An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

doi:10.1186/s12859-015-0819-2

Title: An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Journal Article · Thu Nov 19 00:00:00 EST 2015 · BMC Bioinformatics

DOI:https://doi.org/10.1186/s12859-015-0819-2· OSTI ID:1241035

AlQuraishi, Mohammed ^[1]; Tang, Shengdong ^[1]; Xia, Xide ^[1]

Harvard Medical School, Boston, MA (United States)

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Stanford Univ., CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FG02-05ER64136

OSTI ID:: 1241035

Journal Information:: BMC Bioinformatics, Vol. 16, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 3 works

Citation information provided by
Web of Science

References (83)

Target site choice of the related transposable elements Tc1 and Tc3 of Caenorhabditis elegans van Luenen, Henri G. A. M.; Plasterk, Ronald H. A. Nucleic Acids Research, Vol. 22, Issue 3 https://doi.org/10.1093/nar/22.3.262	journal	January 1994
A Feature-Based Approach to Modeling Protein–DNA Interactions Sharon, Eilon; Lubliner, Shai; Segal, Eran PLoS Computational Biology, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pcbi.1000154	journal	August 2008
The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites Rodgers, David W.; Harrison, Stephen C. Structure, Vol. 1, Issue 4 https://doi.org/10.1016/0969-2126(93)90012-6	journal	December 1993
AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks Palaniswamy, Saranyan K.; James, Stephen; Sun, Hao Plant Physiology, Vol. 140, Issue 3 https://doi.org/10.1104/pp.105.072280	journal	March 2006
Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? 1 1Edited by R. Ebright Pabo, Carl O.; Nekludova, Lena Journal of Molecular Biology, Vol. 301, Issue 3 https://doi.org/10.1006/jmbi.2000.3918	journal	August 2000
Generality of a functional initiator consensus sequence Lo, Kiersten; Smale, Stephen T. Gene, Vol. 182, Issue 1-2 https://doi.org/10.1016/s0378-1119(96)00438-6	journal	December 1996
A census of human transcription factors: function, expression and evolution Vaquerizas, Juan M.; Kummerfeld, Sarah K.; Teichmann, Sarah A. Nature Reviews Genetics, Vol. 10, Issue 4 https://doi.org/10.1038/nrg2538	journal	April 2009
Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro Koudelka, Gerald B.; Harrison, Stephen C.; Ptashne, Mark Nature, Vol. 326, Issue 6116 https://doi.org/10.1038/326886a0	journal	April 1987
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T. Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp950	journal	November 2009
BIPA: a database for protein–nucleic acid interaction in 3D structures Lee, Semin; Blundell, Tom L. Bioinformatics, Vol. 25, Issue 12 https://doi.org/10.1093/bioinformatics/btp243	journal	April 2009
DNA binding activities of the Caenorhabditis elegans Tc3 transposase Colloms, Sean D.; van Luenen, Henri G. A. M.; PIasterk, Ronald H. A. Nucleic Acids Research, Vol. 22, Issue 25 https://doi.org/10.1093/nar/22.25.5548	journal	January 1994
A method for registration of 3-D shapes Besl, P. J.; McKay, Neil D. IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 14, Issue 2 https://doi.org/10.1109/34.121791	journal	February 1992
Divergent homeo box proteins recognize similar DNA sequences in Drosophila Hoey, Timothy; Levine, Michael Nature, Vol. 332, Issue 6167 https://doi.org/10.1038/332858a0	journal	April 1988
Human transcription factor protein interaction networks Göös, Helka; Kinnunen, Matias; Salokas, Kari Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-28341-5	journal	February 2022
Winged helix proteins Gajiwala, Ketan S.; Burley, Stephen K. Current Opinion in Structural Biology, Vol. 10, Issue 1 https://doi.org/10.1016/S0959-440X(99)00057-3	journal	February 2000
AbdB-like Hox proteins stabilize DNA binding by the Meis1 homeodomain proteins. Shen, W. F.; Montgomery, J. C.; Rozenfeld, S. Molecular and Cellular Biology, Vol. 17, Issue 11 https://doi.org/10.1128/MCB.17.11.6448	journal	November 1997
Clustering by Passing Messages Between Data Points Frey, B. J.; Dueck, D. Science, Vol. 315, Issue 5814 https://doi.org/10.1126/science.1136800	journal	February 2007
Prediction of TF target sites based on atomistic models of protein-DNA complexes Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-436	journal	October 2008
Cis requirements for transposition of Tc1-like transposons in C. elegans Fischer, S. E. J.; van Luenen, H. G. A. M.; Plasterk, R. H. A. Molecular and General Genetics MGG, Vol. 262, Issue 2 https://doi.org/10.1007/pl00008641	journal	September 1999
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions Kumar, M. D. S. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj103	journal	January 2006
Maximally Efficient Modeling of DNA Sequence Motifs at All Levels of Complexity Stormo, Gary D. Genetics, Vol. 187, Issue 4 https://doi.org/10.1534/genetics.110.126052	journal	February 2011
Atomistic modeling of protein–DNA interaction specificity: progress and applications Liu, Limin Angela; Bradley, Philip Current Opinion in Structural Biology, Vol. 22, Issue 4 https://doi.org/10.1016/j.sbi.2012.06.002	journal	August 2012
The many faces of the helix-turn-helix domain: Transcription regulation and beyond Aravind, L.; Anantharaman, Vivek; Balaji, Santhanam FEMS Microbiology Reviews, Vol. 29, Issue 2 https://doi.org/10.1016/j.fmrre.2004.12.008	journal	April 2005
Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames Prakash, P.; Yellaboina, S.; Ranjan, A. Bioinformatics, Vol. 21, Issue 10 https://doi.org/10.1093/bioinformatics/bti375	journal	March 2005
Sequence-specific interaction of the Salmonella Hin recombinase in both major and minor grooves of DNA. Hughes, K. T.; Gaines, P. C.; Karlinsey, J. E. The EMBO Journal, Vol. 11, Issue 7 https://doi.org/10.1002/j.1460-2075.1992.tb05335.x	journal	July 1992
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions Newburger, D. E.; Bulyk, M. L. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn660	journal	January 2009
Identification of transcription factor binding sites with variable-order Bayesian networks Ben-Gal, I.; Shani, A.; Gohr, A. Bioinformatics, Vol. 21, Issue 11 https://doi.org/10.1093/bioinformatics/bti410	journal	March 2005
Transcriptional regulatory code of a eukaryotic genome Harbison, Christopher T.; Gordon, D. Benjamin; Lee, Tong Ihn Nature, Vol. 431, Issue 7004 https://doi.org/10.1038/nature02800	journal	September 2004
Transcription Initiation at Its Most Basic Level Marmorstein, Ronen Cell, Vol. 115, Issue 4 https://doi.org/10.1016/s0092-8674(03)00888-2	journal	November 2003
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation Gama-Castro, S.; Jimenez-Jacinto, V.; Peralta-Gil, M. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm994	journal	December 2007
Search for additional replication terminators in the Bacillus subtilis 168 chromosome. Griffiths, A. A.; Wake, R. G. Journal of Bacteriology, Vol. 179, Issue 10 https://doi.org/10.1128/jb.179.10.3358-3361.1997	journal	May 1997
NPIDB: nucleic acid—protein interaction database Kirsanov, Dmitry D.; Zanegina, Olga N.; Aksianov, Evgeniy A. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1199	journal	November 2012
CENP-B box and pJα sequence distribution in human alpha satellite higher-order repeats (HOR) Rosandić, Marija; Paar, Vladimir; Basar, Ivan Chromosome Research, Vol. 14, Issue 7 https://doi.org/10.1007/s10577-006-1078-x	journal	November 2006
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking Chen, Shengfeng; Gunasekera, Angelo; Zhang, Xiaoping Journal of Molecular Biology, Vol. 314, Issue 1 https://doi.org/10.1006/jmbi.2001.5090	journal	November 2001
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila Halfon, M. S.; Gallo, S. M.; Bergman, C. M. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm876	journal	December 2007
The quorum-sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility: TraR decodes its DNA binding site White, Catharine E.; Winans, Stephen C. Molecular Microbiology, Vol. 64, Issue 1 https://doi.org/10.1111/j.1365-2958.2007.05647.x	journal	March 2007
DNA sequence requirements for transcriptional initiator activity in mammalian cells. Javahery, R.; Khachi, A.; Lo, K. Molecular and Cellular Biology, Vol. 14, Issue 1 https://doi.org/10.1128/mcb.14.1.116	journal	January 1994
On the Transcriptional Regulation of Methicillin Resistance: MecI REPRESSOR IN COMPLEX WITH ITS OPERATOR García-Castellanos, Raquel; Mallorquí-Fernández, Goretti; Marrero, Aniebrys Journal of Biological Chemistry, Vol. 279, Issue 17 https://doi.org/10.1074/jbc.M313123200	journal	February 2004
Contacts between gamma delta resolvase and the gamma delta res site. Falvey, E.; Grindley, N. D. The EMBO Journal, Vol. 6, Issue 3 https://doi.org/10.1002/j.1460-2075.1987.tb04824.x	journal	March 1987
Replication Terminator Protein-Based Replication Fork-Arrest Systems in Various Bacillus Species Griffiths, A. A.; Andersen, P. A.; Wake, R. G. Journal of Bacteriology, Vol. 180, Issue 13 https://doi.org/10.1128/jb.180.13.3360-3367.1998	journal	July 1998
Alignment of recombination sites in Hin-mediated site-specific DNA recombination. Moskowitz, I. P.; Heichman, K. A.; Johnson, R. C. Genes & Development, Vol. 5, Issue 9 https://doi.org/10.1101/gad.5.9.1635	journal	September 1991
AthaMap, integrating transcriptional and post-transcriptional data Bulow, L.; Engelmann, S.; Schindler, M. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn709	journal	January 2009
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data Yang, Jian-Hua; Li, Jun-Hao; Jiang, Shan Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1060	journal	November 2012
DNAase footprinting a simple method for the detection of protein-DNA binding specificity Galas, David J.; Schmitz, Albert Nucleic Acids Research, Vol. 5, Issue 9 https://doi.org/10.1093/nar/5.9.3157	journal	January 1978
Genome-Wide Mapping of in Vivo Protein-DNA Interactions Johnson, D. S.; Mortazavi, A.; Myers, R. M. Science, Vol. 316, Issue 5830 https://doi.org/10.1126/science.1141319	journal	June 2007
Identification of DNA-binding protein target sequences by physical effective energy functions. Free energy analysis of lambda repressor-DNA complexes Moroni, E.; Caselle, M.; Fogolari, F. arXiv https://doi.org/10.48550/arxiv.0712.2405	text	January 2007
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information Sierro, Nicolas; Makita, Yuko; de Hoon, Michiel Nucleic Acids Research, Vol. 36, Issue suppl_1 https://doi.org/10.1093/nar/gkm910	journal	October 2007
The many faces of the helix-turn-helix domain: Transcription regulation and beyond Aravind, L.; Anantharaman, V.; Balaji, S. FEMS Microbiology Reviews, Vol. 29, Issue 2 https://doi.org/10.1016/j.femsre.2004.12.008	journal	April 2005
High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA Wilson, David S.; Guenther, Brian; Desplan, Claude Cell, Vol. 82, Issue 5 https://doi.org/10.1016/0092-8674(95)90468-9	journal	September 1995
TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes Matys, V. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj143	journal	January 2006
Binding geometry of α-helices that recognize DNA Suzuki, Masashi; Gerstein, Mark Proteins: Structure, Function, and Genetics, Vol. 23, Issue 4 https://doi.org/10.1002/prot.340230407	journal	December 1995
HNF1, a homeoprotein member of the hepatic transcription regulatory network Tronche, Fran�lois; Yaniv, Moshe BioEssays, Vol. 14, Issue 9 https://doi.org/10.1002/bies.950140902	journal	September 1992
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction Salama, R. A.; Stekel, D. J. Nucleic Acids Research, Vol. 38, Issue 12 https://doi.org/10.1093/nar/gkq274	journal	May 2010
Analysis of a Ubiquitous Promoter Element in a Primitive Eukaryote: Early Evolution of the Initiator Element Liston, David R.; Johnson, Patricia J. Molecular and Cellular Biology, Vol. 19, Issue 3 https://doi.org/10.1128/mcb.19.3.2380	journal	March 1999
Identification and characterization of new DNA replication terminators in Bacillus subtilis Franks, A. H.; Griffiths, A. A.; Wake, R. G. Molecular Microbiology, Vol. 17, Issue 1 https://doi.org/10.1111/j.1365-2958.1995.mmi_17010013.x	journal	July 1995
Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae Yellaboina, Sailu; Ranjan, Sarita; Chakhaiyar, Prachee BMC Microbiology, Vol. 4, Issue 1, p. 38 https://doi.org/10.1186/1471-2180-4-38	journal	January 2004
Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes Huerta, Araceli M.; Francino, M. Pilar; Morett, Enrique PLoS Genetics, Vol. 2, Issue 11 https://doi.org/10.1371/journal.pgen.0020185	journal	January 2006
The Initiator Element: A Paradigm for Core Promoter Heterogeneity within Metazoan Protein-coding Genes Smale, S. T.; Jain, A.; Kaufmann, J. Cold Spring Harbor Symposia on Quantitative Biology, Vol. 63, Issue 0 https://doi.org/10.1101/sqb.1998.63.21	journal	January 1998
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures Lu, Xiang-Jun; Olson, Wilma K. Nature Protocols, Vol. 3, Issue 7 https://doi.org/10.1038/nprot.2008.104	journal	July 2008
Structural Basis of Core Promoter Recognition in a Primitive Eukaryote Schumacher, Maria A.; Lau, Audrey O. T.; Johnson, Patricia J. Cell, Vol. 115, Issue 4 https://doi.org/10.1016/S0092-8674(03)00887-0	journal	November 2003
New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI) Hiroyuki, Sugisaki; Susumu, Kanazawa Gene, Vol. 16, Issue 1-3 https://doi.org/10.1016/0378-1119(81)90062-7	journal	December 1981
Protein-DNA binding specificity predictions with structural models Morozov, A. V. Nucleic Acids Research, Vol. 33, Issue 18 https://doi.org/10.1093/nar/gki875	journal	October 2005
TFinDit: transcription factor-DNA interaction data depository Turner, Daniel; Kim, RyangGuk; Guo, Jun-tao BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-220	journal	January 2012
PRODORIC: prokaryotic database of gene regulation Munch, R. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg037	journal	January 2003
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A. Nucleic Acids Research, Vol. 32, Issue Web Server, p. W665-W667 https://doi.org/10.1093/nar/gkh381	journal	July 2004
The hierarchy of KorB binding at its 12 binding sites on the broad-host-range plasmid RK2 and modulation of this binding by IncC1 protein 1 1Edited by J. Karn Kostelidou, Kalliopi; Thomas, Christopher M. Journal of Molecular Biology, Vol. 295, Issue 3 https://doi.org/10.1006/jmbi.1999.3359	journal	January 2000
Robust and rigorous identification of tissue-specific genes by statistically extending tau score Lüleci, Hatice Büşra; Yılmaz, Alper BioData Mining, Vol. 15, Issue 1 https://doi.org/10.1186/s13040-022-00315-9	journal	December 2022
Improved predictions of transcription factor binding sites using physicochemical features of DNA Maienschein-Cline, Mark; Dinner, Aaron R.; Hlavacek, William S. Nucleic Acids Research, Vol. 40, Issue 22 https://doi.org/10.1093/nar/gks771	journal	August 2012
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Dolinsky, T. J.; Czodrowski, P.; Li, H. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm276	journal	May 2007
Energetics of protein–DNA interactions Donald, Jason E.; Chen, William W.; Shakhnovich, Eugene I. Nucleic Acids Research, Vol. 35, Issue 4 https://doi.org/10.1093/nar/gkl1103	journal	January 2007
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila Gallo, S. M.; Gerrard, D. T.; Miner, D. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq999	journal	October 2010
Direct inference of protein-DNA interactions using compressed sensing methods AlQuraishi, M.; McAdams, H. H. Proceedings of the National Academy of Sciences, Vol. 108, Issue 36 https://doi.org/10.1073/pnas.1106460108	journal	August 2011
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes Kazakov, A. E.; Cipriano, M. J.; Novichkov, P. S. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl865	journal	January 2007
Structural Classification of HTH DNA-binding Domains and Protein – DNA Interaction Modes Wintjens, René; Rooman, Marianne Journal of Molecular Biology, Vol. 262, Issue 2 https://doi.org/10.1006/jmbi.1996.0514	journal	September 1996
Variable structure motifs for transcription factor binding sites Reid, John E.; Evans, Kenneth J.; Dyer, Nigel BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-30	journal	January 2010
Identification of DNA-binding protein target sequences by physical effective energy functions, free energy analysis of lambda repressor-DNA complexes Moroni, Elisabetta; Caselle, Michele; Fogolari, Federico BMC Structural Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1472-6807-7-61	journal	January 2007
Three enhancements to the inference of statistical protein-DNA potentials AlQuraishi, Mohammed; McAdams, Harley H. Proteins: Structure, Function, and Bioinformatics, Vol. 81, Issue 3 https://doi.org/10.1002/prot.24201	journal	November 2012
HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites Jagannathan, V. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj049	journal	January 2006
Visualization and Labeling of Point Clouds in Virtual Reality Stets, Jonathan Dyssel; Sun, Yongbin; Corning, Wiley arXiv https://doi.org/10.48550/arxiv.1804.04111	text	January 2018
3D-footprint: a database for the structural analysis of protein–DNA complexes Contreras-Moreira, Bruno Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp781	journal	September 2009
Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster Down, Thomas A.; Bergman, Casey M.; Su, Jing PLoS Computational Biology, Vol. 3, Issue 1 https://doi.org/10.1371/journal.pcbi.0030007	journal	January 2007
Differential recognition of OR1 and OR3 by bacteriophage 434 repressor and Cro. Koudelka, G. B.; Lam, C. Y. Journal of Biological Chemistry, Vol. 268, Issue 32 https://doi.org/10.1016/S0021-9258(20)80457-8	journal	November 1993

Cited By (2)

Spacer sequences separating transcription factor binding motifs set enhancer quality and strength Guéroult-Bellone, Marion; Nitta, Kazuhiro R.; Kari, Willi bioRxiv https://doi.org/10.1101/098830	journal	January 2017
Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis – An Insight Into the Zinc Homeostasis of the Pathogen Kandari, Divya; Gopalani, Monisha; Gupta, Manish Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03314	journal	January 2019

Similar Records

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

Technical Report · Thu May 26 00:00:00 EDT 2011 · OSTI ID:1241035

Baliga, Nitin S

Sequence-specific alkylation of double-helical DNA by oligonucleotide-directed triple-helix formation

Journal Article · Wed Dec 05 00:00:00 EST 1990 · Journal of the American Chemical Society; (United States) · OSTI ID:1241035

Povsic, T J; Dervan, P B

Structures of carbon catabolite protein A–(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators

Journal Article · Tue Nov 23 00:00:00 EST 2010 · Nucleic Acids Research · OSTI ID:1241035

Schumacher, Maria A.; Sprehe, Mareen; Bartholomae, Maike; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
protein-DNA
database
helix-turn-helix
transcription factors
structure
PWM

Title: An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Citation Formats

References (83)

Cited By (2)

Similar Records

Related Subjects