RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

Journal of Molecular Biology

Volumn 269, Issue 3, 1997, Pages 326-341

  Auffinger, Pascal ^a   Westhof, Eric ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

Hydration; Methylguanine; Particle mesh Ewald; Pseudouridine; tRNA

Indexed keywords

AMMONIA; ASPARTIC ACID TRANSFER RNA; GUANINE DERIVATIVE; PHOSPHATE; PSEUDOURIDINE; WATER;

ANTICODON; ARTICLE; ELECTRICITY; HYDRATION; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; RNA BINDING; RNA CONFORMATION; RNA STRUCTURE;

EID: 0031566427     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1022     Document Type: Article

References (74)

1. 2+in RNA structure and function. Progress in Nucleic Acid Research and Molecular Biology. 1996;Academic Press.
2. Glncomplexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry. 33:1994;7560-7567.
3. Auffinger P., Beveridge D. L. A simple test for evaluating the truncation effects in simulation of systems involving charged groups. Chem. Phys. Letters. 234:1995;413-415.
4. Aspanticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys. J. 71:1996;940-954.
5. Aspin aqueous solution with counterions. J. Am. Chem. Soc. 117:1995;6720-6726.
6. Asp: structuring effects of C-H.O hydrogen bonds and of long-range hydration forces. J. Am. Chem. Soc. 118:1996;1181-1189.
7. Auffinger P., Louise-May S., Westhof E. Hydration of C-H groups in tRNA. Farad. Discuss. 103:1997;151-174.
8. Baeyens K. J., De Bondt H. L., Holbrook S. R. Structure of an RNA double helix including uracil-uracil base-pairs in an internal loop. Nature Struct. Biol. 2:1995;56-62.
9. Benevides J. M., Thomas G. J. A solution structure for poly(rA).poly(dT) with different furanose pucker and backbone geometry in rA and dT strands and intrastrands hydrogen bonding of adenine 8CH. Biochemistry. 27:1988;3868-3873.
10. Berendsen H. J. C., Grigera J. R., Straatsma T. P. The missing term in effective pair potential. J. Phys. Chem. 97:1987;6269-6271.
11. Berman H. M., Olson W. K., Beveridge D. L., Westbrook J., Gelbin A., Demeny T., Hsieh S. H., Srinivasan A. R. The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
12. Betzel C., Lorenz S., Fürste J. P., Bald R., Zhang M., Schneider T. R., Wilson K. S., Erdmann V. A. Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure. FEBS Letters. 351:1994;159-164.
13. Björk G. R., Wikström P. M., Byström A. S. Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science. 244:1989;986-989.
14. Bolton P. H., Kearns D. R. Hydrogen bonding of the 2′ OH in RNA. Biochim. Biophys. Acta. 517:1978;329-337.
15. Cate J. H., Gooding A. R., Podell E., Zhou K. H., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain - principles of RNA packing. Science. 273:1996;1678-1685.
16. Cheatham T. E., III, 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.
17. 2determined by NMR. Nucl. Acids Res. 24:1996;3693-3699.
18. Cruse W. B. T., Saludjian P., Biala E., Strazewski P., Prangé T. Structure of a mispaired RNA double helix at 1.6-Å resolution and implications for the prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA. 91:1994;4160-4164.
19. Darden T., York D., Pedersen L. Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:1993;10089-10092.
20. Davis D. R. Stabilization of RNA stacking by pseudouridine. Nucl. Acids Res. 23:1995;5020-5026.
21. Phefrom hisT mutants: a structural role for pseudouridine. Biochemistry. 30:1991;4223-4231.
22. 2. J. Mol. Biol. 209:1989;459-474.
23. 4′on DNA conformation. Proc. Natl Acad. Sci. USA. 92:1995;180-184.
24. Egli M., Portmann S., Usman N. RNA hydration: a detailed look. Biochemistry. 35:1996;8489-8494.
25. Engler E., Wipff G. MD Draw: A Program of Graphical Representation of Molecular Dynamics Trajectories. 1994;Université Louis Pasteur de Strasbourg.
26. 2in a nonsalt solution. Biopolymers. 32:1992;1035-1059.
27. 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.
28. Forester T. R., McDonald I. R. Molecular dynamics studies of the behavior of water molecules and small ions in concentrated solutions of polymericB -DNA. Mol. Phys. 72:1991;643-660.
29. Fritsch V., Westhof E. Three-center hydrogen bonds in DNA: molecular dynamics of poly(dA).poly(dT). J. Am. Chem. Soc. 113:1991;8271-8277.
30. Fritsch V., Ravishanker G., Beveridge D. L., Westhof E. Molecular dynamics simulations of poly(dA)-(dT): comparisons between implicit and explicit solvent representations. Biopolymers. 33:1993;1537-1552.
31. Alaby alanyl-tRNA synthetase. Science. 271:1996;195-197.
32. Hall K. B., McLauglin L. W. Properties of pseudouridine N1 imino protons located in the major groove of an A -form RNA duplex. Nucl. Acids Res. 20:1992;1883-1889.
33. Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. 1991;Springer-Verlag, Berlin.
34. Karplus P. A., Faerman C. Ordered water in macromolecular structure. Curr. Opin. Struct. Biol. 4:1994;770-776.
35. Kitson D. H., Avbelj F., Moult J., Nguyen D. T., Mertz J. E., Hadzi D., Hagler A. T. On achieving better than 1 Å accuracy in a simulation of a large protein: Streptomyces griseus protease A. Proc. Natl Acad. Sci. USA. 90:1993;8920-8924.
36. Kochoyan M., Leroy J. L. Hydration and solution structure of nucleic acids. Curr. Opin. Struct. Biol. 5:1995;329-333.
37. Kopka M. L., Fratini A. V., Drew H. R., Dickerson R. E. Ordered water structure around a B -DNA dodecamer. A quantitative study. J. Mol. Biol. 163:1983;129-146.
38. Laaksonen A., Nilsson L. G., Jönsson B., Teleman O. Molecular dynamics simulation of double helix Z -DNA in solution. Chem. Phys. 129:1989;175-183.
39. Leonard G. A., Hunter W. N. Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 Å resolution. J. Mol. Biol. 234:1993;198-208.
40. Lietzke S. E., Barnes C. L., Berglund J. A., Kundrot C. E. The structure of an RNA dodecamer shows how tandem U-U base-pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure. 4:1996;917-930.
41. Louise-May S., Auffinger P., Westhof E. Calculation of nucleic acid conformation. Curr. Opin. Struct. Biol. 6:1996;289-298.
42. Lu M., Draper D. E. Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large ribosomal RNA. J. Mol. Biol. 244:1994;572-585.
43. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:1990;585-610.
44. Pearlman D. A., Kim S. H. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211:1990;171-187.
45. Pearlman, D. A. Case, D. A. Caldwell, J. W. Ross, W. S. Cheatham, T. E, III, Ferguson, D. M. Seibel, G. L. Singh, U. C. Weiner, P. K. Kollman, P. A. 1994, AMBER 4.1, San Francisco, California.
46. Pearlman D. A., Case D. A., Caldwell J. W., Ross W. S., Cheatham T. E., III, DeBolt S., Ferguson D., Seibel G., Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91:1995;1-41.
47. Pley H. M., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:1994;68-74.
48. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 194:1976;796-806.
49. Rao S. T., Sundaralingam M. Stereochemistry of nucleic acids and their constituents. XIII. The crystal and molecular structure of 3′-O-acetyl-adenosine. Conformational analysis of nucleosides and nucleotides with syn glycosidic torsion angle. J. Am. Chem. Soc. 92:1970;4963-4970.
50. Aspupon binding to aspartyl-tRNA synthetase. Biochimie. 78:1996;624-631.
51. Asp. Science. 25:1991;1682-1689.
52. 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. Comput. Phys. 23:1977;327-336.
53. Saenger W. Principles of Nucleic Acid Structure. Springer Advanced Text in Chemistry. 1984;Springer-Verlag, New York.
54. Saenger W., Hunter W. N., Kennard O. DNA conformation is determined by economics in the hydration of phosphate groups. Nature. 324:1986;385-388.
55. Schneider B., Cohen D., Berman H. M. Hydration of DNA bases: analysis of crystallographic data. Biopolymers. 32:1992;725-750.
56. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
57. 3in the gas phase. J. Am. Chem. Soc. 109:1987;1607-1614.
58. Smith P. E., Pettitt B. M. Peptides in ionic solutions: a comparison of the Ewald and switching function techniques. J. Chem. Phys. 95:1991;8430-8441.
59. 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 sites. J. Biomol. Struct. Dynam. 6:1989;1093-1122.
60. Subramanian P., Beveridge D. L., Berman H. M. Monte-Carlo studies of the hydration of rGpC. Biopolymers. 29:1990a;771-783.
61. Subramanian P. S., Swaminathan S., Beveridge D. L. Theoretical account of the "spine of hydration" in the minor groove of d(CGCGAATTCGCG). J. Biomol. Struct. Dynam. 7:1990b;1161-1165.
62. Vovelle F., Goodfellow J. M. Hydration sites and hydration bridges around DNA helices. Westhof E. Water and Biological Macromolecules. 1993;The MacMillian Press Ltd, London.
63. Wahl M. C., Ban C., Sekharudu C., Ramakrishnan B., Sundaralingam M. Structure of the purine-pyrimidine alterning RNA double helix, r(GUAUAUA)d(C) with a 3′-terminal deoxy residue. Acta Crystallog. sect. D. 52:1996;655-667.
64. Westhof E. Hydration of oligonucleotides in crystals. Int. J. Biol. Macromol. 9:1987;186-192.
65. Westhof E. Water: an integral part of nucleic acid structure. Annu. Rev. Biophys. Biophys. Chem. 17:1988;125-144.
66. Westhof E. Structural water of nucleic acids. Vasilescu O., Jaz J., Packer L., Pullman B. Water and Ions in Biomolecular Systems - Advances in Life Science. 1990;Birkäuser Verlag, Berlin.
67. Westhof E. Structural water bridges in nucleic acids. Westhof E. Water and Biological Macromolecules. 1993;The MacMillian Press Ltd, London.
68. Westhof E., Beveridge D. L. Hydration of nucleic acids. Franks F. Water Science Reviews 5. 1990;Cambridge University Press, Cambridge.
69. Westhof E., Sundaralingam M. Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry. 25:1986;4868-4878.
70. Westhof E., Dumas P., Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184:1985;119-145.
71. Westhof E., Dumas P., Moras D. Hydration of transfer RNA molecules: a crystallographic study. Biochimie. 70:1988;145-165.
72. Wüthrich K. NMR-this other method for protein and nucleic acid structure determination. Acta. Crystallog. sect. D. 51:1995;249-270.
73. York D. M., Darden T., Pedersen L. G. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99:1993;8345-8348.
74. 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.