Structure-based modeling of protein: DNA specificity

Briefings in Functional Genomics

Volumn 14, Issue 1, 2015, Pages 39-49

  Joyce, Adam P ^a   Zhang, Chi ^c   Bradley, Philip ^b   Havranek, James J ^c  

^a TUFTS UNIVERSITY   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c NONE

Author keywords

Binding specificity; Molecular modeling; Protein: DNA interactions; Structural modeling; Structure prediction; Transcription factor binding sites

Indexed keywords

DNA BINDING PROTEIN; DNA; WATER;

ARTICLE; BINDING SITE; DNA PROTEIN COMPLEX; GENOME; MOLECULAR MODEL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN STRUCTURE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; STRUCTURE ACTIVITY RELATION;

ANIMALS; BASE SEQUENCE; DNA; DNA-BINDING PROTEINS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; STRUCTURE-ACTIVITY RELATIONSHIP; WATER;

EID: 84922434647     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elu044     Document Type: Article

References (74)

1. Alibes A, Nadra AD, De Masi F, et al. Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res 2010;38: 7422-31.
2. Muller PAJ, Vousden KH. p53 mutations in cancer. Nat Cell Biol 2013;15: 2-8.
3. D'Elia AV, Tell G, Paron I, et al. Missense mutations of human homeoboxes: a review. Hum Mutat 2001;18: 361-74.
4. Luscombe NM, Thornton JM. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 2002;320: 991-1009.
5. Borneman AR, Gianoulis TA, Zhang ZD, et al. Divergence of transcription factor binding sites across related yeast species. Science 2007;317: 815-9.
6. Prud'homme B, Gompel N, Carroll SB. Emerging principles of regulatory evolution. Proc Natl Acad Sci USA 2007;104(Suppl. 1):8605-12.
7. Schmidt D, Wilson MD, Ballester B, et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010;328: 1036-40.
8. Wray GA. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 2007;8: 206-16.
9. Luscombe NM, Austin SE, Berman HM, et al. An overview of the structures of protein-DNA complexes. Genome Biol 2000;1: REVIEWS001.
10. Rohs R, Jin X, West SM, et al. Origins of specificity in protein-DNA recognition. Annu Rev Biochem 2010;79: 233-69.
11. Elrod-Erickson M, Rould MA, Nekludova L, et al. Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure 1996;4: 1171-80.
12. Newburger DE, Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 2009;37: D77-82.
13. Schrodinger LLC. The PyMOL Molecular Graphics System. Version 0.99. 2010.
14. Pabo CO, Nekludova L. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol 2000;301: 597-624.
15. Wolfe SA, Ramm EI, Pabo CO. Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers. Structure 2000;8: 739-50.
16. Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with Rosetta. Methods Mol Biol 2014;1123: 265-82.
17. Thyme SB, Baker D, Bradley P. Improved modeling of side-chain-base interactions and plasticity in protein-DNA interface design. J Mol Biol 2012;419: 255-74.
18. Thyme SB, Boissel SJ, Arshiya Quadri S, et al. Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res2014;42: 2564-76.
19. Boas FE, Harbury PB. Potential energy functions for protein design. Curr Opin Struct Biol 2007;17: 199-204.
20. Fornes O, Garcia-Garcia J, Bonet J, et al. On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-dna, and protein-rna interactions. Adv Protein Chem Struct Biol 2014;94: 77-120.
21. Chen CY, Chien TY, Lin CK, et al. Predicting target DNA sequences of DNA-binding proteins based on unbound structures. PLoS One 2012;7: e30446.
22. Siggers TW, Honig B. Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res 2007;35: 1085-97.
23. Xu B, Schones DE, Wang Y, et al. A structural-based strategy for recognition of transcription factor binding sites. PLoS One 2013;8: e52460.
24. Xu B, Yang Y, Liang H, Zhou Y. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins 2009;76: 718-30.
25. AlQuraishi M, McAdams HH. Three enhancements to the inference of statistical protein-DNA potentials. Proteins 2013;81: 426-42.
26. Parisien M, Freed KF, Sosnick TR. On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. PLoS One 2012;7: e32647.
27. Takeda T, Corona RI, Guo JT. A knowledge-based orientation potential for transcription factor-DNA docking. Bioinformatics 2013;29: 322-30.
28. Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Res 2010;38: D91-7.
29. Gabdoulline R, Eckweiler D, Kel A, et al. 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res 2012;40: W180-5.
30. Lin CK, Chen CY. PiDNA: predicting protein-DNA interactions with structural models. Nucleic Acids Res 2013;41: W523-30.
31. Li Z, Lazaridis T. Water at biomolecular binding interfaces. Phys Chem Chem Phys 2007;9: 573-81.
32. Schwabe JW. The role of water in protein-DNA interactions. Curr Opin Struct Biol 1997;7: 126-34.
33. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309: 1868-71.
34. Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007;373: 503-19.
35. Morozov AV, Havranek JJ, Baker D, et al. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 2005;33: 5781-98.
36. Temiz NA, Camacho CJ. Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Res 2009;37: 4076-88.
37. Beierlein FR, Kneale GG, Clark T. Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. BiophysJ 2011;101: 1130-8.
38. Liu LA, Bader JS. Structure-based ab initio prediction of transcription factor-binding sites. Methods Mol Biol 2009;541: 23-41.
39. Seeliger D, Buelens FP, Goette M, et al. Towards computational specificity screening of DNA-binding proteins. Nucleic Acids Res 2011;39: 8281-90.
40. Li Y, Sutch BT, Bui HH, et al. Modeling of the water network at protein-RNA interfaces. J Chem Inf Model 2011;51: 1347-52.
41. Jiang L, Kuhlman B, Kortemme T, et al. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 2005;58: 893-904.
42. Li S, Bradley P. Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model. Proteins 2013;81: 1318-29.
43. van Dijk M, Visscher KM, Kastritis PL, et al. Solvated protein-DNA docking using HADDOCK. J Biomol NMR 2013;56: 51-63.
44. Tucker-Kellogg L, Rould MA, Chambers KA, et al. Engrailed (Gln50! Lys) homeodomain-DNA complex at 1.9 Å resolution: structural basis for enhanced affinity and altered specificity. Structure 1997;5: 1047-54.
45. Schneider B, Cohen D, Berman HM. Hydration of DNA bases: analysis of crystallographic data. Biopolymers 1992;32: 725-50.
46. Robinson CR, Sligar SG. Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions. Biochemistry 1994;33: 3787-93.
47. Kalodimos CG, Bonvin AMJJ, Salinas RK, et al. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator O1 through alternative conformations of its DNA-binding domain. EMBO J 2002;21: 2866-76.
48. Gunther S, Rother K, Frommel C. Molecular flexibility in protein-DNA interactions. Biosystems 2006;85: 126-36.
49. Sunami T, Kono H. Local conformational changes in the DNA interfaces of proteins. PLoS One 2013;8: e56080.
50. Weikl TR, von Deuster C. Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins 2009;75: 104-10.
51. Varnai P, Djuranovic D, Lavery R, et al. Alpha/gamma transitions in the B-DNA backbone. Nucleic Acids Res 2002;30: 5398-406.
52. Endres RG, Schulthess TC, Wingreen NS. Toward an atomistic model for predicting transcription-factor binding sites. Proteins 2004;57: 262-8.
53. Havranek JJ, Duarte CM, Baker D. A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol 2004;344: 59-70.
54. Ashworth J, Havranek JJ, Duarte CM, et al. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006;441: 656-9.
55. Havranek JJ, Baker D. Motif-directed flexible backbone design of functional interactions. Protein Sci 2009;18: 1293-305.
56. Yanover C, Bradley P. Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers. Nucleic Acids Res 2011;39: 4564-76.
57. Cahill M, Cahill S, Cahill K. Proteins wriggle. Biophys J 2002;82: 2665-70.
58. Pérez A, Luque FJ, Orozco M. Frontiers in molecular dynamics simulations of DNA. Acc Chem Res 2011;45: 196-205.
59. Dans PD, Perez A, Faustino I, et al. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res 2012;40: 10668-78.
60. Perez A, Lankas F, Luque FJ, et al. Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res 2008;36: 2379-94.
61. Deremble C, Lavery R, Zakrzewska K. Protein-DNA recognition: breaking the combinatorial barrier. Comp Phys Comm 2008;179: 112-9.
62. Zakrzewska K, Bouvier B, Michon A, et al. Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies. Phys Chem Chem Phys 2009;11: 10712-21.
63. Berger MF, Philippakis AA, Qureshi AM, et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 2006;24: 1429-35.
64. Jolma A, Yan J, Whitington T, et al. DNA-binding specificities of human transcription factors. Cell 2013;152: 327-39.
65. Maerkl SJ, Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors. Science 2007;315: 233-7.
66. Warren CL, Kratochvil NC, Hauschild KE, et al. Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci USA 2006;103: 867-72.
67. Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLoS Comp Biol 2009;5: e1000590.
68. Johnson DS, Mortazavi A, Myers RM, et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007;316: 1497-502.
69. Badis G, Berger MF, Philippakis AA, et al. Diversity and complexity in DNA recognition by transcription factors. Science 2009;324: 1720-3.
70. Gordan R, Shen N, Dror I, et al. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep 2013;3: 1093-104.
71. Berger MF, Badis G, Gehrke AR, et al. Variation in home-odomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 2008;133: 1266-76.
72. Noyes MB, Christensen RG, Wakabayashi A, et al. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 2008;133: 1277-89.
73. Gupta S, Stamatoyannopoulos JA, Bailey TL, et al. Quantifying similarity between motifs. Genome Biol 2007;8: R24.
74. Persikov AV, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res 2014;42: 97-108.