Directional shape complementarity at the protein-DNA interface

Journal of Molecular Recognition

Volumn 16, Issue 4, 2003, Pages 213-222

  Yeh, Ching Sheng ^a   Chen, Fang Ming ^a   Wang, Jaw Yuan ^a   Cheng, Tian Lu ^a   Hwang, Ming Jing ^b   Tzou, Wen Shyong ^a  

^a KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

^b INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

DNA conformation; Normal vector; Protein surface; Shape complementarity; Structural bioinformatics

Indexed keywords

DNA; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION;

EID: 0041627766     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.624     Document Type: Article

References (33)

1. Allemann RK, Egli M. 1997. DNA recognition and bending. Chem. Biol. 4: 643-650.
2. Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B. 1992. The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63: 751-759.
3. Blackburn GM, Gait MJ. 1996. Nucleic Acids in Chemistry and Biology. Oxford University Press: Oxford.
4. 1 subunit interface. Biopolymers 25: 1229-1247.
5. Connolly ML. 1992. Shape distributions of protein topography. Biopolymers 32: 1215-1236.
6. Crothers DM. 1998. DNA curvature and deformation in protein-DNA complexes: a step in the right direction. Proc. Natl Acad. Sci. USA 95: 15163-15165.
7. Dickerson RE. 1989. Definitions and nomenclature of nucleic acid structure parameters. J. Biomol. Struct. Dyn. 6: 627-634.
8. Dickerson RE. 1998. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucl. Acids Res. 26: 1906-1926.
9. Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO. 1996. Zif268 protein-DNA complex refined at 1.6Å: a model system for understanding zinc finger-DNA interactions. Structure 4: 1171-1180.
10. Härd T, Lundbäck T. 1996. Thermodynamics of sequence-specific protein-DNA interactions. Biophys. Chem. 62: 121-139.
11. Jones S, van Heyningen P, Berman HM, Thornton JM. 1999. Protein-DNA interactions: a structural analysis. J. Mol. Biol. 287: 877-896.
12. Kim Y, Geiger JH, Hahn S, Sigler PB. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365: 512-520.
13. Kono H, Sarai A. 1999. Structure-based prediction of DNA target sites by regulatory proteins. Proteins: Struct. Funct. Genet. 35: 114-131.
14. Lawrence MC, Colman PM. 1993. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234: 946-950.
15. Luscombe NM, Laskowski RA, Thornton JM. 1997. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucl. Acids Res. 25: 4940-4945.
16. Luscombe NM, Austin SE, Berman HM, Thornton JM. 2001a. An overview of the structures of protein-DNA complexes. Genome Biol. 1: reviews001.1-reviews001.37.
17. Luscombe NM, Laskowski RA, Thornton JM. 2001b. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucl. Acids Res. 29: 2860-2874.
18. Mandel-Gutfreund Y, Margalit H. 1998. Quantitative parameters for amino acid-base interactions: implications for prediction of protein-DNA binding sites. Nucl. Acids Res. 26: 2306-2312.
19. Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE. 2002. Dimerization allows DNA target site recognition by the NarL response regulator. Nat. Struct. Biol. 9: 771-778.
20. Murphy FV IV, Churchill MEA. 2000. Nonsequence-specific DNA recognition: a structural perspective. Structure 8: R83-R89.
21. Nadassy K, Wodak SJ, Janin J. 1999. Structural features of protein-nucleic acid recognition sites. Biochemistry 38: 1999-2017.
22. Nadassy K, Tomas-Oliveira I, Alberts I, Janin J, Wodak SJ. 2001. Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces. Nucl. Acids Res. 29: 3362-3376.
23. Norel R, Lin SL, Wolfson HJ, Nussinov R. 1994. Shape complementarity at protein-protein interfaces. Biopolymers 34: 933-940.
24. Norel R, Lin SL, Wolfson HJ, Nussinov R. 1995. Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. J. Mol. Biol. 252: 263-273.
25. Pabo CO, Sauer RT. 1992. Transcription factors: structural families and principles of DNA recognition. A. Rev. Biochem. 61: 1053-1095.
26. Patikoglou G, Burley SK. 1997. Eukaryotic transcription factor-DNA complexes. A. Rev. Biophys. Biomol. Struct. 26: 289-325.
27. Rhodes D, Schwabe JWR, Chapman L, Fairall L. 1996. Towards an understanding of protein-DNA recognition. Phil. Trans. Roy. Soc. Ser. B351: 501-509.
28. Segal DJ, Barbas CF III. 2000. Design of novel sequence-specific DNA-binding proteins. Curr. Opin. Chem. Biol. 4: 34-39.
29. Suzuki M, Gerstein M. 1995. Binding geometry of alpha-helices that recognize DNA. Proteins: Struct. Funct. Genet. 23: 525-535.
30. Suzuki M, Yagi N. 1994. DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. Proc. Natl Acad. Sci. USA 91: 12357-12361.
31. Travers AA. 1992. DNA conformation and configuration in protein-DNA complexes. Curr. Opin. Struct. Biol. 2: 71-77.
32. Vorobjev YN, Hermans J. 1997. SIMS: computation of a smooth invariant molecular surface. Biophys. J. 73: 722-732.
33. Young MA, Ravishanker G, Beveridge DL, Berman HM. 1995. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68: 2454-2468.