Influence of DNA stiffness in protein-DNA recognition

Journal of Biotechnology

Volumn 117, Issue 2, 2005, Pages 137-145

  Gromiha, M Michael ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Binding specificity; DNA stiffness; Free energy change; Protein DNA recognition

Indexed keywords

CONFORMATIONS; FREE ENERGY; PARAMETER ESTIMATION; PROTEINS; STIFFNESS; ZINC;

CONFORMATIONAL PROPERTIES; DIRECT ATOMIC CONTACTS; DNA STIFFNESS; GENE EXPRESSION;

DNA;

ENDONUCLEASE; REPRESSOR PROTEIN; ZINC FINGER PROTEIN;

ARTICLE; CORRELATION ANALYSIS; DNA SEQUENCE; ENERGY; GENE MUTATION; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; QUANTITATIVE ANALYSIS;

EID: 16844382945     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2004.12.016     Document Type: Article

References (36)

1. P.V. Benos, A.S. Lapedes, and G.D. Stormo Probabilistic code for DNA recognition by proteins of the EGR family J. Mol. Biol. 323 2002 701 727
2. A.F. da Fonseca, and MA.M. de Aguiar Solving the boundary value problem for finite Kirchhoff rods Physica D 181 2003 53 69
3. A.O. Grillo, M.P. Brown, and C.A. Royer Probing the physical basis for trp repressor-operator recognition J. Mol. Biol. 287 1999 539 554
4. M.M. Gromiha Structure based sequence dependent stiffness scale for trinucleotides: a direct method J. Biol. Phys. 26 2000 43 50
5. M.M. Gromiha, M.G. Munteanu, A. Gabrielian, and S. Pongor Anisotropic elastic bending models of DNA J. Biol. Phys. 22 1996 227 243
6. M.M. Gromiha, M.G. Munteanu, I. Simon, and Pongor S The role of DNA bending in cro protein-DNA interactions Biophys. Chem. 69 1997 153 160
7. M.M. Gromiha, J.G. Siebers, S. Selvaraj, H. Kono, and A. Sarai Intermolecular and intramolecular readout mechanisms in protein-DNA recognition J. Mol. Biol. 337 2004 285 294
8. P.J. Hagerman Flexibility of DNA Annu. Rev. Biophys. Biophys. Chem. 17 1988 265 286
9. R.E. Harrington DNA curving and bending in protein-DNA recognition Mol. Microbiol. 6 1992 2549 2555
10. R.E. Harrington, and I. Winicov New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility Prog. Nucleic Acid Res. Mol. Biol. 47 1994 195 270
11. M.E. Hogan, and R.H. Austin Importance of DNA stiffness in protein-DNA binding specificity Nature 329 1987 263 266
12. S. Jones, P. van Heyningen, H.M. Berman, and J.M. Thornton Protein-DNA interactions: a structural analysis J. Mol. Biol. 287 1999 877 896
13. S. Koizumi, K. Suzuki, Y. Ogra, P. Gong, and F. Otuska Roles of zinc fingers and other regions of the transcription factor human MTF-1 in zinc-regulated DNA binding J. Cell Physiol. 185 2000 464 472
14. H. Kono, and A. Sarai Structure-based prediction of DNA target sites by regulatory proteins Proteins 35 1999 114 131
15. G.B. Koudelka, S.C. Harrison, and M. Ptashne Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and cro Nature 326 1987 886 888
16. N.M. Luscombe, and J.M. Thornton Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity J. Mol. Biol. 320 2002 991 1009
17. T.K. Man, J.S. Yang, and G.D. Stormo Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor Nucleic Acids Res. 32 2004 4026 4032
18. Y. Mandel-Gutfreund, and H. Margalit Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites Nucleic Acids Res. 26 1998 2306 2312
19. A.M. Martin, M.D. Sam, N.O. Reich, and J.J. Perona Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease Nat. Struct. Biol. 6 1999 269 277
20. J.C. Miller, and C.O. Pabo Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition J. Mol. Biol. 313 2001 309 315
21. F. Moreno-Herrero, J. Colchero, and A.M. Baro DNA height in scanning force microscopy Ultramicroscopy 96 2003 167 174
22. K. Nadassy, S.J. Wodak, and J. Janin Structural features of protein-nucleic acid recognition sites Biochemistry 38 1999 1999 2017
23. W.K. Olson, A.A. Gorin, X.J. Lu, L.M. Hock, and V.B. Zhurkin DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl. Acad. Sci. U.S.A. 95 1998 11163 11168
24. W.K. Olson, D. Swigon, and B.D. Coleman Implications of the dependence of the elastic properties of DNA on nucleotide sequence Philos. Transact. Ser. A Math. Phys. Eng. Sci. 362 2004 1403 1422
25. Z. Otwinowski, R.W. Schevitz, R.G. Zhang, C.L. Lawson, A. Joachimiak, R.Q. Marmorstein, B.F. Luisi, and P.B. Sigler Crystal structure of trp repressor/operator complex at atomic resolution Nature 335 1988 321 329
26. G.M. Poon, and RB Macgregor Jr. A thermodynamic basis of DNA sequence selectivity by the ETS domain of murine PU.1 J. Mol. Biol. 335 2004 113 127
27. P. Prabakaran, J. An, M.M. Gromiha, S. Selvaraj, H. Uedaira, H. Kono, and A. Sarai Thermodynamic database for protein-nucleic acid interactions (ProNIT) Bioinformatics 17 2001 1027 1034
28. D.W. Rodgers, and S.C. Harrison The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites Structure 1 1993 227 240
29. A. Sarai, and Y. Takeda Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically Proc. Natl. Acad. Sci. U.S.A. 86 1989 6513 6517
30. A. Sarai, J. Mazur, R. Nussinov, and R.L. Jernigan Sequence dependence of DNA conformational flexibility Biochemistry 28 1989 7842 7849
31. J.W. Schwabe The role of water in protein-DNA interactions Curr. Opin. Struct. Biol. 7 1997 126 134
32. E.B. Starikov Quantum chemistry of nucleic acids: how it could help and when it is necessary J. Photochem. Photobiol. C Photochem. Rev. 3 2002 147 164
33. T. Strick, J. Allemand, V. Croquette, and D. Bensimon Twisting and stretching single DNA molecules Prog. Biophys. Mol. Biol. 74 2000 115 140
34. M. Sundaralingam, and P.K. Ponnuswamy Stability of DNA duplexes with Watson-Crick base pairs: a predicted model Biochemistry 43 2004 16467 16476
35. B.R. Szymczyna, and C.H. Arrowsmith DNA binding specificity studies of four ETS proteins support an intramolecular readout mechanism of protein-DNA recognition J. Biol. Chem. 275 2000 28363 28370
36. A.A. Travers, and J.M. Thompson An introduction to the mechanics of DNA Philos. Transact. Ser. A Math. Phys. Eng. Sci. 362 2004 1265 1279