Role of hydrogen bonds in protein-dna recognition: A comparison of generalized born and finite difference poisson-boltzmann solvation treatments

Journal of Biomolecular Structure and Dynamics

Volumn 16, Issue 2, 1998, Pages 237-242

  Dixit, S B ^a   Jayaram, B ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA PROTEIN COMPLEX; HYDROGEN BOND; MATHEMATICAL ANALYSIS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

EID: 0031758857     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1998.10508242     Document Type: Article

References (38)

1. Seeman, N. C., Rosenberg, J. M., and Rich, A., 1973. Proc. Natl. Acad. Sci. USA, 73:804–808.
2. McClarin, J. A., Frederick, C. A., Wang, B.-C., Greene, P., Boyer, H. W., Grabel, J., and Rosenberg, J. M., 1986. Science, 249:1307–1309.
3. Otwinowski, Z., Schevitz, R. W., Zhang, R. G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., and Sigler, P. B., 1988. Nature, 335:321–329.
4. Matthews, B. W., 1988. Nature, 335:294–295.
5. Schultz, S. C., Shields, G. C., and Steitz, T. A., 1991. Science, 253:1001–1007.
6. Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y. W., Ebright, R. E., and Berman, H. M., 1996. J. Mol. Biol., 260:395–408.
7. Rice, P. A., Yang, S.-W., Mizuuchi, K., and Nash, H. A., 1996. Cell, 87:1295–1306.
8. Dickerson, R. E., 1998. Nucleic Acids Res, 26:1906–26.
9. Travers, A., 1993. DNA-Protein Internerions London:Chapman and Hall.
10. Suzuki, M., Brenner, S. E., Gerstein, M., and Yagi, N., 1995. Protein Engng., 8:319–328.
11. von Hippel, P. H., 1994. Science, 263:769–770.
12. Record, M. T., Jr, Anderson, C. F., Mills, P., Mossing, M., and Roe, J. H., 1985. Adv. Biophys., 20:109–135.
13. Spolar, R. S., and Record, M. T., Jr. 1994. Science, 263:777–784.
14. Jen-Jacobson, L., 1997. Biopoly., 44:153–180.
15. Chaires, J. B., 1997. Biopoly., 44:201–215.
16. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:5179–5197.
17. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheathem, T. E., III, Ferguson, D. M., Seibel, G. E., Singh, U. C., Weiner, P. K., and Kollman, P. A., 1995. Amber Vol. 41, San Francisco:University of California.
18. Honig, B., and Nicholls, A., 1995. Science, 268:1144–1149.
19. Gilson, M. K., and Honig, B., 1988. Proteins Struct. Fund. Genet., 4:7–18.
20. Still, W. C., Tempczyk, A., Hawley, R. C., and Hendrickson, T. J., 1990. J. Am. Chem. Soc., 112:6127–6129.
21. Hawkins, G. D., Cramer, C. J., and Truhlar, D. G., 1996. J. Phys. Chem., 100:19824–19839.
22. Hawkins, G. D., Cramer, C. J., and Truhlar, D. G., 1995. Chem. Phys. Lett., 246:122–129.
23. Jayaram, B., Liu, Y., and Beveridge, D. L., 1998. J. Chem. Phys., 109:1465–1471.
24. Jayaram, B., Sprous, D., and Beveridge, D. L., 1998. J. Phys. Chem, in press
25. Yang, A., and Honig, B., 1995. J. Mol. Biol., 252:351–365.
26. Froloff, N., Windemuth, A., and Honig, B., 1997. Protein Science, 6:1293–1301.
27. Misra, V. K., and Honig, B., 1995. Proc. Natl. Acad. Sci. USA, 92:4691–4695.
28. Misra, V. K., Hecht, J. L., Sharp, K. A., Friedman, R. A., and Honig, B., 1994. J. Mol. Biol., 238:264–280.
29. Jayaram, B., McConnell, K., Dixit, S. B., and Beveridge, D. L., 1998. J. Comp. Phys, submitted
30. Jayaram, B., McConnell, K., Dixit, S. B., and Beveridge, D. L., 1998. manuscript in preparation
31. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R., and Schneider, B., 1992. Biophys. J., 63:751–759.
32. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., 1977. J. Mol. Biol., 112:535–542.
33. NDB Codes of complexes studied:pde00l; pde002; pde003; pde009; pde0l15; pde017; pde020; pde022; pde025; pdeb08; pdr00l; pdr004; pdr008; pdr009; pdr0l0; pdr0l1
34. Lee, B. K., and Richards, F. M., 1971. J. Mol. Biol., 55:379–406.
35. 1993. Delphi Version 2.5 San Diego:Biosym Technologies.
36. Janin, J., 1995. Prog. Biophys. Mol. Biol., 64:145–156.
37. Dixit, S. B., Bhasin, R., Rajasekaran, E., and Jayaram, B., 1997. J. Chem. Soc. Faraday Trans, 93:1105–1113.
38. Sitkoff, D., Sharp, K. A., and Honig, B., 1994. J Phys. Chem., 98:1978–1988.