Molecular flexibility in protein–DNA interactions

Backstrom, 2002, The runx1 runt domain at 1.25a resolution: a structural switch and specifically bound chloride ions modulate dna binding, J. Mol. Biol., 322, 259, 10.1016/S0022-2836(02)00702-7 Barak, 1992, Correlation between phosphorylation of the chemotaxis protein CheY and its activity at the flagellar motor, Biochemistry, 31, 1821, 10.1021/bi00121a034 Berman, 2000, The protein data bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 Betts, 1999, An analysis of conformational changes on protein–protein association: implications for predictive docking, Protein Eng., 12, 271, 10.1093/protein/12.4.271 Dickerson, 1998, DNA bending: the prevalence of kinkiness and the virtues of normality, Nucleic Acids Res., 26, 1906, 10.1093/nar/26.8.1906 Dixit, 2005, Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences, Biophys. J., 88, 3147, 10.1529/biophysj.104.053843 Echols, 2003, Molmovdb: analysis and visualization of conformational change and structural flexibility, Nucleic Acids Res., 31, 478, 10.1093/nar/gkg104 Ferrari, 2004, Soft docking and multiple receptor conformations in virtual screening, J. Med. Chem., 47, 5076, 10.1021/jm049756p Fischer, 1894, Einfluss der configuration auf die wirkung der enzyme, Chem. Ber., 27, 2985, 10.1002/cber.18940270364 Frauenfelder, 1991, The energy landscapes and motions of proteins, Science, 254, 1598, 10.1126/science.1749933 Freire, 1999, The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody d1.3 to lysozyme, Proc. Natl. Acad. Sci. USA, 96, 10118, 10.1073/pnas.96.18.10118 Garvie, 2001, Recognition of specific dna sequences, Mol. Cell, 8, 937, 10.1016/S1097-2765(01)00392-6 Gingeras, 1981, Two new restriction endonucleases from proteus vulgaris, Nucleic Acids Res., 9, 4525, 10.1093/nar/9.18.4525 Goh, 2004, Conformational changes associated with protein–protein interactions, Curr. Opin. Struct. Biol., 14, 104, 10.1016/j.sbi.2004.01.005 Jones, 1999, Protein–DNA interactions: a structural analysis, J. Mol. Biol., 287, 877, 10.1006/jmbi.1999.2659 Koshland, 1958, Application of a theory of enzyme specifity to protein synthesis, Proc. Natl. Acad. Sci. USA, 44, 98, 10.1073/pnas.44.2.98 Lawson, 2004, Catabolite activator protein: DNA binding and transcription activation, Curr. Opin. Struct. Biol., 14, 10, 10.1016/j.sbi.2004.01.012 Li, 2001, Clustering of highly homologous sequences to reduce the size of large protein databases, Bioinformatics, 17, 282, 10.1093/bioinformatics/17.3.282 Li, 2001, Crystal structures of a ddatp-, ddttp-, ddctp, and ddgtp- trapped ternary complex of klentaq1: insights into nucleotide incorporation and selectivity, Protein Sci., 10, 1225, 10.1110/ps.250101 Luscombe, 2002, Protein–DNA interactions: amino acid conservation and the effects of mutations on binding specificity, J. Mol. Biol., 320, 991, 10.1016/S0022-2836(02)00571-5 Mandel-Gutfreund, 1998, Quantitative parameters for amino acid-base interaction: implications for prediction of protein–DNA binding sites, Nucleic Acids Res., 26, 2306, 10.1093/nar/26.10.2306 Matsuo, 2003, The transcription factor ccaat-binding factor cbf/nf-y regulates the proximal promoter activity in the human alpha 1(xi) collagen gene (col11a1), J. Biol. Chem., 278, 32763, 10.1074/jbc.M305599200 Monod, 1965, On the nature of allosteric transitions: a plausible model, J. Mol. Biol., 12, 88, 10.1016/S0022-2836(65)80285-6 Nadassy, 2001, Standard atomic volumes in double-stranded dna and packing in protein–DNA interfaces, Nucleic Acids Res., 29, 3362, 10.1093/nar/29.16.3362 Nadassy, 1999, Structural features of protein-nucleic acid recognition sites, Biochemistry, 38, 1999, 10.1021/bi982362d Otwinowski, 1988, Crystal structure of trp repressor/operator complex at atomic resolution, Nature, 335, 321, 10.1038/335321a0 Passner, 2000, Modeling the camp-induced allosteric transition using the crystal structure of cap-camp at 2.1 a resolution, J. Mol. Biol., 304, 847, 10.1006/jmbi.2000.4231 Pelletier, 1994, Structures of ternary complexes of rat dna polymerase beta, a dna template-primer, and ddctp, Science, 264, 1891, 10.1126/science.7516580 Pelletier, 1996, Crystal structures of human dna polymerase beta complexed with dna: implications for catalytic mechanism, processivity, and fidelity, Biochemistry, 35, 12742, 10.1021/bi952955d Perez-Martin, 1997, Clues and consequences of DNA bending in transcription, Annu. Rev. Microbiol., 51, 593, 10.1146/annurev.micro.51.1.593 Phillips, 1994, Electrostatic activation of escherichia coli methionine repressor, Structure, 2, 309, 10.1016/S0969-2126(00)00032-0 Pingoud, 1997, Recognition and cleavage of dna by type-II restriction endonucleases, Eur. J. Biochem., 246, 1, 10.1111/j.1432-1033.1997.t01-6-00001.x Sawaya, 1997, Crystal structures of human dna polymerase beta complexed with gapped and nicked dna: evidence for an induced fit mechanism, Biochemistry, 36, 11205, 10.1021/bi9703812 Spolar, 1994, Coupling of local folding to site-specific binding of proteins to dna, Science, 263, 777, 10.1126/science.8303294 Stark, 2003, A model for statistical significance of local similarities in structure, J. Mol. Biol., 326, 1307, 10.1016/S0022-2836(03)00045-7 Tahirov, 2001, Structural analyses of dna recognition by the aml1/runx-1 runt domain and its allosteric control by cbfbeta, Cell, 104, 755, 10.1016/S0092-8674(01)00271-9 Tsai, 1999, Folding funnels, binding funnels, and protein function, Protein Sci., 8, 1181, 10.1110/ps.8.6.1181 Ward, 1963, Hierarchical grouping to optimize an objective function, J. Am. Stat. Assoc., 58, 236, 10.2307/2282967 White, 1998, Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex, Nature, 394, 502, 10.1038/28893 Yan, 2004, Cbfbeta allosterically regulates the runx1 runt domain via a dynamic conformational equilibrium, Nat. Struct. Mol. Biol., 11, 901, 10.1038/nsmb819 Yang, 2004, Molecular modelling prediction of ligand binding site flexibility, J. Comput. Aided Mol. Des., 18, 235, 10.1023/B:JCAM.0000046820.08222.83