Comparison of DNA binding across protein Superfamilies

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 1, 2010, Pages 52-62

  Contreras Moreira, Bruno ^a,b,c   Sancho, Javier ^c   Angarica, Vladimir Espinosa ^c  

^a CSIC   (Spain)

^b FUNDACIÓN ARAID   (Spain)

^c UNIVERSITY OF ZARAGOZA   (Spain)

Author keywords

Atomic interactions; Direct and indirect readout; Protein DNA interface; Superfamily

Indexed keywords

DNA BINDING PROTEIN; RESTRICTION ENDONUCLEASE; ZINC FINGER PROTEIN; DNA;

ARTICLE; ELECTRICITY; EVOLUTION; HYDROGEN BOND; HYDROPHOBICITY; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FAMILY; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; ANIMAL; BINDING SITE; CHEMISTRY; COMPARATIVE STUDY; GENETICS; GENOME; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN DATABASE;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; DATABASES, PROTEIN; DNA; DNA-BINDING PROTEINS; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SEQUENCE ALIGNMENT; ZINC FINGERS;

EID: 77949358476     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22525     Document Type: Article

References (55)

1. Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wuthrich K. Homeodomain-DNA. recognition. Cell 1994; 78:211-223.
2. Harrison SC, Aggarwal AK. DNA recognition by proteins with the helix-turn-helix motif. Annu Rev Biochem 1990; 59:933-969.
3. Luscombe NM, Austin SE, Berman HM, Thornton JM. An overview of the structures of protein-DNA complexes. Genome Biol 2000; 1:REVIEWS001.
4. Pabo CO, Sauer RT. Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 1992: 61:1053-1095.
5. Wolfe SA, Nekludova L, Pabo CO. DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct 2000;29:183-212.
6. Berg OG, von Hippel PH. Selection of DNA binding sites by regulatory proteins. Trends Biochem Sci 1988; 13:207-211.
7. 7. Choo Y, Klug A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA. 1994; 91:11168-11172. (Pubitemid 24349647)
8. Mandel-Gutfreund Y, Schueler O, Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J Mol Biol 1995; 253:370-382.
9. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol 1986; 188:415-431.
10. 10. Takeda Y, Sarai A, Rivera VM. Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc Natl Acad Sci USA 1989; 86: 439-443. (Pubitemid 19037760)
11. 11. Berman H, Henrick K, Nakamura. H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007;35(Database issue):D301-D303. (Pubitemid 46056219)
12. Luscombe NM, Laskowski RA, Thornton JM. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 2001; 29:2860-2874.
13. Mandel-Gutfreund Y, Baron A, Margalit H. A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac Symp Biocomput 2001; 6:139-150.
14. 14. Selvaraj S, Kono H, Sarai A. Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding. J Mol Biol 2002; 322: 907-915. (Pubitemid 35266502)
15. 15. Michael Gromiha M, Siebers JG, Selvaraj S, Kono H, Sarai A. Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J Mol Biol. 2004; 337:285-294. (Pubitemid 38293399)
16. 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.
17. Mirny LA, Gelfand MS. Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res 2002; 30:1704-1711.
18. 18. Raviscioni M, Gu P, Saltar M., Cooney AJ, Lichtarge O. Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity. J Mol Biol 2005; 350:402-415. (Pubitemid 40828903)
19. Morozov AV, Havranek JJ, Baker D, Siggia ED. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 2005; 33:5781-5798.
20. Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO. Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure 2001; 9:717-723.
21. 21. Siggers TW, Silkov A, Honig B. Structural alignment of proteinDNA interfaces: insights into the determinants of binding specificity. J Mol Biol 2005; 345:1027-1045. (Pubitemid 40092222)
22. Contreras-Moreira B, Collado-Vides J. Comparative footprinting of DNA-binding proteins. Bioinformatics 2006; 22:e74-e80.
23. Angarica VE, Perez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B. Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics 2008; 9: 436.
24. Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein sidechain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997; 267:1268-1282.
25. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247:536-540.
26. 26. Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001; 313:903-919. (Pubitemid 33063435)
27. 27. Lupyan D, Leo-Macias A, Ortiz AR. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 2005; 21: 3255-3263. (Pubitemid 41418439)
28. Defiance M, Janky R, Sand O, van Helden J. Using RSAT oligoanalysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoč 2008; 3:1589-1603.
29. 29. van Helden J, Rios AF, Collado-Vides J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 2000; 28:1808-1818. (Pubitemid 30199315)
30. 30. van Helden J, Andre B, Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 1998; 281:827-842. (Pubitemid 28408432)
31. Canutescu AA, Shelenkov AA, Dunbrack RL, Jr. A. graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003; 12:2001-2014.
32. 32. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA. DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 2008; 36(Database issue):D88-D92. (Pubitemid 351149701)
33. 33. Lukacs CM, Kučera R, Schildkraut I, Aggarwal AK. Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Nat Struct Biol. 2000; 7: 134-140. (Pubitemid 30082511)
34. 34. Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE. Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA. J Mol Biol 2007; 372:1227-1245. (Pubitemid 47374717)
35. Little EJ, Babic AC, Horton NC. Early interrogation and recognition of DNA sequence by indirect readout. Structure 2008; 16: 1828-1837.
36. 36. Huai Q, Colandene JD, Topal MD, Ke H. Structure of Nael-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Biol 2001; 8:665-669. (Pubitemid 32757923)
37. 37. Deibert M, Grazulis S, Janulaitis A, Siksnys V, Huber R. Crystal structure of Muni restriction endonuclease in complex with cognate DNA at .1.7 A resolution. EMBO J 1999; 18:5805-5816. (Pubitemid 29515657)
38. 38. Burt A, Koufopanou V. Homing endonuclease genes: the rise and fall and rise again of a selfish element. Curr Opin Genet Dev 2004; 14:609-615. (Pubitemid 39505364)
39. Stoddard BL. Homing endonuclease structure and function. Q Rev Biophys 2005; 38:49-95.
40. Locasale JW, Napoli AA, Chen S, Berman HM, Lawson CL. Signatures of protein-DNA recognition in free DNA binding sites. J Mol Biol 2009; 386:1054-1065.
41. 41. Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA. Topology of Type II REases revisited; structural classes and the common conserved, core. Nucleic Acids Res 2007; 35:2227-2237. (Pubitemid 47073710)
42. Lozada-Chavez I, Angarica VE, Collado-Vides J, ContrerasMoreira B. The role of DNA-binding specificity in the evolution of bacterial regulatory networks. J Mol Biol 2008; 379: 627-643.
43. 43. Kono H, Sarai A. Structure-based prediction of DNA target sites by regulatory proteins. Proteins 1999; 35:114-131. (Pubitemid 29128158)
44. Pabo CO, Sauer RT. Protein-DNA recognition. Annu Rev Biochem 1984; 53:293-321.
45. 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.
46. 46. Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams LD. P22 c2 repressor-operator complex: mechanisms of direct and indirect readout. Biochemistry 2008; 47:2325-2338. (Pubitemid 351304538)
47. 47. Belfort M, Roberts RJ. Homing endonucleases: keeping the house in order. Nucleic Acids Res 1997; 25:3379-3388. (Pubitemid 27359210)
48. 48. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali. A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000; 29:291-325. (Pubitemid 30599596)
49. 49. Siggers TW, Honig B. Structure-based prediction of C2H2 zinc-finger binding specificity; sensitivity to docking geometry. Nucleic Acids Res 2007; 35:1085-1097. (Pubitemid 46522964)
50. 50. Contreras-Moreira B, Branger PA, Collado-Vides J. TFmodeller: comparative modelling of protein-DNA complexes. Bioinformatics 2007; 23:1694-1696. (Pubitemid 47244462)
51. 51. Ahmad S, Gromiha MM, Sarai A. Analysis and prediction of DNAbinding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 2004; 20:477-486. (Pubitemid 38344327)
52. Spiro S, Gaston KL, Bell AI, Roberts RE, Busby SJ, Guest JR. Interconversion of the DNA-binding specificities of two related transcription regulators, CRP and FNR. Mol Microbiol 1990; 4:1831-1838.
53. 53. Madan Babu M, Teichmann SA. Evolution, of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 2003; 31:1234-1244. (Pubitemid 36284965)
54. 54. Bouhouche N, Syvanen M, Kado CI. The origin of prokaryotic C2H2 zinc finger regulators. Trends Microbiol 2000; 8:77-81. (Pubitemid 30100331)
55. 55. Martinez-Antonio A, Janga SC, Salgado H, Collado-Vides J. Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol 2006; 14:22-27. (Pubitemid 43063188)