Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation

Biophysical Journal

Volumn 77, Issue 4, 1999, Pages 1782-1800

  Sen, Srikanta ^a   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; SOLVENT; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

AQUEOUS SOLUTION; ARTICLE; CRYSTAL STRUCTURE; DNA PROTEIN COMPLEX; MOLECULAR DYNAMICS; PROTEIN DNA INTERACTION; SOLVATION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0032846562     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77024-4     Document Type: Article

References (52)

1. Alexander, M., J. J. Bonvin, M. Sunnerhagen, G. Otting, and W. F. van Gunsteren. 1998. Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. J. Mol. Biol. 282:859-873.
2. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulations of Liquids. Oxford Science, Oxford.
3. Billeter, M. 1996. Homeodomain-type DNA recognition. Prog. Biophys. Molec. Biol. 56:211-225.
4. Billeter, M., P. Guntert, P. Luginbuhl, and K. Wuthrich. 1996. Hydration and DNA recognition by homeodomains. Cell. 85:1057-1065.
5. Billeter, M., Y. Q. Qian, G. Otting, M. Muller, W. J. Gehring, and K. Wuthrich. 1993. Determination of the nuclear magnetic resonance structure of an Antennapedia homeodomain-DNA complex. J. Mol. Biol. 234:1084-1093.
6. Bishop, T., D. Kosztin, and K. Schulten. 1997. How hormone receptor-DNA binding affects nucleosomal DNA. The role of Symmetry. Biophys. J. 72:2056-2067.
7. Bishop, T., and K. Schulten. 1996. Molecular dynamics study of glucocorticoid receptor-DNA binding. Proteins Struct. Funct. Genet. 24: 115-133.
8. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Com. Chem. 4:187-217.
9. Brooks, C. L., M. Karplus, and B. M. Pettitt. 1989. Proteins: a theoretical perspective of dynamics, structure and thermodynamics. In Advances in Chemical Physics. Wiley, New York. 61.
10. Brooks, III, C. L., and M. Karplus. 1983. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79:6312-6325.
11. Draper, D. E. 1993. Protein-DNA complexes: the cost of recognition. Proc. Natl. Acad. Sci. USA. 90:7429-7430.
12. Dickerson, R. E., and H. R. Drew. 1981. Structure of a B-DNA dodecamer II. Influence of base sequence on helix structure. J. Mol. Biol. 149: 761-786.
13. Duan, Y., P. Wilkosz, and J. M. Rosenberg. 1996. Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases. J. Mol. Biol. 264:546-555.
14. Duan, Y., P. Wilkosz, M. Crowley, and J. M. Rosenberg. 1997. Molecular dynamics simulation study of DNA Dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration. J. Mol. Biol. 272:553-572.
15. Erikssson, M., T. Härd, and L. Nilsson. 1995. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys. J. 68:402-426.
16. Erikssson, M., and L. Nilsson. 1995. Structure, thermodynamics and cooperativity of glucocorticoid receptor DNA-DNA-binding domain in complex with different response elements: molecular dynamics and free energy perturbation study. J. Mol. Biol. 253:453-472.
17. Feig, M., and B. M. Pettitt. 1997. Experiment vs. force fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B. 101:7361-7363.
18. Hirsch, S. D., and A. K. Aggarwal. 1995. Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J. 14:6280-6291.
19. Jeltsch, A., J. Alves, H. Wolfes, G. Maass, and A. Pingoud. 1994. Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA. Biochemistry. 33:10215-10219.
20. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
21. Kandadai, N. S., and M. R. Reddy. 1996. Solution structure of papin as studied by molecular mechanics and molecular dynamics techniques. J. Comp. Chem. 17:1328-1338.
22. Karplus, P. A., and C. Fearman. 1994. Ordered water in macromolecular structure. Curr. Opin. Struct. Biol. 4:770-776.
23. Kim, Y., J. C. Grable, R. Love, P. J. Green, and J. M. Rosenberg. 1990. Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science. 249:1307-1309.
24. Koneshan, S., J. C. Rasaiah, R. M. Lynden-Bell, and S. H. Lee. 1998. Solvent structure, dynamics, and ion mobility in aqueous solution at 25°C. J. Phys. Chem. B. 102:4193-4204.
25. Kosztin, D., T. C. Bishop, and K. Schulten. 1997. Binding of the estrogen receptor to DNA: the role of waters. Biophys. J. 73:557-570.
26. Lavery, R., and H. Sklenar. 1988. The definition of generalised helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6:63-91.
27. Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
28. Lesser, D. R., M. R. Kurpiewski, T. Waters, B. A. Connolly, and L. Jen-Jacobson. 1993. Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. Proc. Natl. Acad. Sci. USA. 90:7548-7552.
29. Lesser, D. R., M. R. Kurpiewski, and L. Jen-Jacobson. 1990. The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science. 250:776-785.
30. Lindahl, E., and O. Edholm. 1998. Solvent diffusion outside macromolecular surfaces. Phys. Rev. E. 57:791-796.
31. Luisi, B. F., W. X. Xu, Z. Otwinowski, L. P. Freedman, K. R. Yamamoto, and P. B. Siglar. 1991. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 352:497-505.
32. MacKerell, A. D. 1997. Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties. J. Phys. Chem. B. 101: 646-656.
33. MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Quo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics. Studies of proteins. J. Phys. Chem. B. 102:3586-3616.
34. MacKerell, Jr., A., J. Wiorkiewicz-Kuczera, and M. Karplus. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-11975.
35. McCammon J. A., and S. C. Harvey. 1987. Molecular Dynamics of Proteins and Nucleic Acids. Cambridge University Press, New York.
36. Misra, V., J. L. Hecht, K. A. Sharp, R. A. Friedman, and B. Honig. 1994. Salt effects on protein-DNA interactions: the λcI repressor and EcoRI endonuclease. J. Mol. Biol. 238:264-280.
37. Newman, M., T. Strzelecka, L. F. Dorner, I. Schildkraut, and A. K. Aggarwal. 1994. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 368:660-664.
38. Otwinoski, Z., R. W. Schevitz, R. G. Zhang, C. L. Lawson A. Joachimiak, R. Q. Marmorstein, B. F. Luisi, and P. B. Sigler. 1988. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 335: 321-329.
39. Qian, Y. Q., G. Otting, and K. Wuthrich. 1993. NMR detection of hydration water in the intermolecular interface of a protein-DNA complex. J. Am. Chem. Soc. 115:1189-1190.
40. Ravishankar, G., S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar. 1989. Conformational and helicoidal analysis of 30ps of molecular dynamics on the d(CGCGAATTCGCG) double helix. J. Biomol. Struct. Dyn. 6:669-699.
41. Robinson, C. R., and S. G. Sligar. 1993. Molecular recognition mediated by bound water: a mechanism for star activity of the restriction endonuclease EcoRI. J. Mol. Biol. 234:302-306.
42. Robinson, C. R., and S. G. Sligar. 1994. Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions. Biochemistry. 33:3787-3793.
43. Rosenberg, J. M. 1991. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 1:104-113.
44. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23: 327-341.
45. Schwabe, J. W., R. L. Chapman, J. T. Finch, and D. Rhodes. 1993. The crystal structure of the estrogen receptor DNA-binding domain bound to the DNA: how receptors discriminate between their response elements. Cell 75:567-578.
46. Sprous, D., Ma. A. Young, and D. L. Beveridge. 1998. Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture: theoretical considerations of the A 219 B transition. J. Phys. Chem. B. 102:4658-4667.
47. Szczelkun, M. D., P. Janscak, K. Firman, and S. E. Halford. 1997. Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I. J. Mol. Biol. 271:112-123.
48. van der Spoel D, P. J. van Maaren, and H. J. C. Berendsen. 1998. A systematic study of water models for molecular simulation: derivation of water models optimized for use with a reaction field. J. Chem. Phys. 108:10220-10230.
49. van Gunsteren 1993. Molecular dynamics and stochastic dynamics simulation: a primer. In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications, Vol 2. ed. by W. F. van Gunsteren, P. K. Weiner and A. J. Wilkinson, Leiden, The Netherlands ESCOM. 3-36.
50. Venclovas, C., A. Timinskas, and V. Syksnys. 1994. Five stranded β-sheet sandwiched with two α-helices: a structural link between restriction nucleases EcoRI and EcoRV. Proteins Struct. Funct. Genet. 20: 279-282.
51. Wing, R., H. R. Drew, T. Takano, C. Broka, S. Tanaka, K, Itakura, and R. E. Dickerson. 1980. Crystal structure analysis of a complete turn of B-DNA. Nature. 287:755-758.
52. Yang, Y., and B. M. Pettitt. 1996. B to A transition of DNA on the nanosecond time scale. J. Phys. Chem. B. 100:2564-2566.