7.5 at 27 C, we calculate a folding lifetime of 180 ns and an unfolding lifetime of 1.4 {mu}s. The {open_quotes}molten globule{close_quotes} form of apomyoglobin (horse, pH*3, 0.15M NaCl) shows similar kinetics for helix that is unconstrained by tertiary structure (helix with an unusually low Amide I frequency, near 1633 cm{sup -1}). In {open_quotes}native{close_quotes} apomyoglobin (horse, pH*5.3, 10 mM NaCl) two very different rates (45 ns and 70 {mu}s) are observed and we infer that a third occurs on a timescales inaccessible to our experiment (> 1 ms). We suggest that the slower processes are due to helix formation that is rate-limited by the formation of tertiary structure.

  8. Protein-folding via divide-and-conquer optimization (Conference) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Protein-folding via divide-and-conquer optimization Citation Details In-Document Search Title: Protein-folding via divide-and-conquer optimization Authors: Oliva, Ricardo ; Crivelli, Silvia ; Meza, Juan Publication Date: 2004-07-11 OSTI Identifier: 882903 Report Number(s): LBNL--55869 R&D Project: 365969; BnR: YN0100000 DOE Contract Number: DE-AC02-05CH11231 Resource Type: Conference Resource Relation: Conference: SIAM Conference on the Life Sciences, Portland,OR, July 11-14,

  9. Deducing the Energetic Cost of Protein Folding in Zinc Finger Proteins Using Designed Metallopeptides

    SciTech Connect (OSTI)

    Reddi,A.; Guzman, T.; Breece, r.; Tierney, D.; Gibney, B.

    2007-01-01

    Zinc finger transcription factors represent the largest single class of metalloproteins in the human genome. Binding of Zn(II) to their canonical Cys4, Cys3His1, or Cys2His2 sites results in metal-induced protein folding events required to achieve their proper structure for biological activity. The thermodynamic contribution of Zn(II) in each of these coordination spheres toward protein folding is poorly understood because of the coupled nature of the metal-ligand and protein-protein interactions. Using an unstructured peptide scaffold, GGG, we have employed fluorimetry, potentiometry, and calorimetry to determine the thermodynamics of Zn(II) binding to the Cys4, Cys3His1, and Cys2His2 ligand sets with minimal interference from protein folding effects. The data show that Zn(II) complexation is entropy driven and modulated by proton release. The formation constants for Zn(II)-GGG with a Cys4, Cys3His1, or Cys2His2 site are 5.6 x 1016, 1.5 x 1015, or 2.5 x 1013 M-1, respectively. Thus, the Zn(II)-Cys4, Zn(II)-Cys3His1, and Zn(II)-Cys2His2 interactions can provide up to 22.8, 20.7, and 18.3 kcal/mol, respectively, in driving force for protein stabilization, folding, and/or assembly at pH values above the ligand pKa values. While the contributions from the three coordination motifs differ by 4.5 kcal/mol in Zn(II) affinity at pH 9.0, they are equivalent at physiological pH, ?G = -16.8 kcal/mol or a Ka = 2.0 x 1012 M-1. Calorimetric data show that this is due to proton-based enthalpy-entropy compensation between the favorable entropic term from proton release and the unfavorable enthalpic term due to thiol deprotonation. Since protein folding effects have been minimized in the GGG scaffold, these peptides possess nearly the tightest Zn(II) affinities possible for their coordination motifs. The Zn(II) affinities in each coordination motif are compared between the GGG scaffold and natural zinc finger proteins to determine the free energy required to fold the latter

  10. Exploration in the Sub Andean thrust/fold belt of northwest Argentina

    SciTech Connect (OSTI)

    Schulz, A.; Alarcon, M.; Aramayo, F.; Santiago, M.; Ashby, W.J.

    1996-08-01

    A significant portion of the 15,000 square kilometer Aguarague exploration permit is located with the Sub Andean zone of northwest Argentina bordering Bolivia. The Sub Andean sedimentary section is dominated by a succession of tectonostratigraphic cycles of Silurian to recent age. These cycles display a complex geological history prior to the onset of the Andean deformation of Upper Miocene age. As the structures are complex, several different exploration techniques were combined, including satellite imagery, aeromagnetics, geological mapping, geochemistry, microtectonic studies, magneto stratigraphy, seismic modeling and seismic with pre- and post-stack depth migration. The interpretation of these techniques produced three dimensional structural models, at regional and prospect scales, that demonstrated the deformation mechanism, sequence and timing of the structures; these were then linked to the timing of generation/expulsion of hydrocarbons. The physical properties of the sedimentary sequence produces three structural environs, each with distinct fold and fault mechanisms. 1. (Upper): A product of the cumulative deformation of the underlying environs; 2. (Middle): The presence of an incompetent shale, the principal source rock, within this unit produces {open_quotes}fold disharmony {close_quotes} (horizontally and vertically) between the overlying and underlying environs. 3. (Lower): Characterized by folds developed by Fault Bend Fold processes. Hydrocarbon fields and exploration prospects are present within all three environs. The work performed has permitted the successful evaluation of several structures within the Sub Andean of the UTE Aguarague.

  11. Long range correlations and folding angle with applications to ?-helical proteins

    SciTech Connect (OSTI)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden)] [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Nicolis, Stam, E-mail: Stam.Nicolis@lmpt.univ-tours.fr [Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France)] [Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-03-07

    The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. Unlike particles, chains can bend, twist, and even become knotted. Thus chains might also display a much richer phase structure. Unfortunately, it is not very easy to characterize the phase of a long chain. Essentially, the only known attribute is the radius of gyration. The way how it changes when the degree of polymerization becomes different, and how it evolves when the ambient temperature and solvent properties change, is commonly used to disclose the phase. But in any finite length chain there are corrections to scaling that complicate the detailed analysis of the phase structure. Here we introduce a quantity that we call the folding angle to identify and scrutinize the phase structure, as a complement to the radius of gyration. We argue for a mean-field level relationship between the folding angle and the scaling exponent in the radius of gyration. We then estimate the value of the folding angle in the case of crystallographic ?-helical protein structures in the Protein Data Bank. We also show how the experimental value of the folding angle can be obtained computationally, using a semiclassical Born-Oppenheimer description of ?-helical chiral chains.

  12. Microscopic Description of the Exotic Nuclei Reactions by Using Folding model Potentials

    SciTech Connect (OSTI)

    Ibraheem, Awad A.; Hassanain, M. A.; Mokhtar, S. R.; El-Azab Farid, M.; Zaki, M. A.; Mahmoud, Zakaria M. M.

    2011-10-27

    A microscopic folding approach based upon the effective M3Y nucleon-nucleon interaction and the nuclear matter densities of the interacting nuclei has been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering reaction at four different laboratory energies near the Coulomb barrier. The corresponding reaction cross sections are also considered.

  13. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein`s amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate.

  14. High-resolution structure of a retroviral protease folded as a monomer

    SciTech Connect (OSTI)

    Gilski, Miroslaw [A. Mickiewicz University, 60-780 Poznan (Poland); Polish Academy of Sciences, 61-704 Poznan (Poland); Kazmierczyk, Maciej; Krzywda, Szymon [A. Mickiewicz University, 60-780 Poznan (Poland); Zbransk, Helena [Academy of Sciences of the Czech Republic, 166 10 Prague (Czech Republic); Cooper, Seth; Popovi?, Zoran [University of Washington, Box 352350, Seattle, WA 98195 (United States); Khatib, Firas; DiMaio, Frank; Thompson, James; Baker, David [University of Washington, Box 357350, Seattle, WA 98195 (United States); Pichov, Iva [Academy of Sciences of the Czech Republic, 166 10 Prague (Czech Republic); Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl [A. Mickiewicz University, 60-780 Poznan (Poland); Polish Academy of Sciences, 61-704 Poznan (Poland)

    2011-11-01

    The crystal structure of MasonPfizer monkey virus protease folded as a monomer has been solved by molecular replacement using a model generated by players of the online game Foldit. The structure shows at high resolution the details of a retroviral protease folded as a monomer which can guide rational design of protease dimerization inhibitors as retroviral drugs. MasonPfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C{sup ?} deviations are large and the active-site DTG loop (here NTG) deviates up to 2.7 from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 ) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including

  15. Isolation, folding and structural investigations of the amino acid transporter OEP16

    SciTech Connect (OSTI)

    Ni, Da Qun; Zook, James; Klewer, Douglas A.; Nieman, Ronald A.; Soll, J.; Fromme, Petra

    2011-12-01

    Membrane proteins compose more than 30% of all proteins in the living cell. However, many membrane proteins have low abundance in the cell and cannot be isolated from natural sources in concentrations suitable for structure analysis. The overexpression, reconstitution, and stabilization of membrane proteins are complex and remain a formidable challenge in membrane protein characterization. Here we describe a novel, in vitro folding procedure for a cation-selective channel protein, the outer envelope membrane protein 16 (OEP16) of pea chloroplast, overexpressed in Escherichia coli in the form of inclusion bodies. The protein is purified and then folded with detergent on a Ni-NTA affinity column. Final concentrations of reconstituted OEP16 of up to 24 mg/ml have been achieved, which provides samples that are sufficient for structural studies by NMR and crystallography. Reconstitution of OEP16 in detergent micelles was monitored by circular dichroism, fluorescence, and NMR spectroscopy. Tryptophan fluorescence spectra of heterologous expressed OEP16 in micelles are similar to spectra of functionally active OEP16 in liposomes, which indicates folding of the membrane protein in detergent micelles. CD spectroscopy studies demonstrate a folded protein consisting primarily of a-helices. 15N-HSQC NMR spectra also provide evidence for a folded protein. We present here a convenient, effective and quantitative method to screen large numbers of conditions for optimal protein stability by using microdialysis chambers in combination with fluorescence spectroscopy. Recent collection of multidimensional NMR data at 500, 600 and 800 MHz demonstrated that the protein is suitable for structure determination by NMR and stable for weeks during data collection.

  16. Geology of oil and gas accumulations in the Papuan fold and thrust belt

    SciTech Connect (OSTI)

    Foo, W.K. )

    1990-06-01

    The high level of exploration interest in Papua New Guinea has developed in large part because of recent discoveries in the western Papuan fold and thrust belt and shows in the adjacent foreland region. Results from recent drilling in the Iagifu/Hedinia area by a Chevron-led joint venture have outlined several pools in culminations along a 50 km long structural axis. Oil and gas are sourced from a thick succession of Jurassic marine shales that were deposited along the rifted northern margin of the Australian plate. Generation and migration is interpreted to have peaked coincident with development of the fold and thrust belt during the Neogene. Trapping occurred as anticlines and thrust sheets developed sequentially from northeast to southwest. Several trends remain untested on lands held by various groups, primarily in the area west of the Juha gas condensate pool.

  17. MitoNEET is a Uniquely Folded Outer Mitochondrial Membrane Protein

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

    Stabilized by Diabetes Drugs MitoNEET is a Uniquely Folded Outer Mitochondrial Membrane Protein Stabilized by Diabetes Drugs The rise in obesity in the United States parallels a dramatic increase in obesity-associated diseases, most notably type-2 diabetes. This disease is predicted to reach epidemic proportions in the next several decades (Zimmet et al 2001, Urek et al 2007). Thus, understanding the biochemical processes underlying type-2 diabetes and identifying new targets for therapeutic

  18. In the OSTI Collections: Determining How Proteins Fold | OSTI, US Dept of

    Office of Scientific and Technical Information (OSTI)

    Energy Office of Scientific and Technical Information Determining How Proteins Fold Article Acknowledgement: Dr. William N. Watson, Physicist DOE Office of Scientific and Technical Information Investigations Focused on Direct Experiments Investigations Focused on Computation References Research Organizations Reports available through OSTI's SciTech Connect Additional References Proteins are the materials in living cells whose primary structures are specified by the cell's DNA. These primary

  19. Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition

    SciTech Connect (OSTI)

    Wang, Jin; Lu, Qiang N.; Lu, H PETER.

    2006-07-01

    The study of associations between two biomolecules is the key to understand molecular recognition and function. Molecular function is often thought to be determined by the underlying structures. Here, combining single molecule study of protein binding with an energy landscape inspired microscopic model, we found strong evidences that bio-molecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse grained molecular dynamics performed on the residue level with the energy function biased towards the native binding structure (Go model). With our model, the underlying free energy landscape of the binding can be explored. Two distinct conformational states as free energy minimum, one with partially folding of CBD and significant binding of CBD to CDC42, and another with native folding of CBD and native binding of CBD to CDC42, are clearly seen. This shows the binding process proceeds with significant interface binding of CBD with CDC42 first without complete folding of CBD. Finally binding and folding are coupled with each other cooperatively to reach the native binding state. The single molecule experimental finding of the dynamic fluctuations between the loosely bound and closely bound conformational states can be identified with theoretically calculated free energy minimum and quantitatively explained in our model as a result of binding associated with large conformational changes. Theoretical predictions have identified certain key residues for binding which are consistent with mutational experiments. The combined study provides a test ground for fundamental mechanisms as well as insights into design and further explorations on biomolecular recognition with large conformational changes.

  20. Structural Analysis of Protein Folding by the Long-Chain Archaeal Chaperone FKBP26

    SciTech Connect (OSTI)

    E Martinez-Hackert; W Hendrickson

    2011-12-31

    In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called 'Insert-in-Flap' or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.

  1. Wang-Landau sampling of the interplay between surface adsorption and folding of HP lattice proteins

    SciTech Connect (OSTI)

    Li, Ying Wai [ORNL] [ORNL; Wuest, Thomas [Swiss Federal Research Institute, Switzerland] [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA] [University of Georgia, Athens, GA

    2014-01-01

    Generic features associated with the adsorption of proteins on solid surfaces are reviewed within the framework of the hydrophobic-polar (HP) lattice protein model. The thermodynamic behavior and structural properties of various HP protein sequences interacting with attractive surfaces have been studied using extensive Wang-Landau sampling with different types of surfaces, each of which attracts either: all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. Consequently, different types of folding behavior occur for varied surface strengths. Analysis of the combined patterns of various structural observables, e.g., the derivatives of the numbers of interaction contacts, together with the specific heat, leads to the identification of fundamental categories of folding and transition hierarchies. We also inferred a connection between the transition categories and the relative surface strengths, i.e., the ratios of the surface attractive strengths to the intra-chain attraction among H monomers. We thus believe that the folding hierarchies and identification scheme are generic for different HP sequences interacting with attractive surfaces, regardless of the chain length, sequence, or surface attraction.

  2. Geometry and controls on fracturing in a natural fault-bend fold: Rosario field, Maracaibo basin, Venezuela

    SciTech Connect (OSTI)

    Apotria, T.G.; Wilkerson, M.S.; Knewtson, S.L.

    1996-08-01

    The Rosario oil field lies between the Perija Mountain front and Lake Maracaibo and produces from fractured Cretaceous carbonates and Tertiary clastics. We interpret the structure as a detached fault-bend fold which ramps through Cretaceous Cogollo and La Luna carbonates and flattens into an upper detachment at the base of the Upper Cretaceous Colon Shale. The structural relief formed primarily during the Mid Miocene and younger. Seismic and well control on the three-dimensional geometry illustrates the effects of (1) lithology and displacement variation on fold geometry, (2) an oblique footwall ramp on hangingwall faulting, and (3) fold curvature on fracturing and hydrocarbon production. Fold geometry at different structural levels is strongly controlled by lithology. Stiff Cogollo and La Luna carbonates exhibit kink-style folding above the upper fault-bend. The weak Colon Shale decouples the faulted carbonates from the concentrically folded Tertiary clastics. Regions of enhanced faulting and fracturing of Cretaceous carbonates are a function of structural position. We observe normal faults in the hangingwall where the strike of the footwall ramp changes from N20{degrees}E to N65{degrees}E. Fold curvature highlights fold hinges, yet distributed faulting is seismically imaged in the forelimb, suggesting that rocks fracture as they migrate through the ramp-upper flat fault-bend. Production rates are higher near the forelimb relative to the flat crestal region.

  3. Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding

    SciTech Connect (OSTI)

    Huang, David M.; Chandler, David

    2000-04-01

    The Lum-Chandler-Weeks theory of hydrophobicity [J. Phys. Chem. 103, 4570 (1999)] is applied to treat the temperature dependence of hydrophobic solvation in water. The application illustrates how the temperature dependence for hydrophobic surfaces extending less than 1nm differs significantly from that for surfaces extending more than 1nm. The latter is the result of water depletion, a collective effect, that appears at length scales of 1nm and larger. Due to the contrasting behaviors at small and large length scales, hydrophobicity by itself can explain the variable behavior of protein folding.

  4. Protein folding and non-conventional drug design: a primer for nuclear structure physicists

    SciTech Connect (OSTI)

    Broglia, R.A. [Dipartimento di Fisica, Universita di Milano, Via Celoria 16, I-20133 Milan (Italy); INFN, Sezione di Milano, Via Celoria 16, I-20133 Milan (Italy); Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen (Denmark); Tiana, G.; Provasi, D. [Dipartimento di Fisica, Universita di Milano, Via Celoria 16, I-20133 Milan (Italy); INFN, Sezione di Milano, Via Celoria 16, I-20133 Milan (Italy)

    2004-02-27

    Some of the paradigms emerging from the study of the phenomena of phase transitions in finite many-body systems, like e.g. the atomic nucleus can be used at profit to solve the protein folding problem within the framework of simple (although not oversimplified) models. From this solution a paradigm emerges for the design of non-conventional drugs, which inhibit enzymatic action without inducing resistance (mutations). The application of these concepts to the design of an inhibitor to the HIV-protease central in the life cycle of the HIV virus is discussed.

  5. Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymerase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mejia, Yara X.; Nudler, Evgeny; Bustamante, Carlos

    2014-12-31

    Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP’s pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kineticmore » model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. The model suggests a finely tuned mechanism that balances transcription speed and fidelity.« less

  6. Trigger loop folding determines transcription rate of Escherichia colis RNA polymerase

    SciTech Connect (OSTI)

    Mejia, Yara X.; Nudler, Evgeny; Bustamante, Carlos

    2014-12-31

    Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAPs pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. The model suggests a finely tuned mechanism that balances transcription speed and fidelity.

  7. THE INFLUENCE OF FOLD AND FRACTURE DEVELOPMENT ON RESERVOIR BEHAVIOR OF THE LISBURNE GROUP OF NORTHERN ALASKA

    SciTech Connect (OSTI)

    Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen; Michael T. Whalen

    2002-01-01

    The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. The Lisburne in the main axis of the Brooks Range is characteristically deformed into imbricate thrust sheets with asymmetrical hanging wall anticlines and footwall synclines. In contrast, the Lisburne in the northeastern Brooks Range is characterized by symmetrical detachment folds. The focus of our 2000 field studies was at the boundary between these structural styles in the vicinity of Porcupine Lake, in the Arctic National Wildlife Refuge. The northern edge of thrust-truncated folds in Lisburne is marked by a local range front that likely represents an eastward continuation of the central Brooks Range front. This is bounded to the north by a gently dipping panel of Lisburne with local asymmetrical folds. The leading edge of the flat panel is thrust over Permian to Cretaceous rocks in a synclinal depression. These younger rocks overlie symmetrically detachment-folded Lisburne, as is extensively exposed to the north. Six partial sections were measured in the Lisburne of the flat panel and local range front. The Lisburne here is about 700 m thick and is interpreted to consist primarily of the Wachsmuth and Alapah Limestones, with only a thin veneer of Wahoo Limestone. The Wachsmuth (200 m) is gradational between the underlying Missippian Kayak Shale and the overlying Mississippian Alapah, and

  8. Protein Folding Dynamics Detected By Time-Resolved Synchrotron X-ray Small-Angle Scattering Technique

    SciTech Connect (OSTI)

    Fujisawa, Tetsuro; Takahashi, Satoshi [RIKEN Harima Institute, SPring-8 Center, Laboratory for Biometal Science, Hyogo 679-5148 (Japan); Institute for Protein Research, Osaka University Suita Osaka 565-0871/CREST, JST (Japan)

    2007-03-30

    The polypeptide collapse is an essential dynamics in protein folding. To understand the mechanism of the collapse, in situ observation of folding by various probes is necessary. The changes in secondary and tertiary structures in the folding process of globular proteins, whose chain lengths are less than 300 polypeptides, were observed by circular dichrosim and intrinsic fluorescence spectroscopies, respectively. On the other hand, those in protein compactness could be only detected by using time-resolved synchrotron x-ray small-angle scattering technique. The observed dynamics for several proteins with different topologies suggested a common folding mechanism termed 'collapse and search' dynamics, in which the polypeptide collapse precedes the formation of the native contact formation. In 'collapse and search' dynamics, the most outstanding feature lied in the compactness of the initial intermediates. The collapsed intermediates demonstrated the scaling relationship between radius of gyration (Rg) and chain length with a scaling exponent of 0.35 {+-} 0.11, which is close to the value (1/3) predicted by mechano-statistical theory for the collapsed globules of polymers in poor solvent. Thus, it was suggested that the initial collapse is caused by the coil-globule transition of polymers. Since the collapse is essential to the folding of larger proteins, further investigations on the collapse likely lead to an important insight into the protein folding phenomena.

  9. Variscan fold belt and its foreland in western Europe from late Carboniferous to Permian time

    SciTech Connect (OSTI)

    Mascle, A.; Benard, F.; Cazes, M.; Le Gall, B.

    1988-08-01

    The Variscan front was emplaced in the Later Carboniferous with a south-to-north or southeast-to-northwest-trending vergence of thrusting. At the same time, folds were formed in the foreland. In England and southern Scotland, such structures were induced by an east-west direction of shortening, followed by a more subdued north-south compressive event. In Stephanian time, isolated basins developed on the Hercynian belt. In the Massif Central Marues Massif, they are closely related to transcurrent faults which developed in response to north-south-trending compressive stresses. The distribution of stresses completely changed in Early Permian time when extension dominated almost everywhere. Three kinds of basins developed at that time: those related to the relaxation of stresses on the Hercynian range, a north-south-trending rift system in the western United Kingdom and the North Sea, and a broad flexural evaporitic basin from eastern England to Poland.

  10. Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

    SciTech Connect (OSTI)

    Yao, Shuhuai [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bakajin, Olgica [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2007-08-01

    Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

  11. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-08-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  12. Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-06-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  13. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    SciTech Connect (OSTI)

    Martinez-Hackert, E.; Hendrickson, W

    2009-01-01

    Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.

  14. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

    SciTech Connect (OSTI)

    Agarwala, R. [National Institutes of Health, Bethesda, MD (United States); Batzoglou, S. [MIT Lab. for Computer Science, Cambridge, MA (United States); Dancik, V. [Univ. of Southern California, Los Angeles, CA (United States)] [and others

    1997-12-01

    A long standing problem in molecular biology is to determine the three-dimensional structure of a protein, given its amino acid sequence. A variety of simplifying models have been proposed abstracting only the {open_quotes}essential physical properties{close_quotes} of real proteins. In these models, the three dimensional space is often represented by a lattice. Residues which are adjacent in the primary sequence (i.e. covalently linked) must be placed at adjacent points in the lattice. A conformation of a protein is simply a self-avoiding walk along the lattice. The protein folding problem STRING-FOLD is that of finding a conformation of the protein sequence on the lattice such that the overall energy is minimized, for some reasonable definition of energy. This formulation leaves open the choices of a lattice and an energy function. Once these choices are made, one may then address the algorithmic complexity of optimizing the energy function for the lattice. For a variety of such simple models, this minimization problem is in fact NP-hard. In this paper, we consider the Hydrophobic-Polar (HP) Model introduced by Dill. The HP model abstracts the problem by grouping the 20 amino acids into two classes: hydrophobic (or non-polar) residues and hydrophilic (or polar) residues. For concreteness, we will take our input to be a string from (H,P){sup +}, where P represents polar residues, and H represents hydrophobic residues. Dill et.al. survey the literature analyzing this model. 8 refs., 2 figs., 1 tab.

  15. Hydrocarbon exploration through remote sensing and field work in the onshore Eastern Papuan Fold Belt, Gulf province, Papua New Guinea

    SciTech Connect (OSTI)

    Dekker, F.; Balkwill, H.; Slater, A. ); Herner, R. ); Kampschuur, W. )

    1990-05-01

    Over the years several types of remote sensing surveys have been acquired of the Eastern Papuan Fold Belt, in the Gulf Province of Papua New Guinea. These include aerial photographs, Landsat Multispectral Scanner (MSS), and Synthetic Aperture Radar (SAR). Each has been used by Petro-Canada Inc. for interpreting the geologic structure and stratigraphy of onshore hydrocarbon prospects. Analysis of available remotely sensed imagery reveals greater structural complexity than is shown on published geologic maps. Foremost among the images is SAR because of its low, artificial sun angle. Hence, a comprehensive view of the area has been acquired revealing many structural elements previously not appreciated. A distinct difference in structural style is found between the northern and southern segment of the Eastern Papuan fold belt in the study area. The northern segment shows discontinuous, open folds with widely separated anticlines set in featureless valleys. The southern segment is tightly folded, possessing few anticlines and synclines clearly recognizable on the imagery. However, structural components can be traced easily for tens of miles. Recent field work supports an SAR structural interpretation suggesting most, if not all, anticlines in the northern segment are overturned. The combination of remote sensing and field work proved invaluable in understanding the fold belt tectonics and has aided considerably in the selection of drilling locations.

  16. The Influence of fold and fracture development on reservoir behavior of the Lisburne Group of northern Alaska

    SciTech Connect (OSTI)

    Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen: Michael T. Whalen; Paul Atkinson; Joseph Brinton; Thang Bui; Margarete Jadamec; Alexandre Karpov; John Lorenz; Michelle M. McGee; T.M. Parris; Ryan Shackleton

    2004-07-01

    The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is folded and thrust faulted where it is exposed throughout the Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study were to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. Symmetrical detachment folds characterize the Lisburne in the northeastern Brooks Range. In contrast, Lisburne in the main axis of the Brooks Range is deformed into imbricate thrust sheets with asymmetrical hangingwall anticlines and footwall synclines. The Continental Divide thrust front separates these different structural styles in the Lisburne and also marks the southern boundary of the northeastern Brooks Range. Field studies were conducted for this project during 1999 to 2001 in various locations in the northeastern Brooks Range and in the vicinity of Porcupine Lake, immediately south of the Continental Divide thrust front. Results are summarized below for the four main subject areas of the study.

  17. Discriminating trpzip2 and trpzip4 peptides folding landscape using the two-dimensional infrared spectroscopy: A simulation study

    SciTech Connect (OSTI)

    Wu, Tianmin; Zhang, Ruiting; Li, Huanhuan; Zhuang, Wei, E-mail: wzhuang@dicp.ac.cn, E-mail: lijiangy@pku.edu.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning (China)] [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning (China); Yang, Lijiang, E-mail: wzhuang@dicp.ac.cn, E-mail: lijiangy@pku.edu.cn [College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871 (China)] [College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871 (China)

    2014-02-07

    We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two ?-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB{sup OBC} implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.

  18. Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri

    SciTech Connect (OSTI)

    Davis, Jamaine; Wang, Jiawei; Tropea, Joseph E.; Zhang, Di; Dauter, Zbigniew; Waugh, David S.; Wlodawer, Alexander

    2009-01-28

    VirA, a secreted effector protein from Shigella sp., has been shown to be necessary for its virulence. It was also reported that VirA might be related to papain-like cysteine proteases and cleave {alpha}-tubulin, thus facilitating intracellular spreading. We have now determined the crystal structure of VirA at 3.0 {angstrom} resolution. The shape of the molecule resembles the letter 'V,' with the residues in the N-terminal third of the 45-kDa molecule (some of which are disordered) forming one clearly identifiable domain, and the remainder of the molecule completing the V-like structure. The fold of VirA is unique and does not resemble that of any known protein, including papain, although its N-terminal domain is topologically similar to cysteine protease inhibitors such as stefin B. Analysis of the sequence conservation between VirA and its Escherichia coli homologs EspG and EspG2 did not result in identification of any putative protease-like active site, leaving open a possibility that the biological function of VirA in Shigella virulence may not involve direct proteolytic activity.

  19. The role of hydrogen bonds in protein folding and protein association

    SciTech Connect (OSTI)

    Ben-Naim, A. (National Inst. of Health, Bethesda, MD (USA))

    1991-02-07

    The contribution of a pair of functional groups that can form either intermolecular or intramolecular hydrogen bonds to the total standard free energy of the process of protein folding or protein association is examined. It is found that this contribution can be quite large, either positive or negative, depending on the particular process and on the solvent density. This is in contrast to the common belief that the hydrogen-bond energies tend to be compensated in these processes. For the binding process, in which the two functional groups are completely removed from the aqueous environment, the contribution of such a pair of functional groups to {Delta}G can be as high as +6.4 kcal/mol. This is the main reason why hydrophobic rather than hydrophilic surfaces tend to attach to each other. In contrast, when the two functional groups are only partially removed from the aqueous environment, as in the case of the formation of {alpha}-helix, their contribution to {Delta}G can be negative and of the order of about 1 kcal/mol.

  20. Predicting methane accumulations generated from humic Carboniferous coals in the Donbas fold belt (Ukraine)

    SciTech Connect (OSTI)

    Alsaab, D.; Elie, M.; Izart, A.; Sachsenhofer, R.F.; Privalov, V.A.

    2008-08-15

    The numerical modeling of the Ukrainian part of the Donbas fold belt indicates that the coalification pattern was controlled mainly by the maximum burial depth of coal seams and the heat flow (HF) (40-75 mW/m{sup 2}) during the Permian. The coalification pattern was overprinted by magmatic events during the Late Permian in the south syncline (150 mW/m{sup 2}) and during the Permian-Triassic in the north of the Krasnoarmeisk region (120 mW/m{sup 2}). The coalification pattern shows a strong increase in vitrinite reflectance values toward the east and southeastern parts of the study area likely caused by (1) an eastward increase in burial depth, (2) a probable eastward increase in HF, and, (3) probable magmatic activity. An increase in total erosion toward the eastern and southeastern parts was also observed with a maximum erosional amount of approximately 8 km (5 mi) in the southeastern part of the study area. The basin modeling of this area predicts that the main phase of hydrocarbon generation occurred during the Carboniferous-Early Permian subsidence. The magmatic events that occurred during the Permian-Triassic caused renewed pulses of hydrocarbon generation. A large amount of the generated hydrocarbons was lost to the surface because of a lack of seals. However, the numerical simulation predicts accumulations of about 2 tcf (57 billion m{sup 3}) of methane generated from Carboniferous coals in the south and main synclines, where Lower Permian seal rocks are preserved. Finally, this study provides data on methane resources along the northern flank

  1. Energy and Mass Dependences of the Parameters of the Semimicroscopic Folding Model for Alpha Particles at Low and Intermediate Energies

    SciTech Connect (OSTI)

    Kuterbekov, K.A.; Zholdybayev, T.K.; Kukhtina, I.N.; Penionzhkevich, Yu.E.

    2005-06-01

    The energy and mass dependences of the parameters of the semimicroscopic alpha-particle potential are investigated for the first time in the region of low and intermediate energies. Within the semimicroscopic folding model, both elastic and inelastic differential and total cross sections for reactions on various nuclei are well described by using global parameters obtained in this study.

  2. Pattern of extensional faulting in pelagic carbonates of the Unbria-Marche Apennines of central Italy

    SciTech Connect (OSTI)

    Alvarez, W. )

    1990-05-01

    The Umbria-Marche Apennines provide a new region in which the nature passive-margin extensional faulting can be studied in outcrop. In these dominantly pelagic carbonate rocks of Jurassic and Cretaceous age, horsts acted as shallow, nonvolcani seamounts, while tilted half grabens formed deeper basins. One well-exposed seamount-basin transition agrees in general with the model of listric normal faulting and tilted half grabens, but shows interesting and significant divergences when studied in detail. A small sedimentary wedge at the faulted margin of a horst-block seamount thickens unexpectedly toward the adjacent basin. This wedge developed because of local convex-upward curvature of the shallowest part of a fault which at depth must have concave-up, listric geometry. The local sedimentary wedge resulted from deposition on the hanging wall as it tilted, followed by differential compaction of younger limestones that lapped onto the gentle slope leading from the horst-block seamount toward the basin. The map pattern of listric normal faulting in the Umbria-Marche Apennines suggests that both principal strain axes were extensional, in contrast to the usual pattern of listric faults crossed by transfer faults.

  3. The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

    SciTech Connect (OSTI)

    Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel; Korolev, Sergey (Birbeck); (St. Louis-MED); (WU-MED)

    2010-07-20

    Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragment adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.

  4. A Summary of Information on the Behavior of the Yakima Fold Belt as a Structural Entity -- Topical Report

    SciTech Connect (OSTI)

    Last, George V.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis (PSHA) of the Hanford Site. The purpose of this report is to summarize available data and analyses relevant to the Yakima Fold Belt (YFB) that may bear on the question of whether or not the YFB behaves as a single seismotectonic province in which activity along one fold structure is representative of behavior along all other fold structures. This topic has met with a fairly high level of contention in the expert community and has the potential to result in significant impacts on an evaluation of seismic hazard at the Hanford Site. This report defines the relevant alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, it suggests some possible approaches for reducing uncertainties regarding this issue.

  5. Magnetostratigraphic constraints on the development of paired fold-thrust belts/foreland basins in the Argentine Andes

    SciTech Connect (OSTI)

    Reynolds, J.H. ); Damanti, J.F. ); Jordan, T.E. )

    1991-03-01

    Development of a paired fold thrust-thrust belt/foreland basin is correlated to the flattening of the subducting Nazca plate between 28-33{degree}S. Magnetostratigraphic studies in neogene basin-filling continental strata determine local basin subsidence rates and provide relatively precise chronostratigraphic correlation between different depositional environments. The data demonstrate that most existing lithostratigraphic units are diachronous and require new tectonic interpretations. Increases in sediment accumulation rates closely correspond to changes in provenance and indicate that the Frontal Cordillera, on the Chile-Argentina border was a positive topographic province by 18 Ma. The Precordillera evolved from {approx}16 Ma to the present as thrusting migrated from west to east. Published ages from intercalated airfall tuffs constrain some sedimentary sections in the eastern Sierras Pampeanas where the earliest uplift occurred since 10 Ma. The youngest uplifts are on the west side close to continuing thrusting in the Precordillera. Not all fold-thrust belt/foreland basin pairs are associated with flat subduction, suggesting that tectonic controls exceeding the scale of individual plate segments may be important. The hydrocarbon-producing Subandean fold-thrust belt/foreland basin, located in the area of 'steep' subduction that underlies northern Argentina and Bolivia (18-24{degree}S), is also believed to have evolved since middle Miocene time. Recently initiated magnetostratigraphic studies in the Subandean foreland basin will attempt to temporally constrain the Neogene tectonic evolution for comparison with the southern region.

  6. Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S. [Sandia National Labs., Albuquerque, NM (United States). Algorithms and Discrete Mathematics Dept.

    1996-08-09

    This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.

  7. Assessment of substrate-stabilizing factors for DnaK on the folding of aggregation-prone proteins

    SciTech Connect (OSTI)

    Ryu, Kisun; Kim, Chul Woo; Kim, Byung Hee [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Han, Kyoung Sim [Protheon Incorporated, Yonsei Engineering Research Center B120E, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Kim, Kyun-Hwan [Department of Pharmacology, School of Medicine, and Center for Diagnostic Medicine, Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701 (Korea, Republic of); Choi, Seong Il [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Institute of Life Science and Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of)], E-mail: seongilchoi@daum.net; Seong, Baik L. [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Protheon Incorporated, Yonsei Engineering Research Center B120E, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Institute of Life Science and Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of)], E-mail: blseong@yonsei.ac.kr

    2008-08-15

    Hydrophobic interactions between molecular chaperones and their nonnative substrates have been believed to be mainly responsible for both substrate recognition and stabilization against aggregation. However, the hydrophobic contact area between DnaK and its substrate proteins is very limited and other factors of DnaK for the substrate stabilization could not be excluded. Here, we covalently fused DnaK to the N-termini of aggregation-prone proteins in vivo. In the context of a fusion protein, DnaK has the ability to efficiently solubilize its linked proteins. The point mutation of the residue of DnaK critical for the substrate recognition and the deletion of the C-terminal substrate-binding domain did not have significant effect on the solubilizing ability of DnaK. The results imply that other factors of DnaK, distinct from the hydrophobic shielding of folding intermediates, also contributes to stabilization of its noncovalently bound substrates against aggregation. Elucidation of the nature of these factors would further enhance our understanding of the substrate stabilization of DnaK for expedited protein folding.

  8. Laser-induced temperature jump/time-resolved infrared study of the fast events in protein folding

    SciTech Connect (OSTI)

    Woodruff, W.H.; Dyer, R.B.; Williams, S. [Los Alamos National Laboratory, NM (United States); Callender, H.; Gilmanshin, R. [CUNY, NY (United States)

    1996-10-01

    Laser-induced temperature jump followed by time-resolved infrared probe of reaction dynamics are used to study the temporal evolution of polypeptide structure during protein folding and unfolding. Reactions are initiated in times of 50 ps or longer by T-jumps of 10`s of degrees, obtained by laser excitation of water overtone absorbances. Observation of the Amide I transient absorbances reveal melting lifetimes of helices unconstrained by tertiary structure to be ca. 160 ns in a model 21-peptide and ca. 30 ns in {open_quotes}molten globule{close_quotes} apomyoglobin. No other processes are observed in these systems over the timescale 50 ps to 2 ms. Equilibrium data suggest the corresponding helix formation lifetimes to be ca. 16 and 1 ns, respectively. In {open_quotes}native{close_quotes} apomyoglobin two helix melting lifetimes are observed and we infer that a third occurs on a timescale inaccessible to our experiment (> 1 ms). The shorter observed lifetime, as in the molten globule, is ca. 30 ns. The longer lifetime is ca. 70 {mu}s. We suggest that the slower process is helix melting that is rate-limited by the unfolding of tertiary structure. Equilibrium data suggest a lifetime of ca. 1 {mu}s for the development of these tertiary folds.

  9. Deputy-Director

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

    Berkeley Lab Deputy Director Horst Simon horst-simon Horst Simon is an internationally recognized expert in computer science and applied mathematics and the Deputy Director of ...

  10. Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation

    SciTech Connect (OSTI)

    Wang, T.; Li, H.; Darwin, K. H.

    2010-11-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  11. Binding-induced Folding of Prokaryotic Ubiquitin-like Protein on the Mycobacterium Proteasomal ATPase Targets Substrates for Degradation

    SciTech Connect (OSTI)

    T Wang; K Heran Darwin; H Li

    2011-12-31

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  12. A Summary of Coupled, Uncoupled, and Hybrid Tectonic Models for the Yakima Fold Belt--Topical Report

    SciTech Connect (OSTI)

    Chamness, Michele A.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis of the Hanford Site. The purpose of this report is to summarize the range of opinions and supporting information expressed by the expert community regarding whether a coupled or uncoupled model, or a combination of both, best represents structures in the Yakima Fold Belt. This issue was assessed to have a high level of contention with up to moderate potential for impact on the hazard estimate. This report defines the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some possible approaches for reducing uncertainties regarding this issue.

  13. Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b)

    SciTech Connect (OSTI)

    Singh, Priya; Sarkar, Subir K.; Bandyopadhyay, Pradipta

    2014-07-07

    We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energyalong with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5?k{sub B}T higher than the value at the global minimum.

  14. 'Let the phage do the work': Using the phage P22 coat protein structures as a framework to understand its folding and assembly mutants

    SciTech Connect (OSTI)

    Teschke, Carolyn M., E-mail: Teschke@uconn.ed [Departments of Molecular and Cell Biology, and Chemistry, 91 N. Eagleville Rd., U-3125, University of Connecticut, Storrs, CT 06269-3125 (United States); Parent, Kristin N. [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA (United States)

    2010-06-05

    The amino acid sequence of viral capsid proteins contains information about their folding, structure and self-assembly processes. While some viruses assemble from small preformed oligomers of coat proteins, other viruses such as phage P22 and herpesvirus assemble from monomeric proteins (Fuller and King, 1980). The subunit assembly process is strictly controlled through protein:protein interactions such that icosahedral structures are formed with specific symmetries, rather than aberrant structures. dsDNA viruses commonly assemble by first forming a precursor capsid that serves as a DNA packaging machine. DNA packaging is accompanied by a conformational transition of the small precursor procapsid into a larger capsid for isometric viruses. Here we highlight the pseudo-atomic structures of phage P22 coat protein and rationalize several decades of data about P22 coat protein folding, assembly and maturation generated from a combination of genetics and biochemistry.

  15. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect (OSTI)

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variantwhile the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  16. 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)

    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)

    2010-07-19

    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.

  17. Investigation of the reaction {sup 208}Pb({sup 18}O, f): Folding angular distributions of fission fragments and gamma-ray multiplicity

    SciTech Connect (OSTI)

    Rusanov, A. Ya. Itkis, M. G.; Kondratiev, N. A.; Pokrovsky, I. V.; Salamatin, V. S.; Chubarian, G. G.

    2007-10-15

    Correlations between folding angular distributions of fission fragments and the gamma-ray multiplicity are studied for {sup 18}O + {sup 208}Pb interactions at energies of the beam of {sup 18}O ions in the range E{sub lab} = 78-198.5 MeV. The probabilities are determined for complete-and incomplete-fusion processes inevitably followed by the fission of nuclei formed in these processes. It is found that the probability of incomplete fusion followed by fission increases with increasing energy of bombarding ions. It is shown that, for the incomplete-fusion process, folding angular distributions of fission fragments have a two-component structure. The width of folding angular distributions (FWHM) for complete fusion grows linearly with increasing energy of {sup 18}O ions. The multiplicity of gamma rays from fission fragments as a function of the linear-momentum transfer behaves differently for different energies of projectile ions. This circumstance is explained here by the distinction between the average angular momenta of participant nuclei in the fusion and fission channels, which is due to the difference in the probabilities of fission in the cases where different numbers of nucleons are captured by the target nucleus.

  18. Development of transfer zones and location of oil and gas fields in frontal part of Bolivian Andean fold-and-thrust belt

    SciTech Connect (OSTI)

    Baby, P. ); Specht, M.; Colletta, B.; Letouzey, J. ); Mendez, E. ); Guillier, B. )

    1993-02-01

    The frontal part of the Bolivian Andean thrust belt consists of a thick series of paleozoic to cenozoic sedimentary rocks (5 to 8 km thick) which are folded and thrusted towards the east on a sole thrust at the base of paleozoic series. The front of this tectonic wedge is characterized by transfer zones of various scales and geometries. The main oil and gas fields are located in these transfer zones. A study realized from YPFB (Yacimientos Petroliferos Fiscales Bolivianos) seismic data shows that in all the cases, the deformation is controlled by the geometry and thickness variations of the paleozoic basin. The most spectacular transfer zone appears at the bolivian orocline scale and corresponds to the famous bending of the andean thrust front close to Santa Cruz. More to the south (19 to 22[degrees] S) the southern foreland fold and thrust belt is characterized by a set of local right lateral offset transfer zones ([open quotes]en echellon[close quotes] folds). The difference of geometry and scale of the transfer zones seems to be related to the variation of the angle value between the shortening direction and the direction of the paleozoic basin borders. In order to test our interpretation, to constrain the boundary conditions and to study the thrust propagation sequence, we performed a set of analog model experiments whose 3D visualization was analyzed by computerized X-ray tomography.

  19. Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycHYopH chaperoneeffector complex

    SciTech Connect (OSTI)

    Vujanac, Milos; Stebbins, C. Erec, E-mail: stebbins@rockefeller.edu [The Rockefeller University, New York, NY 10065 (United States)

    2013-04-01

    The structure of a SycHYopH chaperoneeffector complex from Yersinia reveals the bacterial state of a protein that adopts different folds in the host and pathogen environments. Yersinia pestis injects numerous bacterial proteins into host cells through an organic nanomachine called the type 3 secretion system. One such substrate is the tyrosine phosphatase YopH, which requires an interaction with a cognate chaperone in order to be effectively injected. Here, the first crystal structure of a SycHYopH complex is reported, determined to 1.9 resolution. The structure reveals the presence of (i) a nonglobular polypeptide in YopH, (ii) a so-called ?-motif in YopH and (iii) a conserved hydrophobic patch in SycH that recognizes the ?-motif. Biochemical studies establish that the ?-motif is critical to the stability of this complex. Finally, since previous work has shown that the N-terminal portion of YopH adopts a globular fold that is functional in the host cell, aspects of how this polypeptide adopts radically different folds in the host and in the bacterial environments are analysed.

  20. Geometry and evolution of the frontal part of the Magallanes foreland thrust and fold belt (Vicuna Area), Tierra del Fuego, southern Chile

    SciTech Connect (OSTI)

    Alvarez-Marron, J.; McClay, K.R. ); Harambour, S.; Rojas, L.; Skarmeta, J. )

    1993-11-01

    The Magallanes foreland thrust and fold belt is a thin-skinned foreland thrust and fold belt of Paleocene to Oligocene age that deforms Upper Jurassic through Tertiary volcanic, volcaniclastic, and siliciclastic strata of the Magallanes basin, southern Andean Cordillera, Chile. This paper is a detailed description and analysis of the geology and structural evolution of the thrust front (Vicuna area of southern Tierra del Fuego). Reflection seismic and well data, together with 1:50,000 scale geological mapping, have been used in the analysis. In the southern part of the Vicuna area, two different thrust systems have been found: an upper imbricate fan that deforms Upper Jurassic and Cretaceous strata, and a younger, lower duplex composed of Cretaceous and probably Upper Jurassic rocks. The imbricate fan is characterized by fault-propagation folding in which listric thrust faults merge downward into a sole thrust that probably is located within the Upper Jurassic stratigraphy. The sole thrust of the upper imbricates forms the roof thrust of the underlying duplex. In the northern part of the Vicuna area, the syntectonic sedimentary wedge of the foredeep consists of Late Cretaceous through Tertiary siliciclastics that have been deformed and uplifted by passive back thrusting at the triangle zone. The structural style in the foreland region shows three main subhorizontal detachment levels located within the sedimentary wedge as a result of the progressive transfer of slip from the thrust belt to the foreland. Minor blind thrusts produce stacked [open quotes]pop up[close quotes] and triangle structures that result in complex geometries in the cores of anticlines. A forward-breaking sequence of thrusting is interpreted. During deformation, the active foredeep wedge migrated at least 10 km northward. Balanced geological cross sections indicate approximately 60% (-30 km) shortening for this part of the Magallanes thrust belt.

  1. Galectin-1 as a fusion partner for the production of soluble and folded human {beta}-1,4-galactosyltransferase-T7 in E. coli

    SciTech Connect (OSTI)

    Pasek, Marta; Boeggeman, Elizabeth; Ramakrishnan, Boopathy; Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 2170 ; Qasba, Pradman K.

    2010-04-09

    The expression of recombinant proteins in Escherichia coli often leads to inactive aggregated proteins known as the inclusion bodies. To date, the best available tool has been the use of fusion tags, including the carbohydrate-binding protein; e.g., the maltose-binding protein (MBP) that enhances the solubility of recombinant proteins. However, none of these fusion tags work universally with every partner protein. We hypothesized that galectins, which are also carbohydrate-binding proteins, may help as fusion partners in folding the mammalian proteins in E. coli. Here we show for the first time that a small soluble lectin, human galectin-1, one member of a large galectin family, can function as a fusion partner to produce soluble folded recombinant human glycosyltransferase, {beta}-1,4-galactosyltransferase-7 ({beta}4Gal-T7), in E. coli. The enzyme {beta}4Gal-T7 transfers galactose to xylose during the synthesis of the tetrasaccharide linker sequence attached to a Ser residue of proteoglycans. Without a fusion partner, {beta}4Gal-T7 is expressed in E. coli as inclusion bodies. We have designed a new vector construct, pLgals1, from pET-23a that includes the sequence for human galectin-1, followed by the Tev protease cleavage site, a 6x His-coding sequence, and a multi-cloning site where a cloned gene is inserted. After lactose affinity column purification of galectin-1-{beta}4Gal-T7 fusion protein, the unique protease cleavage site allows the protein {beta}4Gal-T7 to be cleaved from galectin-1 that binds and elutes from UDP-agarose column. The eluted protein is enzymatically active, and shows CD spectra comparable to the folded {beta}4Gal-T1. The engineered galectin-1 vector could prove to be a valuable tool for expressing other proteins in E. coli.

  2. A two-fold interpenetrating 3D metal-organic framework material constructed from helical chains linked via 4,4'-H{sub 2}bpz fragments

    SciTech Connect (OSTI)

    Xie Yiming; Zhao Zhenguo; Wu Xiaoyuan; Zhang Qisheng; Chen Lijuan; Wang Fei; Chen Shanci; Lu Canzhong

    2008-12-15

    A 3-connected dia-f-type metal-organic framework compound {l_brace}[Ag(L){sub 3/2}H{sub 2}PO{sub 4}]{r_brace}{sub n} (1) has been synthesized by self-assembly of 4,4'-H{sub 2}bpz (L=4,4'-H{sub 2}bpz=3,3',5,5'-tetramethyl-4,4'-bipyrazole) and Ag{sub 4}P{sub 2}O{sub 7} under hydrothermal conditions. It crystallizes in the tetragonal space group I4{sub 1}/acd with a=21.406(4) A, b=21.406(4) A, c=36.298(8) A, Z=32. X-ray single-crystal diffraction reveals that 1 has a three-dimensional framework with an unprecedented alternate left- and right-handed helices structure, featuring a non-uniform two-fold interpenetrated (4.14{sup 2}) net. Photoluminescent investigation reveals that the title compound displays interesting emissions in a wide region, which shows that the title compound may be a good potential candidate as a photoelectric material. - Graphical abstract: A 3-connected dia-f-type metal-organic framework compound [Ag(4,4'-bpz){sub 3/2}H{sub 2}PO{sub 4}] shows unprecedented alternating left- and right-handed helices structure, featuring a non-uniform two-fold interpenetrated (4.14{sup 2}) net.

  3. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

    SciTech Connect (OSTI)

    Oshima, Hiraku; Kinoshita, Masahiro

    2015-04-14

    In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient

  4. Structure of the N-terminal domain of the protein Expansion: an ‘Expansion’ to the Smad MH2 fold

    SciTech Connect (OSTI)

    Beich-Frandsen, Mads; Aragón, Eric; Llimargas, Marta; Benach, Jordi; Riera, Antoni; Pous, Joan; Macias, Maria J.

    2015-04-01

    Expansion is a modular protein that is conserved in protostomes. The first structure of the N-terminal domain of Expansion has been determined at 1.6 Å resolution and the new Nα-MH2 domain was found to belong to the Smad/FHA superfamily of structures. Gene-expression changes observed in Drosophila embryos after inducing the transcription factor Tramtrack led to the identification of the protein Expansion. Expansion contains an N-terminal domain similar in sequence to the MH2 domain characteristic of Smad proteins, which are the central mediators of the effects of the TGF-β signalling pathway. Apart from Smads and Expansion, no other type of protein belonging to the known kingdoms of life contains MH2 domains. To compare the Expansion and Smad MH2 domains, the crystal structure of the Expansion domain was determined at 1.6 Å resolution, the first structure of a non-Smad MH2 domain to be characterized to date. The structure displays the main features of the canonical MH2 fold with two main differences: the addition of an α-helical region and the remodelling of a protein-interaction site that is conserved in the MH2 domain of Smads. Owing to these differences, to the new domain was referred to as Nα-MH2. Despite the presence of the Nα-MH2 domain, Expansion does not participate in TGF-β signalling; instead, it is required for other activities specific to the protostome phyla. Based on the structural similarities to the MH2 fold, it is proposed that the Nα-MH2 domain should be classified as a new member of the Smad/FHA superfamily.

  5. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

    SciTech Connect (OSTI)

    Lu, Jun; Wu, Ruiying; Adkins, Joshua N.; Joachimiak, Andrzej; Glover, Mark

    2014-09-16

    In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

  6. Exploration of multi-fold symmetry element-loaded superconducting radio frequency structure for reliable acceleration of low- & medium-beta ion species

    SciTech Connect (OSTI)

    Huang, Shichun; Geng, Rongli

    2015-09-01

    Reliable acceleration of low- to medium-beta proton or heavy ion species is needed for future high current superconducting radio frequency (SRF) accelerators. Due to the high-Q nature of an SRF resonator, it is sensitive to many factors such as electron loading (from either the accelerated beam or from parasitic field emitted electrons), mechanical vibration, and liquid helium bath pressure fluctuation etc. To increase the stability against those factors, a mechanically strong and stable RF structure is desirable. Guided by this consideration, multi-fold symmetry element-loaded SRF structures (MFSEL), cylindrical tanks with multiple (n>=3) rod-shaped radial elements, are being explored. The top goal of its optimization is to improve mechanical stability. A natural consequence of this structure is a lowered ratio of the peak surface electromagnetic field to the acceleration gradient as compared to the traditional spoke cavity. A disadvantage of this new structure is an increased size for a fixed resonant frequency and optimal beta. This paper describes the optimization of the electro-magnetic (EM) design and preliminary mechanical analysis for such structures.

  7. Soro West: A non-seismically defined, fault cut-off prospect in the Papuan Fold and Thrust Belt, Papua New Guinea

    SciTech Connect (OSTI)

    Robinson, W.F. ); Swift, C.M. Jr. )

    1996-01-01

    Soro West is a fault cut-off prospect located in the frontal portion of the Papuan Fold and Thrust Belt. Prospective Toro and Imburu sandstones are interpreted to be in the hanging wall of the Soro Thrust. Truncation against the thrust, both updip and through lateral ramps, provides the trapping mechanism. The Soro West Prospect was defined using geological, geochemical, remote sensing, and geophysical data. The definition and location of the trap is a primary risk and work was focused on this aspect. Surface geological data (lithology, strikes, and dips) topography and synthetic aperture radar imagery were incorporated into the evaluation. Statistical curvature analysis techniques helped define the shape of the structure and the locations of the lateral ramps. Strontium isotope analyses of Darai Limestone surface samples refined erosional levels using a locally-derived reference curve. Severe karst precludes the acquisition of coherent surface seismic data, so the primary geophysical tool used was magnetotellurics (MT). A detailed, pre-survey feasibility study defined expected responses from alternative structural models. The MT data demonstrated that the limestone at surface is underlain by thick conductive clastics and not another Darai Limestone sheet. The data also constrained the range of fault cut-off positions significantly. Multiple, three-dimensionally consistent, restorable alternative structural models were created using results from all analyses. These led to a positive assessment of the prospect and an exploratory test is to be drilled in 1996.

  8. Soro West: A non-seismically defined, fault cut-off prospect in the Papuan Fold and Thrust Belt, Papua New Guinea

    SciTech Connect (OSTI)

    Robinson, W.F.; Swift, C.M. Jr.

    1996-12-31

    Soro West is a fault cut-off prospect located in the frontal portion of the Papuan Fold and Thrust Belt. Prospective Toro and Imburu sandstones are interpreted to be in the hanging wall of the Soro Thrust. Truncation against the thrust, both updip and through lateral ramps, provides the trapping mechanism. The Soro West Prospect was defined using geological, geochemical, remote sensing, and geophysical data. The definition and location of the trap is a primary risk and work was focused on this aspect. Surface geological data (lithology, strikes, and dips) topography and synthetic aperture radar imagery were incorporated into the evaluation. Statistical curvature analysis techniques helped define the shape of the structure and the locations of the lateral ramps. Strontium isotope analyses of Darai Limestone surface samples refined erosional levels using a locally-derived reference curve. Severe karst precludes the acquisition of coherent surface seismic data, so the primary geophysical tool used was magnetotellurics (MT). A detailed, pre-survey feasibility study defined expected responses from alternative structural models. The MT data demonstrated that the limestone at surface is underlain by thick conductive clastics and not another Darai Limestone sheet. The data also constrained the range of fault cut-off positions significantly. Multiple, three-dimensionally consistent, restorable alternative structural models were created using results from all analyses. These led to a positive assessment of the prospect and an exploratory test is to be drilled in 1996.

  9. Exploiting parameter space in MOFs: a 20-fold enhancement of phosphate-ester hydrolysis with UiO-66-NH 2

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Katz, Michael J.; Moon, Su-Young; Mondloch, Joseph E.; Beyzavi, M. Hassan; Stephenson, Casey J.; Hupp, Joseph T.; Farha, Omar K.

    2015-02-24

    The hydrolysis of nerve agents is of primary concern due to the severe toxicity of these agents. Using a MOF-based catalyst (UiO-66), we have previously demonstrated that the hydrolysis can occur with relatively fast half-lives of 50 minutes. However, these rates are still prohibitively slow to be efficiently utilized for some practical applications (e.g., decontamination wipes used to clean exposed clothing/skin/vehicles). We thus turned our attention to derivatives of UiO-66 in order to probe the importance of functional groups on the hydrolysis rate. Three UiO-66 derivatives were explored; UiO-66-NO2 and UiO-66-(OH)2 showed little to no change in hydrolysis rate. However,more » UiO-66-NH2 showed a 20 fold increase in hydrolysis rate over the parent UiO-66 MOF. Half-lives of 1 minute were observed with this MOF. In order to probe the role of the amino moiety, we turned our attention to UiO-67, UiO-67-NMe2 and UiO-67-NH2. In these MOFs, the amino moiety is in close proximity to the zirconium node. We observed that UiO-67-NH2 is a faster catalyst than UiO-67 and UiO-67-NMe2. We conclude that the role of the amino moiety is to act as a proton-transfer agent during the catalytic cycle and not to hydrogen bond or to form a phosphorane intermediate.« less

  10. Preliminary analysis of gravity and aeromagnetic surveys of the Timber Mountain Area, southern Nevada

    SciTech Connect (OSTI)

    Kane, M.F.; Webring, M.W.; Bhattacharyya, B.K.

    1981-12-31

    Recent (1977 to 1978) gravity and aeromagnetic surveys of the Timber Mountain region, southern Nevada, have revealed new details of subsurface structure and lithology. The data strongly suggest that deformation caused by volcanic events has been accommodated along straight-line faults combining in such a fashion as to given a curvilinear appearance to regional structure. The magnetic data suggest that rock units in the central graben and along the southeast margin of Timber Mountain may have been altered, perhaps thermally, from their original state. The gravity data indicate that the south part of the Timber Mountain is underlain by relatively dense rock possibly intrusive rock, like that which crops out along its southeast side. The gravity data also suggest that the Silent Canyon caldera may extend considerably south of its presently indicated southern limit and may underlie much of the area of Timber Mountain. The moat areas appear to be more rectangular or triangular than annular in shape. The southern part of Timber Mountain caldera is separated from the Yucca Mountain area to the south by a triangular horst. The structural relations of the rock units making up the horst are complex. Several linear terrain features in the southern part of the caldera area are closely aligned with geophysical features, implying that the terrain features are fault-controlled.

  11. About the Deputy Director: Short Scientific Biography

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

    Lab Deputy Director Horst Simon Horst Simon is an internationally recognized expert in computer science and applied mathematics and the Deputy Director of Lawrence Berkeley...

  12. UFO (UnFold Operator) user guide

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F. ); Marking, T.R. )

    1991-06-01

    UFO is a collection of interactive utility programs for estimating unknown functions of one variable using a wide-ranging class of information as input, for miscellaneous data-analysis applications, for performing feasibility studies, and for supplementing our other software. Inverse problems, which include spectral unfolds, inverse heat-transfer problems, time-domain deconvolution, and unusual or difficult curve-fit problems, are classes of applications for which UFO is well suited. Extensive use of B-splines and (X,Y)-datasets is made to represent functions. The (X,Y)-dataset representation is unique in that it is not restricted to equally-spaced data. This feature is used, for example, in a table-generating algorithm that evaluates a function to a user-specified interpolation accuracy while minimizing the number of points stored in the corresponding dataset. UFO offers a variety of miscellaneous data-analysis options such as plotting, comparing, transforming, scaling, integrating; and adding, subtracting, multiplying, and dividing functions together. These options are often needed as intermediate steps in analyzing and solving difficult inverse problems, but they also find frequent use in other applications. Statistical options are available to calculate goodness-of-fit to measurements, specify error bands on solutions, give confidence limits on calculated quantities, and to point out the statistical consequences of operations such as smoothing. UFO is designed to do feasibility studies on a variety of engineering measurements. It is also tailored to supplement our Test Analysis and Design codes, SRAD Test-Data Archive software, and Digital Signal Analysis routines.

  13. Evolution on folding landscapes in combinatorial structures

    SciTech Connect (OSTI)

    Fraser, S.M.; Reidys, C.M.

    1997-11-01

    In this paper the authors investigate the evolution of molecular structures by random point mutations. They will consider two types of molecular structures: (a) (RNA) secondary structures, and (b) random structures. In both cases structure consists of: (1) a contact graph, and (2) a family of relations imposed on its adjacent vertices. The vertex set of the contact graph is simply the set of all indices of a sequence, and its edges are the bonds. The corresponding relations associated with the edges are viewed as secondary base pairing rules and tertiary interaction rules respectively. Mapping of sequences into secondary and random structures are modeled and analyzed. Here, the set of all sequences that map into a particular structure is modeled as a random graph in the sequence space, the so called neutral network and they study how neutral networks are embedded in sequence space. A basic replication of deletion experiment reveals how effective secondary and random structures can be searched by random point mutations and to what extent the structure effects the dynamics of this optimization process. In particular the authors can report a nonlinear relation between the fraction of tertiary interactions in random structures, and the times taken for a population of sequences to find a high fitness target random structure.

  14. A novel second-order non-linear optical coordination polymer with three-fold interpenetrated CdSO{sub 4}-type network constructed by carboxylate–sulfonate ligands and strontium ions

    SciTech Connect (OSTI)

    Guan, Lei; Wang, Ying

    2015-10-15

    A novel strontium carboxylate–sulfonate coordination polymer, [Sr(HSIP)(H{sub 2}O){sub 3}]{sub n·}nH{sub 2}O (1) (NaH{sub 2}SIP=5-sulfoisophthalic monosodium salt) has been synthesized by hydrothermal reaction. It was characterized by X-ray single crystal diffraction, infrared spectroscopy, elemental and thermogravimetric analysis. Each strontium atom is eight-coordinate with a distorted bicapped trigonal prismatic arrangement. The whole HSIP{sup 2−} ligand acts as a η{sup 5}μ{sup 4} bridge to generate three-fold interpenetrated CdSO{sub 4}-type network structure, which is constructed from the left- and right-handed helixes paralleled to each other bridged by the HSIP{sup 2−} ligands. The luminescence spectrum indicates an emission maximum at 459 nm. Compound 1 shows a second harmonic generation (SHG) response that is 4 times that of KH{sub 2}PO{sub 4}. - Graphical abstract: The whole HSIP{sup 2−} ligands act as η{sup 5}μ{sup 4} bridges with strontium ions, and the strontium ion is eight-coordinated, showing a distorted bicapped trigonal prism geometry. - Highlights: • A novel coordination polymer with a CdSO{sub 4}-type network structure was synthesized. • It shows a second harmonic generation response that is 4 times that of KH{sub 2}PO{sub 4}. • It is constructed from the helixes paralleled to each other.

  15. Preliminary survey of tuff distribution in Esmeralda, Nye, and Lincoln Counties, Nevada

    SciTech Connect (OSTI)

    Smith, G.V.; Pink, T.S.; Lawrence, J.R.; Woodward, L.A.; Keil, K.; Lappin, A.R.

    1981-02-01

    This report inventories the surface distribution of silicic tuffs in Nye, Esmeralda, and Lincoln Counties, NV, based on a review of available literature. The inventory was taken to provide a data base in evaluating tuff sites for the disposal of high-level nuclear waste. Silicic ash-flow tuffs that are about 11 to 34 million years (my) old are widespread in these counties. These rocks are locally deformed by right-lateral movement along Walker Lane and the Las Vegas Shear Zone, and left-lateral movement along a zone from near the Nevada Test Site (NTS) to the Utah border, and are commonly offset by steeply dipping normal faults. The normal faults that bound horsts, grabens, and tilted-fault blocks of the Basin-and-Range Province began to form 30 my ago; some are still active. Tuff distribution is discussed on a regional basis. Tuff thicknesses and alterations, structural complexity, and proximity to recent faulting, recent volcanism, and mineral resources are discussed for each area. Although the literature on which it is based is often incomplete and sketchy, this report is intended to serve as a basis for future, more detailed work that includes initial field inspection, detailed field and laboratory studies, and extrapolations to the subsurface.

  16. Petroleum geology of Azov-Black Sea region

    SciTech Connect (OSTI)

    Lukin, A.; Trofimenko, G.

    1995-08-01

    The main features of tectonics, stratigraphy, paleogeography, lithology, hydrogeology, geothermics and hydrocarbon-bearingness of Azov-Black Sea Region are characterized on the basis of present-day data. Among the most prospective petroliferous complexes one ought to mention: Paleozoic (S - D - C{sub 1}) of Near-Dobrudga foredeep, Triassic - Jurassic of the Black Sea (shelf and continental slope); Lower Cretaceous of the various parts of the Region; Upper Cretaceous of the Black Sea shelf; Paleocene-Eocene of Azov Sea. In addition certain prospects are connected with Precambrian and Paleozoic basements within conjunction zone between Eastern-Europe platform and Scythian plate. Geodynamic evolution of the Region is considered with determination of tension and compression stages and characteristic of the main regularities of diapirs, mud volcanos, swells, horsts and grabens distribution. There determined the most interesting types of hydrocarbon traps connected with various tectonic forms, river and deltaic channels, bars, conturites, carbonate reefs, etc. Paleogeothermic and paleogeodynamic reconstructions allow to determine the main phases of oil and gas accumulation. The most prospective oil-gas-bearing zones and areas are mapped.

  17. User Coupled Confirmation Drilling Program case study: City of Alamosa, Colorado, Alamosa No. 1 geothermal test well

    SciTech Connect (OSTI)

    Zeisloft, J.; Sibbett, B.S.

    1985-08-01

    A 7118 ft (2170 m) deep geothermal test well was drilled on the south edge of the city of Alamosa, Colorado as part of the Department of Energy's User Coupled Confirmation Drilling Program. The project was selected on the bases of a potential direct heat geothermal resource within the Rio Grande rift graben and resource users in Alamosa. The well site was selected on the hypothesis of a buried horst along which deep thermal fluids might be rising. In addition, there were city wells that were anomalous in temperature and the location was convenient to potential application. The Alamosa No. 1 penetrated 2000 ft (610 m) of fine clastic rocks over 4000 ft (1219 m) of volcaniclastic rock resting on precambrian crystalline rock at a depth of 6370 ft (1942 m). Due to poor hole conditions, geophysical logs were not run. The stabilized bottom hole temperature was 223/sup 0/F (106/sup 0/C) with a gradient of 2.6/sup 0/F/100 ft (47/sup 0/C/km). Limited testing indicated a very low production capacity. 16 refs., 6 figs.

  18. Geology of the lower Yellow Creek Area, Northwestern Colorado

    SciTech Connect (OSTI)

    Hail, W.J.

    1990-01-01

    The lower Yellow Creek area is located in Rio Blanco and Moffat Counties of northwestern Colorado, about midway between the towns of Rangely and Meeker. The study area is in the northwestern part of the Piceance Creek basin, a very deep structural and sedimentary basin that formed during the Laramide orogeny. Potentially important resources in the area are oil shale and related minerals, oil and gas, coal, and uranium. Topics discussed in the report include: Stratigraphy (Subsurface rocks, Cretaceous rocks, Tertiary rocks, and Quaternary deposits); Structure (Midland anticline, graben at Pinyon Ridge, and Crooked Wash syncline, Folds and faults in the vicinity of the White River, Red Wash syncline and central graben zone, Yellow Creek anticlinal nose); Economic geology (Oil shale and associated minerals, Coal, Oil and gas, Uranium, Gravel).

  19. Mesozoic and cenozoic tectonic evolution of the Maranon Basin in Southeastern Columbia, Eastern Ecuador and Northeastern Peru

    SciTech Connect (OSTI)

    Aleman, A.M.; Marksteiner, M. )

    1993-02-01

    The Late Triassic to Early Jurassic in the Maranon was characterized by tectonic quiescence and carbonate shelf deposition. During Middle to Late Jurassic, a northeast-southwest extensional event occurred which is documented by the presence of northwest oriented grabens filled with red beds and volcaniclastic rocks. Cretaceous deposition commenced during the Aptian and continued to the Early Campanian within the vast South America Cretaceous Seaway (SACS) that extended from Venezuela to Central Peru. These strata comprised of shallow marine clastics sources from the Brazilian and Guyana cratons to the east. Retreat of the SACS resulted from the Late Cretaceous (Peruvian) phase of the Andean Orogeny. Deposition became largely continental with sediments derived from the west. The deformation was comtemporaneous with oblique collision and accretion of an allochthonous terrain present in Colombia and Ecuador, as well as uplift of the Putumayo, Napo, Cutucu and Cenepa (PNCC) Mountains, westward erosion of the Napo/Chonta Formations, widespread deposition of red beds, volcanic activity in the foreland and the subtle inversion of half grabens. The Middle Eocene (Inca) phase of the Andean Orogeny, correlated to a relative increase in convergence rates along the western margin of South America (SA). This orogeny was characterized by the development of folds and reverse faults within a narrow and elongated belt, the reactivation of the PNCC Uplifts, the deposition of varicolored fluviatile deposits, the renewed inversion of half grabens, and volcanic activity close to the hinterland. The three main pulses of the Late Miocene to Pliocene phase of the Andean Orogeny correlate with high rates of convergence along the SA margin. This orogenic phase was characterized by thick fluviatile deposition, reactivation of the PNCC uplifts, eastward propagation of the fold and thrust belt, renewed inversion of the half grabens and alkaline volcanism in the foreland.

  20. Method of identifying hairpin DNA probes by partial fold analysis

    DOE Patents [OSTI]

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2008-10-28

    Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  1. Method of identifying hairpin DNA probes by partial fold analysis

    DOE Patents [OSTI]

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2009-10-06

    Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  2. DOE Science Showcase - Protein Folding | OSTI, US Dept of Energy...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect - reports from DOE science, technology and engineering programs. ... National Library of EnergyBeta - search results from across the DOE Complex. Science.gov - ...

  3. New Crystal Structures Lift Fog around Protein Folding

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

    genetic code embodied by the nucleotide sequences in DNA and collected in the form of genes is well known. Biological macromolecules like proteins comprise strings of amino acids...

  4. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    Publication Date: 2013-07-11 OSTI Identifier: 1103786 Type: Publisher's Accepted Manuscript Journal Name: Physical Review Letters Additional Journal Information: Journal Volume: ...

  5. Folding and association of a homotetrameric protein complex in...

    Office of Scientific and Technical Information (OSTI)

    Publication Date: 2013-01-11 OSTI Identifier: 1101879 Type: Publisher's Accepted Manuscript Journal Name: Physical Review E Additional Journal Information: Journal Volume: 87; ...

  6. New Crystal Structures Lift Fog around Protein Folding

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

    lid. A Molecular Origami Machine The genetic code embodied by the nucleotide sequences in DNA and collected in the form of genes is well known. Biological macromolecules like...

  7. Tank 19F Folding Crawler Final Evaluation, Rev. 0

    SciTech Connect (OSTI)

    Nance, T.

    2000-10-25

    The Department of Energy (DOE) is committed to removing millions of gallons of high-level radioactive waste from 51 underground waste storage tanks at the Savannah River Site (SRS). The primary radioactive waste constituents are strontium, plutonium,and cesium. It is recognized that the continued storage of this waste is a risk to the public, workers, and the environment. SRS was the first site in the DOE complex to have emptied and operationally closed a high-level radioactive waste tank. The task of emptying and closing the rest of the tanks will be completed by FY28.

  8. VERIFI code optimization yields three-fold increase in engine...

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

    Greg Cunningham at (630) 252-8232 or media@anl.gov. Connect Find an Argonne expert by subject. Follow Argonne on Twitter, Facebook, Google+ and LinkedIn. For inquiries on...

  9. Brochure (8 1/2 x 11, landscape, 2-fold)

    National Nuclear Security Administration (NNSA)

    kind found. You should also determine whether any administrative or disciplinary action needs to be taken against the individuals who created HWE/ harassment. In doing so, you should consult the Department's Table of Penalties, your EEO Manager or OHCM EMRB. What if the inquiry indicates that there is no harassment or hostile work environment. Do I still need to do anything? You should reaffirm your commitment to nondiscrimination and harassment in the workplace with your employees. You should

  10. Energy Landscapes: From Protein Folding to Molecular Assembly

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

    like kinesin, the efflux pump machinery, ATP synthase, the ribosome, and many others. ... often function by undergoing conformational changes under weak physiological signals. ...

  11. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    Close Cite: Bibtex Format Close 0 pages in this document matching the terms "" Search For Terms: Enter terms in the toolbar above to search the full text of this document for ...

  12. Protein-folding via divide-and-conquer optimization (Conference...

    Office of Scientific and Technical Information (OSTI)

    Berkeley, CA (US) Sponsoring Org: USDOE Laboratory Directed Research andDevelopment Country of Publication: United States Language: English Subject: 60 APPLIED LIFE SCIENCES

  13. UFO (UnFold Operator) default data format

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F. ); Marking, T.R. )

    1991-05-01

    The default format for the storage of x,y data for use with the UFO code is described. The format assumes that the data stored in a file is a matrix of values; two columns of this matrix are selected to define a function of the form y = f(x). This format is specifically designed to allow for easy importation of data obtained from other sources, or easy entry of data using a text editor, with a minimum of reformatting. This format is flexible and extensible through the use of inline directives stored in the optional header of the file. A special extension of the format implements encoded data which significantly reduces the storage required as compared wth the unencoded form. UFO supports several extensions to the file specification that implement execute-time operations, such as, transformation of the x and/or y values, selection of specific columns of the matrix for association with the x and y values, input of data directly from other formats (e.g., DAMP and PFF), and a simple type of library-structured file format. Several examples of the use of the format are given.

  14. Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses...

    Office of Science (SC) Website

    ... Data presented in this article were acquired at the Center for Electron Microscopy and Microanalysis at the University of Southern California. Work at the Molecular Foundry was ...

  15. Brochure (8 1/2 x 11, landscape, 2-fold)

    National Nuclear Security Administration (NNSA)

    with the employee who raised the issue. You might also invite the EEO Manager to be present with you during this meeting. The EEO Manager may need to issue the employee a Notice ...

  16. Protein-folding via divide-and-conquer optimization (Conference...

    Office of Scientific and Technical Information (OSTI)

    Authors: Oliva, Ricardo ; Crivelli, Silvia ; Meza, Juan Publication Date: 2004-07-11 OSTI Identifier: 882903 Report Number(s): LBNL--55869 R&D Project: 365969; BnR: YN0100000 DOE ...

  17. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    None USDOE United States 2013-07-01 English Journal Article Journal Name: Physical Review Letters; Journal Volume: 111; Journal Issue: 2 Medium: X OSTI ID: 1103786, Legacy ID:...

  18. New Crystal Structures Lift Fog around Protein Folding

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

    incorrect or "misfolding" of proteins has been linked to many diseases, including Alzheimer's, Parkinson's, and some forms of cancer. So far, however, a complete...

  19. Heavy metal ions are potent inhibitors of protein folding

    SciTech Connect (OSTI)

    Sharma, Sandeep K. [Biochemisches Institut, Universitaet Zuerich, CH-8057 Zuerich (Switzerland); Departement de Biologie Moleculaire Vegetale, Universite de Lausanne, CH-1015 Lausanne (Switzerland); Goloubinoff, Pierre [Departement de Biologie Moleculaire Vegetale, Universite de Lausanne, CH-1015 Lausanne (Switzerland); Christen, Philipp [Biochemisches Institut, Universitaet Zuerich, CH-8057 Zuerich (Switzerland)], E-mail: christen@bioc.uzh.ch

    2008-07-25

    Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd{sup 2+}, Hg{sup 2+} and Pb{sup 2+} proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC{sub 50} in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.

  20. Modified Microbes Tolerate 50-Fold More Organic Acid - Energy...

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

    UW-Madison researchers have genetically modified microorganisms to better tolerate organic acids like 3HP, acrylic acid and propionic acid. The modified microorganisms are ...

  1. Rift Zone | Open Energy Information

    Open Energy Info (EERE)

    - increased volcanic activity and the formation of graben structures (reference: science-art.com) Rift valleys occur at divergent plate boundaries, resulting in large graben...

  2. NREL: Sustainable NREL - Media Contacts for the Research Support...

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

    viable. With this building, DOE leads by example and hopes to spur innovation and replication throughout government and the commercial building sector. John Horst U.S....

  3. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... ; Lee, Sooheyong ; Walther, Michael ; Schulte-Schrepping, Horst ; Franz, Hermann ; Gray, Amber ; Sikorski, Marcin ; Fuoss, Paul H. ; Stephenson, G.Brian ; Robert, Aymeric ; et ...

  4. Presentations

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

    Horst Simon | Scheduled for Monday, November 18, 2002 at the Marriot Inner Harbor Hotel West Ballroom, in Baltimore, Maryland. The meeting will coincide with SC2002, the...

  5. Geologic evolution and aspects of the petroleum geology of the northern East China Sea shelf basin

    SciTech Connect (OSTI)

    Lee, G.H.; Kim, B.Y.; Shin, K.S.; Sunwoo, D.

    2006-02-15

    Analysis of multichannel seismic reflection profiles reveals that the northern East China Sea shelf basin experienced two phases of rifting, followed by regional subsidence. The initial rifting in the Late Cretaceous created a series of grabens and half grabens, filled by alluvial and fluviolacustrine deposits. Regional uplift and folding (Yuquan movement) in the late Eocene-early Oligocene terminated the initial rifting. Rifting resumed in the early Oligocene, while alluvial and fluviolacustrine deposition continued to prevail. A second phase of uplift in the early Miocene terminated the rifting, marking the transition to the postrift phase. The early postrift phase (early Miocene-late Miocene) is characterized by regional subsidence and westward and northwestward marine transgression. Inversion (Longjing movement) in the late Miocene interrupted the postrift subsidence, resulting in an extensive thrust-fold belt in the eastern part of the area. The entire area entered a stage of regional subsidence again and has become a broad continental shelf. Source rocks include synrift lacustrine facies, fluvial shales, and coal beds. Synrift fluvial, lacustrine, and deltaic deposits, postrift littoral and/or shallow-marine sandstones, and fractured basement have the potential to provide reservoirs. Various types of hydrocarbon traps (e.g., faulted anticlines, overthrusts, rollover anticlines, faults, unconformity traps, combination structural-stratigraphic traps, weathered basement, and stratigraphic traps) are recognized, but many of these traps have not been tested.

  6. Structure of Mesita del Buey at TA-54, Los Alamos National Laboratory, New Mexico

    SciTech Connect (OSTI)

    Reneau, S.L.; Broxton, D.E.; Carney, J.S.; LaDelfe, C.

    1998-04-23

    The geological structure of Mesita del Buey at Technical Area 54 (TA-54) was examined using precise surveying of the contact between units 1v and 2 of the Tshirege Member of the Bandelier Tuff at 3.5 km along the north wall of Pajarito Canyon and 0.6 km along the north wall of a tributary to Canada del Buey. Estimated structure contours on this contact indicate typical strikes of N40E to N70E along this part of Mesita del Buey, although the apparent strike of the tuff is E-W at the western part of the survey. Typical dips are 1.0{degree} to 2.0{degree} to the east or southeast, with an estimated maximum dip of 3.2{degree} near the west end of Material Disposal Area G. Thirty seven faults with vertical displacements of 5 to 65 cm were observed in outcrop along the Pajarito Canyon traverse, and, due to the incomplete exposure of the unit 1v-unit 2 contact, many more faults of this magnitude undoubtedly exist. The faults have a wide range in strike and have either down-to-the-west and down-to-the-east components of offset, although about 65% of the observed displacement is down-to-the-west or northwest. These faults are not clearly associated with major fault zones, indicated by the general absence of larger-scale offsets or inflections along the unit 1v-unit 2 contact in areas where the small-scale faults were observed; they may instead record distributed secondary deformation across the Pajarito Plateau associated with large earthquakes on the main Pajarito fault zone 8--11 km to the west, or perhaps other faults in the region. The survey data also suggest that a 150--250 m wide zone of greater magnitude faulting is present near the west end of the traverse associated with a horst-and-graben structure displaying about 1.5--3.5 m of offset on individual faults, although the total amount of offset across this structure and its orientation are not known.

  7. Protein folding of the H0P model: A parallel Wang-Landau study

    SciTech Connect (OSTI)

    Shi, Guangjie; Wuest, Thomas; Li, Ying Wai; Landau, David P

    2015-01-01

    We propose a simple modication to the hydrophobic-polar (HP) protein model, by introducing a new type of monomer, "0", with intermediate hydrophobicity of some amino acids between H and P. With the replica-exchange Wang-Landau sampling method, we investigate some widely studied HP sequences as well as their H0P counterparts and observe that the H0P sequences exhibit dramatically reduced ground state degeneracy and more signicant transition signals at low temperature for some thermodynamic properties, such as the specific heat.

  8. Analyses of Candida Cdc13 Orthologues Revealed a Novel OB Fold...

    Office of Scientific and Technical Information (OSTI)

    Resource Type: Journal Article Resource Relation: Journal Name: Molecular and Cellular Biology; Journal Volume: 32; Journal Issue: (1) ; 01, 2012 Research Org: Advanced Photon ...

  9. Protein-Folding Landscapes in Multi-Chain Systems Major Classification...

    Office of Scientific and Technical Information (OSTI)

    ... Average radius of gyration (per chain): single-chain (blue), two-chain (red), and four chain systems (green) as functions of temperature (lower right). Figure 3. Free-energy ...

  10. Discovering The Folding Rules That Proteins Obey FY08 LDRD Final...

    Office of Scientific and Technical Information (OSTI)

    Sponsoring Org: USDOE Country of Publication: United States Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES Word Cloud More Like This Full Text preview image File size N...

  11. How to Achieve a Four-Fold Productivity Increase at Fenton Hill...

    Open Energy Info (EERE)

    rate of 340 gpm and at a production temperature of 204C (400F). Author Donald W. Brown Conference GRC Annual Meeting; Salt Lake City, Utah; 19941002 Published Geothermal...

  12. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article...

    Office of Scientific and Technical Information (OSTI)

    Authors: Cellmer, Troy ; Bratko, Dusan ; Prausnitz, John M. ; Blanch, Harvey Publication Date: 2005-06-20 OSTI Identifier: 861262 Report Number(s): LBNL--57925 R&D Project: 402201; ...

  13. Protein-Folding Landscapes in Multi-Chain Systems Major Classification...

    Office of Scientific and Technical Information (OSTI)

    ... The twelve beads listed in Table I, and shown within the context of the native state in ... A decrease in the entropy gain is indeed observed in our model upon increasing the number ...

  14. Kinks, loops, and protein folding, with protein A as an example

    SciTech Connect (OSTI)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden)] [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Liwo, Adam, E-mail: adam@chem.univ.gda.pl [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland)] [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland); Maisuradze, Gia G., E-mail: gm56@cornell.edu; Scheraga, Harold A., E-mail: has5@cornell.edu [Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301 (United States); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours, France and Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-01-14

    The dynamics and energetics of formation of loops in the 46-residue N-terminal fragment of the B-domain of staphylococcal protein A has been studied. Numerical simulations have been performed using coarse-grained molecular dynamics with the united-residue (UNRES) force field. The results have been analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrdinger (DNLS) equation. In the case of proteins, the DNLS equation arises from a C{sup ?}-trace-based energy function. Three individual kink profiles were identified in the experimental three-?-helix structure of protein A, in the range of the Glu16-Asn29, Leu20-Asn29, and Gln33-Asn44 residues, respectively; these correspond to two loops in the native structure. UNRES simulations were started from the full right-handed ?-helix to obtain a clear picture of kink formation, which would otherwise be blurred by helix formation. All three kinks emerged during coarse-grained simulations. It was found that the formation of each is accompanied by a local free energy increase; this is expressed as the change of UNRES energy which has the physical sense of the potential of mean force of a polypeptide chain. The increase is about 7 kcal/mol. This value can thus be considered as the free energy barrier to kink formation in full ?-helical segments of polypeptide chains. During the simulations, the kinks emerge, disappear, propagate, and annihilate each other many times. It was found that the formation of a kink is initiated by an abrupt change in the orientation of a pair of consecutive side chains in the loop region. This resembles the formation of a Bloch wall along a spin chain, where the C{sup ?} backbone corresponds to the chain, and the amino acid side chains are interpreted as the spin variables. This observation suggests that nearest-neighbor side chainside chain interactions are responsible for initiation of loop formation. It was also found that the individual kinks are reflected as clear peaks in the principal modes of the analyzed trajectory of protein A, the shapes of which resemble the directional derivatives of the kinks along the chain. These observations suggest that the kinks of the DNLS equation determine the functionally important motions of proteins.

  15. New structural limits on magma chamber locations at the Valley of Ten Thousand Smokes, Katmai National Park, Alaska

    SciTech Connect (OSTI)

    Wallmann, P.C.; Pollard, D.D. ); Hildreth, W. ); Eichelberger, J.C. )

    1990-12-01

    New structural data from the Novarupta basin, Katmai National Park, Alaska, site of the largest volcanic eruption of this century (1912), provide limits for the location of magma chambers associated with this eruption. To investigate the subsurface structure of the 1912 vents, and to support an interdisciplinary study of this young volcanic system, a project of geologic mapping of surficial and bedrock structures in the vent region of the 1912 eruption has been undertaken. Landslide scarps, arcuate grabens, a monoclinal fold, and truncated ridges circumscribe the Novarupta basin, marking the inferred outer rim of the vent. A set of radial fissures crosses the southern margin of the basin, striking {approximately}140{degree}, subparallel to the dominant bedrock joint set. These fissures and joints, along with the local plate-motion vector and the inferred regional stress orientation, are consistent with a feeder dike propagating from a reservoir beneath Trident volcano to the eruptive vent.

  16. Technical Sessions W. F. Dabberdt, C. ~,1artin, H. L. Cole, J...

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

    W. F. Dabberdt, C. ,1artin, H. L. Cole, J. Dudhia, T. Horst, Y. H. Kuo, :3. Oncley, and ... K. S. Gage, W. Ecklund, D. Carter, R. Strauch, and E. R. Westwater National Oceanic and ...

  17. Berkeley Lab Transportation and Parking Demand Management Committee

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

    510-486-6647 JMDahlgard@lbl.gov Mat Vail Facilities 510-495-2849 MEVail@lbl.gov Doug Goodman OCFO 510-486-7632 DGoodman@lbl.gov Blair Horst Facilities 510-486-4902...

  18. Agenda

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

    Implications of Upcoming Security Guidance Bill Kramer 15:30 Break 16:00 Meeting of PAC members Horst Simon (Attendees who are not PAC members are free) 17:00 End of today's...

  19. Distribution of Quaternary Rhyolite Dome of the Coso Range California...

    Open Energy Info (EERE)

    rhyolite of similar major element chemical composition were erupted over the past 1 m.y. from vents arranged in a crudely S-shaped array atop a granitic horst in the Coso...

  20. Distribution of quaternary rhyolite dome of the Coso Range, California...

    Open Energy Info (EERE)

    rhyolite of similar major element chemical composition were erupted over the past 1 m.y. from vents arranged in a crudely S-shaped array atop a granitic horst in the Coso...

  1. Agenda

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

    Survey results Francesca Verdier 10:00 Review of new allocations process Horst Simon - lessons learned 10:15 Break 10:35 NERSC-3 status plans Bill Kramer 11:35 New Building...

  2. Microsoft Word - Document1

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

    of NERSC Address Horst Simon Director, NERSC Division Bill Kramer Director, High Performance Computing Department NERSC Accomplishments in 1996 Horst Simon - 1/28/97 http://www.nersc.gov/research/whitepaper/whitepaper.html NERSC Mission Statement Provide reliable, high quality, state of the art computing resources and client support in a timely manner-- independent of client location--while wisely advancing the state of computational and computer science. Major Milestones Feb 96 Four NERSC

  3. U.S. Department of Energy Wind and Hydropower Technologies: Top 10 Program Accomplishments (Tri-fold Brochure)

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

    Wind and Hydropower Technologies Top 10 Program Accomplishments Wind Powered Electricity Although the wind has been harnessed to deliver power for centuries, it was only as recently as the 1970s, through the efforts of the U.S. Department of Energy's (DOE's) new Wind Energy Program, that wind power evolved into a viable source for clean commercial power. During that decade, the Wind Energy Program designed, built, and tested the 100-kilowatt (kW) "Mod" series (100 kW was the benchmark

  4. Integrated Geophysical Exploration of a Known Geothermal Resource...

    Open Energy Info (EERE)

    a half-graben basin. This basin-bounding fault serves as the primary conduit for deep water circulation. Potential field, electrical, and seismic data characterize this major...

  5. Germencik Geothermal Area | Open Energy Information

    Open Energy Info (EERE)

    graben, Turkey. Geothermics. 32(1):669-678. Benjamin Matek. Geo-energy Internet. Geothermal Energy Association. updated 20150428;cited 20150428. Available from:...

  6. Gumuskoy Geothermal Area | Open Energy Information

    Open Energy Info (EERE)

    graben, Turkey. Geothermics. 32(1):669-678. Benjamin Matek. Geo-energy Internet. Geothermal Energy Association. updated 20150428;cited 20150428. Available from:...

  7. File:GM-79 A-Aprime.pdf | Open Energy Information

    Open Energy Info (EERE)

    section through the Valles Caldera. The section transects the Valles and Toledo ring fracture zones, the Redondo Creek Graben, and the Sulphur Springs hydrothermal system at core...

  8. Stratigraphic Record Of The Yellowstone Hotspot Track, Neogene...

    Open Energy Info (EERE)

    grabens diverted the Middle Miocene drainage patterns in southwest Montana. Authors James W. Sears, Marc S. Hendrix, Robert C. Thomas and William J. Fritz Published Journal...

  9. Hydrogeological And Isotopic Survey Of Geothermal Fields In The...

    Open Energy Info (EERE)

    Hydrogeological And Isotopic Survey Of Geothermal Fields In The Buyuk Menderes Graben, Turkey Jump to: navigation, search OpenEI Reference LibraryAdd to library Journal Article:...

  10. Presentations

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

    Science Driven Computing: NERSC's Five-Year Plan for 2005 - 2010 October 4, 2005 | Author(s): Horst Simon and Bill Kramer | Download File: NUGStrategyOverview.ppt | ppt | 4.8 MB NERSC/LBNL Data Analytics Project October 4, 2005 | Author(s): Wes Bethel | Download File: NERSC-analytics-04Oct2005.pdf | pdf | 440 KB Progress in Supercomputing: The Top Three Breakthroughs of the Last 20 Years and the Top Three Challenges for the Next 20 Years October 4, 2005 | Author(s): Horst Simon | Download File:

  11. Agenda

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

    Agenda Agenda Energy Research Scientific Computing Users Group (ERSUG) Schedule April 6, 1998 Monday April 6, 1998 Berkeley Lab - Perseverance Hall Time Scheduled Event Speaker / Session Leader 08:00 Continental Breakfast 08:30 Welcome Ricky Kendall 08:35 View From Washington Tom Kitchens 08:55 New NERSC Staff Introductions Horst Simon 09:00 NERSC Research Efforts (Leverage to the NERSC Program) Horst Simon 09:30 Strategic Computing Initiative Bill McCurdy 10:00 ERCAP Changes Tom Kitchens 10:20

  12. Challenge for Mesozoic hydrocarbon exploration in the Eastern Indonesia

    SciTech Connect (OSTI)

    Abdullah, S.; Rukmiati, M.G.; Sitompul, N.

    1996-12-31

    The eastern part of Indonesia covers approximately 3 million square kilometers, 35 percent being landmass and 65 percent covered by ocean. Only three of 38 sedimentary basins are producing hydrocarbon (Salawati, Bintuni, and Seram Basins). Oil and gas have discovered in the Lariang, Bone, Timor, Banggai, Sula and Biak Basins, however the discoveries have not developed yet. Hydrocarbon systems in Northern Australia and Papua New Guinea give the major contributions to the geological idea of Pre-Tertiary section in the less explored area in the Eastern Indonesia. The Triassic-Middle Jurassic marine carbonaceous shale sequences are the main hydrocarbon source rock in the Irian Jaya and surrounding area (Buton, gula and Seram basins). The main Mesozoic reservoir are the Kembelangan Formation in the Bintuni Basin of Irian Jaya and Bobong Formation in the North Sula Region. Exploration play types in the Eastern Indonesia can be divided into five types: 1 - Peri Cratonic, 2 - Marginal Rift Graben, 3 - Thrust Fold Belt Island Arc, 4 - Early Collision and 5 -Microcontinental Block - Advanced Collision. Recent discoveries through Mesozoic section in Eastern Indonesia are: Roabiba-1 (1990) in Bintuni Basin-Irian Jaya (Kambelangan Formation); Loku- 1 (1990) in North Sula region (Pre-Tertiary sediments); Oseil-1 (1993/94) in Bula-Seram Basin (Jurassic Manusela Formation); Elang-1 (1 994); Kakaktua-1 (1994) and Laminaria-1 in North Bonaparte Basin (Upper Jurassic Sands).

  13. Challenge for Mesozoic hydrocarbon exploration in the Eastern Indonesia

    SciTech Connect (OSTI)

    Abdullah, S.; Rukmiati, M.G.; Sitompul, N. )

    1996-01-01

    The eastern part of Indonesia covers approximately 3 million square kilometers, 35 percent being landmass and 65 percent covered by ocean. Only three of 38 sedimentary basins are producing hydrocarbon (Salawati, Bintuni, and Seram Basins). Oil and gas have discovered in the Lariang, Bone, Timor, Banggai, Sula and Biak Basins, however the discoveries have not developed yet. Hydrocarbon systems in Northern Australia and Papua New Guinea give the major contributions to the geological idea of Pre-Tertiary section in the less explored area in the Eastern Indonesia. The Triassic-Middle Jurassic marine carbonaceous shale sequences are the main hydrocarbon source rock in the Irian Jaya and surrounding area (Buton, gula and Seram basins). The main Mesozoic reservoir are the Kembelangan Formation in the Bintuni Basin of Irian Jaya and Bobong Formation in the North Sula Region. Exploration play types in the Eastern Indonesia can be divided into five types: 1 - Peri Cratonic, 2 - Marginal Rift Graben, 3 - Thrust Fold Belt Island Arc, 4 - Early Collision and 5 -Microcontinental Block - Advanced Collision. Recent discoveries through Mesozoic section in Eastern Indonesia are: Roabiba-1 (1990) in Bintuni Basin-Irian Jaya (Kambelangan Formation); Loku- 1 (1990) in North Sula region (Pre-Tertiary sediments); Oseil-1 (1993/94) in Bula-Seram Basin (Jurassic Manusela Formation); Elang-1 (1 994); Kakaktua-1 (1994) and Laminaria-1 in North Bonaparte Basin (Upper Jurassic Sands).

  14. VisGreenWorkshop Findings

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

    "Visualization Greenbook" Future Visualization Needs of the DOE Computational Science Community Hosted at NERSC Report Prepared by: Bernd Hamann, UC Davis E. Wes Bethel, LBNL/NERSC Horst Simon, LBNL/NERSC Juan Meza, LBNL/NERSC October 2002 Lawrence Berkeley National Laboratory - 1 - 1 Executive Summary .................................................................................................... 3 2

  15. INNOVATIVE METHODOLOGY FOR DETECTION OF FRACTURE-CONTROLLED SWEET SPOTS IN THE NORTHERN APPALACHIAN BASIN

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2001-06-30

    In the structure task, the authors completed reducing the data they had collected from a N-S transect on the east side of Seneca Lake. They have calculated the fracture frequency for all the fracture sets at each site, and constructed modified rose diagrams that summarize the fracture attributes at each site. These data indicate a N-striking fault near the southeastern shore of Seneca Lake, and also indicate NE and ENE-trending FIDs and faults north of Valois. The orientation and existence of the ENE-striking FIDs and faults are thought to be guided by faults in the Precambrian basement. These basement faults apparently were sufficiently reactivated to cause faulting in the Paleozoic section. Other faults are thrust ramps above the Silurian salt section that were controlled by a far-field Alleghanian stress field. Structure contour maps and isopach maps have been revised based on additional well log analyses. Except for the Glodes Corners Field, the well spacing generally is insufficient to definitely identify faults. However, relatively sharp elevational changes east of Keuka Lake support the contention that faults occur along the east side of Keuka Lake. Outcrop stratigraphy along the east side of Seneca Lake indicates that faults and gentle folds can be inferred from some exposures along Seneca Lake, but the lensing nature of the individual sandstones can preclude long-distance definite correlations and structure identification. Soil gas data collected during the 2000 field season was reduced and displayed in the previous semiannual report. The seismic data that Quest licensed has been reprocessed. Several grabens observed in the Trenton reflector are consistent with surface structure, soil gas, and aeromagnetic anomalies. In this report they display an interpreted seismic line that crosses the Glodes Corners and Muck Farms fields. The final report from the subcontractor concerning the completed aeromagnetic survey is included. Prominent magnetic anomalies

  16. INNOVATIVE METHODOLOGY FOR DETECTION OF FRACTURE-CONTROLLED SWEET SPOTS IN THE NORTHERN APPALACHIAN BASIN

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2002-01-30

    In the structure task, we completed reducing the data we had collected from a N-S transect on the east of Seneca Lake. We have calculated the fracture frequency for all the fracture sets at each site, and constructed modified rose diagrams that summarize the fracture attributes at each site. These data indicate a N-striking fault near the southeastern shore of Seneca Lake, and also indicate NE and ENE-trending FIDs and faults north of Valois. The orientation and existence of the ENE-striking FIDs and faults are thought to be guided by faults in the Precambrian basement; these basement faults apparently were sufficiently reactivated to cause faulting in the Paleozoic section. Other faults are thrust ramps above the Silurian salt section that were controlled by a far-field Alleghanian stress field. Structure contour maps and isopach maps have been revised based on additional well log analyses. Except for the Glodes Corners Field, the well spacing generally is insufficient to definitively identify faults. However, relatively sharp elevational changes east of Keuka Lake support the contention that faults occur along the east side of Keuka Lake. Outcrop stratigraphy along the east side of Seneca Lake indicates that faults and gentle folds can be inferred from the some exposures along Seneca Lake, but the lensing nature of the individual sandstones can preclude long-distance definitive correlations and structure identification. Soil gas data collected during the 2000 field season was reduced and displayed in the previous semiannual report. The seismic data that Quest licensed has been reprocessed. Several grabens observed in the Trenton reflector are consistent with surface structure, soil gas, and aeromagnetic anomalies. In this report we display an interpreted seismic line that crosses the Glodes Corners and Muck Farm fields. The final report from the subcontractor concerning the completed aeromagnetic survey is included. Prominent magnetic anomalies suggest that

  17. Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-Monophosphate

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tian, Yuanyuan; Cui, Wenjun; Huang, Manna; Robinson, Howard; Wan, Yiqian; Wang, Yousheng; Ke, Hengming

    2014-08-05

    Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli. Recombinant yPDE1 has a KM of 110 μM and a kcat of 16.9 s⁻¹ for cAMP and a KM of 105 μM and a kcat of 11.8 s₅⁻¹ for cGMP. Thus, the specificity constant (kcat/KMcAMP)/(kcat/KMcGMP) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural foldingmore » that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.« less

  18. A two-fold reduction in measurement time for neutron assay: Initial tests of a prototype dual-gated shift register

    SciTech Connect (OSTI)

    Stewart, J.E.; Bourret, S.C.; Krick, M.S.; Hansen, W.J.; Harker, W.C.

    1996-09-01

    Neutron coincidence counting (NCC) is used routinely around the world for nondestructive mass assay of uranium and plutonium in many forms, including waste. Compared with other methods, NCC is generally the most flexible, economic, and rapid. Many applications of NCC would benefit from a reduction in counting time required for a fixed random error. We have developed and tested the first prototype of a dual- gated, shift-register-based electronics unit that offers the potential of decreased measurement time for all passive and active NCC applications.

  19. CX-012266: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles CX(s) Applied: A9 Date: 06/26/2014 Location(s): California Offices(s): National Energy Technology Laboratory

  20. Regional Gravity Survey of the Northern Great Salt Lake Desert...

    Open Energy Info (EERE)

    of about -196 mgal over the alluvium-covered graben areas. The gravity high over the Raft River Mountains apparently corresponds with the Raft River Mountains anticline. A belt...

  1. Southern Basin and Range Geothermal Region | Open Energy Information

    Open Energy Info (EERE)

    faults form the western edge of the Sierra Madre Occidental plateau in northeastern Sonora. These faults and associated half-grabens extend over a distance of more than 300 km...

  2. EERE PowerPoint 97-2004 Template: Green Version

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

    Plan View B is production, A is deep regional d after J. Faulds Purging sample port on ... Cascades graben Advances in Structural Geology Analysis Central Oregon LiDAR Coverage ...

  3. CX-012265: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles… CX(s) Applied: B3.1 Date: 06/26/2014 Location(s): California, California, California Offices(s): National Energy Technology Laboratory

  4. CX-010451: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles CX(s) Applied: B3.16 Date: 06/17/2013 Location(s): California Offices(s): National Energy Technology Laboratory

  5. Phanerozoic tectono-stratigraphic evolution of the Trans-Pecos and Permian basin regions (Mexico, Texas, New Mexico) using Landsat imagery, subsurface and outcrop data

    SciTech Connect (OSTI)

    Markello, J.R.; Sarg, J.F.

    1996-08-01

    Integrating regional Landsat imagery, outcrop field studies, and subsurface data has resulted in a more comprehensive understanding and delineation of the tectono-stratigraphic evolution of the Trans-Pecos region. Landsat imagery were acquired and registered to the existing 1:25000 scale maps and mosaiced to create a regional view of the Trans-Pecos and Permian basin region. The imagery were used to extrapolate and map key stratigraphic and tectonic elements after calibration from documented outcrop and subsurface data. The interpretations aided in the extrapolation of scattered control information and were critical in the complete reconstruction of the geologic history of the area. The Trans-Pecos Phanerozoic history comprises five tectono-depositional phases, and these have controlled the shape of the modem landscape: (1) Late Proterozoic rifting (Gondwana from Laurentia), and development of the Early-Middle Paleozoic Tobosa basin; (2) Pennsylvanian collision (South and North Americas), and differentiation of the Tobosa basin into the Midland, Delaware, Orogrande, and Pedregosa basins separated by basement blocks: Central Basin Platform, Diablo Platform, Burro-Florida Platform; (3) Middle Mesozoic transtensional rifting (Mexico from North America), and Late Jurassic failed rifting of the Mexican Chihuahua and Coahuila Troughs west and south of the Diablo Platform; (4) Late Mesozoic Laramide collision (Mexico and Texas), and development of the Chihuahua fold/thrust belt limited by the western margin of the Diablo Platform; (5) Late Cenozoic North American basin and Range rifting, and development of Rio Grande grabens, block-faulted mountains, and volcanics. The Tobosa basin was a passive-margin interior sag; its continental margin was south of the Marathons.

  6. Monitoring

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

    Monitoring the US ATLAS Network Infrastructure with perfSONAR-PS For the ATLAS Collaboration, Shawn McKee 1 , Andrew Lake 2 , Philippe Laurens 3 , Horst Severini 4 , Tomasz Wlodek 5 , Stephen Wolff 6 and Jason Zurawski 6 1 University of Michigan Physics Department 2 Lawrence Berkeley National Laboratory 3 Michigan State University Physics and Astronomy Department 4 University of Oklahoma, Physics/IT 5 Brookhaven National Laboratory 6 Internet2 E-mail: smckee@umich.edu, andy@es.net,

  7. NERSC Celebrates 40 Years at the Forefront

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

    Celebrates 40 Years of Supercomputing NERSC Celebrates 40 Years at the Forefront DOE supercomputing facility has been supporting broad-based scientific research since 1974 January 29, 2014 Contact: Kathy Kincade, KKincade@lbl.gov, +1 510 495 2124 horstsimon2013 Horst Simon This year, the Department of Energy's (DOE) National Energy Research Scientific Computing Center (NERSC) is celebrating yet another milestone: its 40th anniversary. Since its founding in 1974, NERSC has become the primary

  8. NERSC in the News

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

    Top500 List Released July 7, 2009 | Source: HPCWire | The TOP500 Supercomputer Sites is compiled by Hans Meuer of the University of Mannheim, Germany; Erich Strohmaier and Horst Simon of NERSC/Lawrence Berkeley National Laboratory; and Jack Dongarra of the University of Tennessee, Knoxville. New Way to Determine Protein Structures Revealed July 23, 2009 | Source: SciCasts: SciTech Trade News Network | Department of Energy's (DOE) Lawrence Berkeley National Laboratory have developed a fast and

  9. NUG 1998

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

    NUG 1998 Dates April 8 & 9, 1998 Location Lawrence Berkeley National Lab NERSC's Web Site Presentations Agenda Energy Research Scientific Computing Users Group (ERSUG) Schedule April 6, 1998 Monday April 6, 1998 Berkeley Lab - Perseverance Hall Time Scheduled Event Speaker / Session Leader 08:00 Continental Breakfast 08:30 Welcome Ricky Kendall 08:35 View From Washington Tom Kitchens 08:55 New NERSC Staff Introductions Horst Simon 09:00 NERSC Research Efforts (Leverage to the NERSC Program)

  10. Notes for Visualization Requirememnts

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

    Notes for Vis Requirements Notes for Visualization Requirememnts Notes from June 5, 2002, Visualization Requirements for DOE-Sponsored Computational Science and Engineering Applications A DOE Workshop to Be Held 
at Lawrence Berkeley National Laboratory,
Berkeley, California, June 5, 2002 Workshop Co-organizers: Bernd Hamann 
University of California-Davis Lawrence Berkeley National Lab. E. Wes Bethel 
Lawrence Berkeley National Lab. Horst D. Simon
Lawrence Berkeley National Lab.