Changes in thermodynamic properties of dna base pairs in protein-dna recognition

Journal of Biomolecular Structure and Dynamics

Volumn 27, Issue 4, 2010, Pages 429-442

  Samanta, Sudipta ^a   Chakrabarti, Jaydeb ^a   Bhattacharyya, Dhananjay ^b  

^a S N BOSE NATIONAL CENTRE FOR BASIC SCIENCES   (India)

^b SAHA INSTITUTE OF NUCLEAR PHYSICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; CONTROLLED STUDY; CRYSTALLOGRAPHY; GENE STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN SECONDARY STRUCTURE; TATA BOX; THERMODYNAMICS;

EID: 75149142448     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2010.10507328     Document Type: Article

References (57)

1. Brown, T. A., 2002. Genomes. New York:Wiley-Liss.
2. Neidle, S., 2002. Nucleic Acid Structure and Recognition Oxford:Oxford University Press.
3. Jones, S., van Heyningen, P., Berman, H. M., and Thornton, J. M., 1999. J Mol Biol, 287:877–896.
4. Luscombe, N. M., and Thronton, J. M., 2002. J Mol Biol, 320:991–1009.
5. Mandel-Gutfreund, Y., Margalit, H., Jernigan, R. L., and Zhurkin, V. B., 1998. J Mol Biol, 277:1129–1140.
6. Nadassy, K., Wodak, S. J., and Janin, J., 1999. Biochemistry, 38:1999–2017.
7. Nelson, H. C., 1995. Current Opinion in Genetics and Development, 5:180–189.
8. Gurlie, R., and Zakrzewska, K., 2001. Theor Chem Acc, 106:83–90.
9. Gromiha, M. M., Siebers, J. G., Selvaraj, S., Kono, H., and Sarai, A., 2004. J Mol Biol, 337:285–294.
10. Hogan, M. E., and Austin, R. H., 1987. Nature, 329:263–266.
11. Sarai, A., Mazur, J., Nussinov, R., and Jernigan, R. L., 1989. Biochemistry, 28:7842–7849.
12. Harrington, R. E., and Winicov, I., 1994. Prog Nucl Acid Res & Mol Biol, 47:195–270.
13. O'Flanagan, A. R., Paillard, G., Lavery, R., and Sengupta, A. M., 2005. Bioinfomatics, 21:2254–2263.
14. Faiger, H., Ivanchenko, M., and Haran, T. E., 2007. Nucl Acids Res, 35:4409–4419.
15. Flatters, D., and Lavery, R., 1998. Biophys J, 75:372–381.
16. Librizzi, D. M., Brenowitz, M., and Willis, I. M., 1998. J Biol Chem, 273:4563–4568.
17. Luscombe, N. M., Laskowski, R. A., and Thornton, J. M., 1997. Nucl Acids Res, 25:4940–4945.
18. Kunkel, G. R., and Martinson, H. G., 1981. Nucl Acids Res, 9:6869–6888.
19. Albert, I., Mavrich, T. N., Tomsho, L. P., Qi, J., Zanton, S. J., Schuster, S. C., and Pugh, B. F., 2007. Nature, 446:572–576.
20. Hunter, C. A., 1993. J Mol Biol, 230:1025–1054.
21. Mohanty, D., and Bansal, D. M., 1991. J Biomol Struct Dyn, 9:127–142.
22. Samanta, S., Mukherjee, S., Chakrabarti, J., and Bhattacharyya, D., 2009. J Chem Phys, 130:115103–115114.
23. Brukner, I., Sanchez, R., Suck, D., and Pongor, S., 1995. EMBO, J14:1812–1818.
24. Lu, X., Shakked, Z., and Olson, W. K., 2000. J Mol Biol, 300:819–840.
25. Olson, W. K., Bansal, M., Burley, S. K., Dickerson, R. E., Gerstein, M., Harvey, S. C., Heinemann, U., Lu, X., Neidle, S., Shakked, Z., Sklenar, H., Suzuki, M., Tung, C., Westhof, E., Wolberger, C., and Berman, H. M., 2001. J Mol Biol, 313:229–237.
26. Bhattacharyya, D., and Bansal, M., 1990. J Biomol Struct Dynam, 8:539–572.
27. Dickerson, R. E., 1989. Nucl Acids Res, 17:1797–1803.
28. Bhattacharyya, D., Kundu, S., Thakur, A. R., and Majumdar, R., 1999. J Biomol Struct Dynam, 17:289–300.
29. Olson, W. K., Gorin, A. A., Lu, X., Hock, L. M., and Zhurkin, V., 1998. Proc Natl Acad Sci USA, 95:11163–11168.
30. Faiger, H., Ivanchenko, M., Cohen, I., and Haran, T. E., 2006. Nucl Acids Res, 34:104–119.
31. Subirana, J. A., and Faria, T., 1997. Biophys J, 73:333–338.
32. Bandyopadhyay, D., and Bhattacharyya, D., 2000. J Biomol Struct Dynam, 18:29–43.
33. Beveridge, D. L., Barreiro, G., Byun, K. S., Case, D. A., Cheatham, T. E., III, Dixit, S. B., Giudice, E., Lankas, F., Lavery, R., Maddocks, J. H., Osman, R., Seibert, E., Sklenar, H., Stoll, G., Thayer, K. M., Varnai, P., and Young, M. A., 2004. Biophys J, 87:3799–3813.
34. Dixit, S. B., Beveridge, D. L., Case, D. A., Cheatham, T. E., III, Giudice, E., Lankas, F., Lavery, R., Maddocks, J. H., Osman, R., Sklenar, H., Thayer, K. M., and Varnai, P., 2005. Biophys J, 89:3721–3740.
35. Bandyopadhyay, D., and Bhattacharyya, D., 2002. J Biomol Struct Dyn, 19:659–667.
36. Fujii, S., Kono, H., Takenaka, S., Go, N., and Sarai, A., 2007. Nucl Acids Res, 35:6063–6074.
37. Greenbaum, J. A., Pang, B., and Tullius, T. D., 2007. Genome Res, 17:947–953.
38. Chaikin, P. M., and Lubensky, T. C., 1998. Principles of Condensed matter Physics Cambridge
39. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2000. Nucl Acids Res, 28:235–242.
40. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983. J Comp Chem, 4:187–217.
41. Mackerell, A. D., and Banavali, N., 2000. J Comput Chem, 21:105–120.
42. Chandrasekaran, R., and Arnott, S., 1996. J Biomol Struct Dyn, 13:1015–1027.
43. Allen, M. P., and Tildesley, D. J., 1987. Computer Simulations of Liquids New York:Oxford University Press.
44. Bansal, M., Bhattacharyya, D., and Ravi, B., 1995. Comput Appl Biosci, 11:281–287.
45. Barlow, R. J., 1989. Statistics New York:Wiley.
46. Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr. 2000. “ Nucleic Acids Structures ”. In Properties and Functions California:University Science Books. Sausalito.
47. Mukherjee, S., Majumdar, S., and Bhattacharyya, D., 2005. J Phys Chem B, 109:10484–10492.
48. Schaftenaar, G., and Noordik, J. H., 2000. J Comput-Aided Mol Des, 14:123–134.
49. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. J., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M., and Montgomery, J. A., 1993. J Comput Chem, 14:1347–1363.
50. Morokuma, K., 1971. J Chem Phys, 55:1236–1244.
51. Jin, R., and Breslauer, K. J., 1988. Proc Natl Acad Sci USA, 85:8939–8942.
52. Snedecor, G. W., and Cochran, W. G., 1989. Statistical Methods Ames, Iowa:Iowa State University Press.
53. Kim, J. L., and Burley, S. K., 1994. Nature Struct & Mol Biol, 1:638–653.
54. Kim, J., Nikolov, D. B., and Burley, S. K., 1993. Nature, 365:520–527.
55. Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B., 1993. Nature, 365:512–520.
56. Pedone, F., Mazzei, F., and Barone, F., 2001. Biophys Chem, 94:175–184.
57. Fujimoto, B. S., and Schurr, J. M., 1990. Nature, 344:175–178.