Water molecules in DNA recognition II: A molecular dynamics view of the structure and hydration of the trp operator

Journal of Molecular Biology

Volumn 282, Issue 4, 1998, Pages 859-873

  Bonvin, Alexandre M J J ^a   Sunnerhagen, Maria ^b   Otting, Gottfried ^b   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

^b S 171 77 ^*  (Sweden)

Author keywords

DNA hydration; Hydrogen bonds; Molecular dynamics; Residence time; trp operator

Indexed keywords

DOUBLE STRANDED DNA; WATER;

ARTICLE; CRYSTAL STRUCTURE; DIFFUSION; DNA CONFORMATION; DNA STRUCTURE; HYDRATION; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; OPERATOR GENE; PRIORITY JOURNAL; REPRESSOR GENE; SIMULATION;

EID: 0032475912     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2034     Document Type: Article

References (48)

1. Arnott S., Campbell-Smith P.J., Chandrasekaran R. Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA, and DNA-RNA helices. CRC Handbook of Biochemistry and Molecular Biology. 1976;411-422 CRC Press, Boca Raton, FL
2. Auffinger P., Beveridge D.L. A simple test for evaluating the truncation effects in simulations of systems involving charged groups. Chem. Phys. Letters. 234:1995;413-415
3. Aspanticodon hairpin. J. Mol. Biol. 269:1997;326-341
4. 6meA-T-C-G- a β-DNA helix with 10.6 base-pairs per turn. J. Mol. Biol. 231:1993;768-784
5. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J. Interaction models for water in relation to proteins hydration. Pullman B. Intermolecular Forces. 1981;331-342 Reidel, Dordrecht
6. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:1984;3684-3690
7. Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., Schneider B. The Nucleic Acid Database a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759
8. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.E. Jr, Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542
9. Beveridge D.L., Ravishanker G. Molecular dynamics studies of DNA. Curr. Opin. Struct. Biol. 4:1994;246-255
10. Billeter M., Güntert P., Louginbühl P., Wüthrich K. Hydration and DNA recognition by homeodomains. Cell. 85:1996;1057-1065
11. Brünger A.T. A memory-efficient fast Fourier transformation algorithm for crystallographic refinement on super-computers. Acta Crystallog. sect. A. 44:1989;270-282
12. Brünger A.T. X-PLOR Version 3.1 A System for X-ray Crystallography and NMR. 1993;Yale University Press, New Haven, CT
13. Brunne R.M., Liepinsh E., Otting G., Wüthrich K., van Gunsteren W.F. Hydration of proteins A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231:1993;1040-1048
14. Cheatham T.E., Miller J.L., Fox T., Darden T.A., Kollman P.A. Molecular dynamics simulations on solvated biomolecular systems the particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins. J. Am. Chem. Soc. 117:1995;4193-4194
15. DeLano W.L., Brünger A.T. Helix packing in proteins prediction and energetic analysis of dimeric, trimeric and tetrameric GCN4 coiled coil structures. Proteins: Struct. Funct. Genet. 20:1994;105-123
16. de Vlieg J., Berendsen H.J.C., van Gunsteren W.F. An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution. Proteins: Struct. Funct. Genet. 6:1989;104-127
17. Dickerson R.E., Goodsell D.S., Neidle S. "...the tyranny of the lattice..." Proc. Natl Acad. Sci. USA. 91:1994;3579-3583
18. Eriksson M.A.L., Härd T., Nilsson L. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys. J. 68:1995;402-426
19. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103:1995;8577-8593
20. Evans S.V. SETOR hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graphics. 11:1993;134-138
21. Gu W., Schoenborn B.P. Molecular dynamics simulation of hydration in myoglobin. Proteins: Struct. Funct. Genet. 22:1995;20-26
22. Hindman J.C. Relaxation processes in water viscosity, self-diffusion, and spin-lattice relaxation. A kinetic model. J. Chem. Phys. 60:1974;4488-4496
23. Hubbard S.J., Thornton J.M. "NACCESS", Computer Program. 1993;Department of Biochemistry and Molecular BiologyUniversity College, London
24. Hummer G., Soumpasis D.M. Statistical mechanical treatment of the structural hydration of biological macromolecules results for B-DNA. Phys. Rev. E50:1994;5085-5095
25. Hummer G., Garcia A.E., Soumpasis D.M. Hydration of nucleic acid fragments Comparison of theory and experiment for high-resolution crystal structures of RNA, DNA and DNA-drug complexes. Biophys. J. 68:1995;1639-1652
26. Joachimiak A., Haran T.E., Sigler P.B. Mutagenesis supports water mediated recognition in the trp repressor/operator system. EMBO J. 13:1994;367-372
27. 17O and some related results. Ber. Bunsenges Phys. Chem. 86:1982;215-221
28. Lawson C.L., Carey J. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature. 366:1993;178-182
29. Louise-May S., Auffinger P., Westhof E. Calculations of nucleic acid conformations. Curr. Opin. Struct. Biol. 6:1996;289-298
30. Lu X.-J., El Hussein M.A., Hunter C.A. Structure and conformation of helical nucleic acids analysis programs (SCHNAaP). J. Mol. Biol. 273:1997;668-680
31. Luty B.A., van Gunsteren W.F. Calculating electrostatic interactions using the particle-particle particle-mesh method with nonperiodic long-range interactions. J. Phys. Chem. 100:1996;2581-2587
32. Luty B.A., Tironi I.G., van Gunsteren W.F. Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J. Chem. Phys. 103:1995;3014-3021
33. Olson W.K., Gorin A.A., Lu X.-J., Hock L.M., Zhurkin V.B. DNA sequence-dependent deformability deduced from proteins-DNA crystal complexes. Proc. Natl Acad. Sci. USA. 1998;. in the press
34. Otwinowski Z., Schevitz R.W., Zhang R.G., Lawson C.L., Joachimiak A., Marmorstein R.Q., Luisi B.F., Sigler P.B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 335:1988;321-329
35. Ravishanker G., Swaminathan S., Beveridge D.L., Lavery R., Sklenar H. Conformational and helicoidal analysis of 30 ps of molecular dynamics on the d(CGCGAATTCGCG) double helix "Curves", dials and windows. J. Biomol. Struct. Dynam. 6:1998;669-700
36. Ryckaert J.-P., Ciccotti G., Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints molecular dynamics of n-alkanes. J. Comp. Phys. 23:1977;327-341
37. Schneider B., Berman H.M. Hydration of the DNA bases in local. Biophys. J. 69:1995;2661-2669
38. Shakked Z. The influence of the environment of DNA structures determined by X-ray crystallography. Curr. Opin. Struct. Biol. 1:1991;446-451
39. Shakked Z., Guzikevich-Guerstein G., Frolow F., Rabinovich D., Joachimiak A., Sigler P.B. Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature. 368:1994;469-473
40. Smith P.E., van Gunsteren W.F. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K. J. Chem. Phys. 100:1994;3169-3174
41. Smith S.A., Rajur S.B., McLaughlin L.W. Specific purine N7-nitrogens are critical for high affinity binding by the trp repressor. Nature Struct. Biol. 1:1994;18-22
42. Subramanian P.S., Beveridge D.L. A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG) Monte Carlo simulation and comparison with crystallographic ordered water site. J. Biomol. Struct. Dynam. 6:1989;1093-1122
43. Sunnerhagen M., Denisov V.P., Venu K., Bonvin A.M.J.J., Carey J., Halle B., Otting G. Water molecules in DNA recognition I Hydration lifetimes in the trp operator in solution measured by NMR spectroscopy. J. Mol. Biol. 282:1998;847-858
44. Tironi I.G., Sperb R., Smith P.E., van Gunsteren W.F. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102:1995;5451-5459
45. van Gunsteren W.F., Berendsen H.J.C. Computer simulation of molecular dynamics methodology, applications and perspectives in chemistry. Agnew. Chem. Int. Ed. Engl. 29:1990;992-1023
46. van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott W.R.P., Tironi I.G. Biomolecular Simulation: The GROMOS96 Manual and User guide. 1996;1-1042 Vdf Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland
47. York D.M., Yang W., Lee H., Darden T., Pedersen L.G. Toward the accurate modeling of DNA the importance of long-range electrostatics. J. Am. Chem. Soc. 117:1995;5001-5002
48. Young M.A., Ravishanker G., Beveridge D.L. A 5-nanosecond molecular dynamics trajectory for B-DNA analysis of structure, motions and solvation. Biophys. J. 73:1997;2313-2336