Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids

Annual Reports in Computational Chemistry

Volumn 1, Issue C, 2005, Pages 75-89

  Cheatham III, Thomas E ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33847651004     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(05)01006-6     Document Type: Review

References (134)

1. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
2. Cheatham III T.E., Cieplak P., and Kollman P.A. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16 (1999) 845-862
3. Wang J., Cieplak P., and Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J. Comput. Chem. 21 (2000) 1049-1074
4. Foloppe N., and MacKerell Jr. A.D. All-atom empirical force field for nucleic acids. 1) Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21 (2000) 86-104
5. MacKerell Jr. A.D., and Banavali N. All-atom empirical force field for nucleic acids. 2) Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem. 21 (2000) 105-120
6. Langley D.R. Molecular dynamics simulations of environment and sequence dependent DNA conformation: the development of the BMS nucleic acid force field and comparison with experimental results. J. Biomol. Struct. Dyn. 16 (1998) 487-509
7. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
8. Sagui C., and Darden T.A. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Ann. Rev. Biophys. Biomol. Struct. 28 (1999) 155-179
9. Steinbach P.J., and Brooks B.R. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 15 (1994) 667-683
10. Norberg J., and Nilsson L. On the truncation of long-range electrostatic interactions in DNA. Biophys. J. 79 (2000) 1537-1553
11. Strauss J.K., Roberts C., Nelson M.G., Switzer C., and Maher III L.J. DNA bending by hexamethylene-tethered ammonium ions. Proc. Natl Acad. Sci. 93 (1996) 9515-9520
12. Young M.A., Jayaram B., and Beveridge D.L. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J. Am. Chem. Soc. 119 (1997) 59-69
13. Chiu T.K., Kaczor-Grzeskowiak M., and Dickerson R.E. Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG. J. Mol. Biol. 292 (1999) 589-608
14. McConnell K.J., and Beveridge D.L. DNA structure: what's in charge?. J. Mol. Biol. 304 (2000) 803-820
15. Hamelberg D., McFail-Isom L., Williams L.D., and Wilson W.D. Flexible structure of DNA: ion dependence of minor-groove structure and dynamics. J. Am. Chem. Soc. 122 (2001) 10513-10520
16. Hud N.V., and Polak M. DNA-cation interactions: the major and minor grooves are flexible ionophores. Curr. Opin. Struct. Biol. 11 (2001) 293-301
17. Tereshko V., Wilds C.J., Minasov G., Prakash T.P., Maier M.A., Howard A., Wawrzak Z., Manoharan M., and Egli M. Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res. 29 (2001) 1208-1215
18. Egli M. DNA-cation interactions: quo vadis?. Chem. Biol. 9 (2002) 277-286
19. + in the minor groove of B-DNA. Biopolymers 68 (2003) 471-485
20. Subirana J.A., and Soler-Lopez M. Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. Annu. Rev. Biophys. Biomol. Struct. 32 (2003) 27-45
21. Draper D.E. A guide to ions and RNA structure. RNA 10 (2004) 335-343
22. Auffinger P., Bielecki L., and Westhof E. Anion binding to nucleic acids. Structure 12 (2004) 379-388
23. Auffinger P., and Westhof E. RNA solvation: a molecular dynamics simulation perspective. Biopolymers 56 (2000) 266-274
24. Beveridge D.L., and McConnell K.J. Nucleic acids: theory and computer simulation, Y2K. Curr. Opin. Struct. Biol. 10 (2000) 182-196
25. Cheatham III T.E., and Kollman P.A. Molecular dynamics simulation of nucleic acids. Ann. Rev. Phys. Chem. 51 (2000) 435-471
26. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D.A., and Cheatham III T.E. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33 (2000) 889-897
27. Lane A.N., and Jenkins T.C. Thermodynamics of nucleic acids and their interactions with ligands. Q. Rev. Biophys. 33 (2000) 255-306
28. Cheatham III T.E., and Young M.A. Molecular dynamics simulations of nucleic acids: successes, limitations and promise. Biopolymers 56 (2001) 232-256
29. Major F., and Griffey R. Computational methods for RNA structure determination. Curr. Opin. Struct. Biol. 11 (2001) 282-286
30. Wang W., Donini O., Reyes C.M., and Kollman P.A. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Ann. Rev. Biophys. Biomol. Struct. 30 (2001) 211-243
31. Giudice E., and Lavery R. Simulations of nucleic acids and their complexes. Acc. Chem. Res. 35 (2002) 350-357
32. Lavery R., LeBrun A., Allemand J.F., Bensimon D., and Croquette V. Structure and mechanics of single biomolecules: experiment and simulation. J. Phys. Condens. Matter 14 (2002) R383-R414
33. Makarov V., Pettitt B.M., and Feig M. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc. Chem. Res. 35 (2002) 376-384
34. Norberg J., and Nilsson L. Molecular dynamics applied to nucleic acids. Acc. Chem. Res. 35 (2002) 465-472
35. Orozco M., Perez A., Noy A., and Javier Luque F. Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev. 32 (2003) 350-364
36. Sponer J., and Hobza P. Molecular interactions of nucleic acid bases. A review of quantum-chemical studies. Collect. Czech. Chem. Commun. 68 (2003) 2231-2282
37. Vorobjev Y.N. In silico modeling and conformational mobility of DNA duplexes. Mol. Biol. 37 (2003) 210-222
38. Beveridge D.L., Dixit S.B., Barreiro G., and Thayer K.M. Molecular dynamics simulation of DNA curvature and flexibility: helix phasing and premelting. Biopolymers 73 (2004) 380-403
39. Lankas F. DNA sequence-dependent deformability - insights from computer simulations. Biopolymers 73 (2004) 327-339
40. Cheatham III T.E., Brooks B.R., and Kollman P.A. Molecular modeling of nucleic acid structure. In: Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A. (Eds). Current Protocols in Nucleic Acid Chemistry Vol. 1 (2000), Wiley, New York 7.5.1, 7512
41. Cheatham III T.E., Brooks B.R., and Kollman P.A. Molecular modeling of nucleic acid structure: setup and analysis. In: Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A. (Eds). Current Protocols in Nucleic Acid Chemistry Vol. 1 (2001), Wiley, New York 7.10.1, 71018
42. Cheatham III T.E., Brooks B.R., and Kollman P.A. Molecular modeling of nucleic acid structure: electrostatics and solvation. In: Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A. (Eds). Current Protocols in Nucleic Acid Chemistry Vol. 1 (2001), Wiley, New York 7.9.1, 7921
43. Cheatham III T.E., Brooks B.R., and Kollman P.A. Molecular modeling of nucleic acid structure: energy and sampling. In: Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A. (Eds). Current Protocols in Nucleic Acid Chemistry Vol. 1 (2001), Wiley, New York 7.8.1, 7820
44. Hud N.V., and Plavec J. A unified model for the origin of DNA sequence-directed curvature. Biopolymers 69 (2003) 144-158
45. Cheatham III T.E. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 14 (2004) in press
46. Isaacs R.J., and Spielmann H.P. Insight into G-T mismatch recognition using molecular dynamics with time-averaged restraints derived from NMR spectroscopy. J. Am. Chem. Soc. 126 (2004) 583-590
47. Tolstorukov M.Y., Jernigan R.L., and Zhurkin V.B. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J. Mol. Biol. 337 (2004) 65-76
48. Bingman C.A., Zon G., and Sundaralingam M. Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis. J. Mol. Biol. 227 (1992) 738-756
49. Dickerson R.E., Goodsell D.S., and Neidle S. "...the tyranny of the lattice...". Proc. Natl Acad. Sci. USA 91 (1994) 3579-3583
50. Owczarzy R., You Y., Moreira B.G., Manthey J.A., Huang L., Behlke M.A., and Walder J.A. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43 (2004) 3537-3554
51. Reddy S.Y., Leclerc F., and Karplus M. DNA polymorphism: a comparison of force fields for nucleic acids. Biophys. J. 84 (2003) 1421-1449
52. Lankas F., Cheatham III T.E., Hobza P., Langowski J., Spackova N., and Sponer J. Critical effect of the N2 amino group on structure, dynamics and elasticity of DNA polypurine tracts. Biophys. J. 82 (2002) 2592-2609
53. Lankas F., Sponer J., Langowski J., and Cheatham III T.E. DNA base-pair step deformability inferred from molecular dynamics simulation. Biophys. J. 85 (2003) 2872-2883
54. Lankas F., Sponer J., Langowski J., and Cheatham III T.E. DNA deformability at the base pair level. J. Am. Chem. Soc. 126 (2004) 4124-4125
55. Varnai P., Djuranovic D., Lavery R., and Hartmann B. alpha/gamma transitions in the B-DNA backbone. Nucleic Acids Res. 30 (2002) 5398-5406
56. I. J. Am. Chem. Soc. 125 (2003) 14990-14991
57. Trieb M., Rauch C., Wellenzohn B., Wibowo F.R., Loerting T., and Liedl K.R. Dynamics of DNA: B-I and B-II phosphate backbone transitions. J. Phys. Chem. B 108 (2004) 2470-2476
58. Trieb M., Rauch C., Wellenzohn B., Wibowo F.R., Loerting T., Mayer E., and Liedl K.R. Daunomycin intercalation stabilizes distinct backbone conformations of DNA. J. Biomol. Struct. Dyn. 21 (2004) 713-724
59. Djuranovic D., and Hartmann B. DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Biopolymers 73 (2004) 356-368
60. Varnai P., and Lavery R. Base flipping in DNA: pathways and energetics studied with molecular dynamics simulations. J. Am. Chem. Soc. 124 (2002) 7272-7273
61. Giudice E., and Lavery R. Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations. J. Am. Chem. Soc. 125 (2003) 4998-4999
62. Giudice E., Varnai P., and Lavery R. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res. 31 (2003) 1434-1443
63. Huang N., Banavali N.K., and MacKerell Jr. A.D. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl Acad. Sci. 100 (2003) 68-73
64. Bosch D., Campillo M., and Pardo L. Binding of proteins to the minor groove of DNA: what are the structural and energetic determinants for kinking a basepair step?. J. Comput. Chem. 24 (2003) 682-691
65. Seibert E., Ross J.B.A., and Osman R. Role of DNA flexibility in sequence-dependent activity of uracil DNA glycosylase. Biochemistry 41 (2002) 10976-10984
66. Seibert E., Ross J.B.A., and Osman R. Contribution of opening and bending dynamics to specific recognition of DNA damage. J. Mol. Biol. 330 (2003) 687-703
67. Pinak M. 8-Oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: a molecular dynamics study. J. Comput. Chem. 24 (2003) 898-907
68. Allawi H.T., Kaiser M.W., Onufriev A.V., Ma W.P., Brogaard A.E., Case D.A., Neri B.P., and Lyamichev V.I. Modeling of flap endonuclease interactions with DNA substrate. J. Mol. Biol. 328 (2003) 537-554
69. Wellenzohn B., Flader W., Winger R.H., Hallbrucker A., Mayer E., and Liedl K.R. Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions. Biochemistry 41 (2002) 4088-4095
70. Byun K.S., and Beveridge D.L. Molecular dynamics simulations of papilloma virus E2 DNA sequences: dynamical models for oligonucleotide structures in solution. Biopolymers 73 (2004) 369-379
71. Arthanari H., McConnell K.J., Berger R., Young M.A., Beveridge D.L., and Bolton P.H. Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers 68 (2003) 3-15
72. Nguyen B., Lee M.P.H., Hamelberg D., Joubert A., Bailly C., Brun R., Neidle S., and Wilson W.D. Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove. J. Am. Chem. Soc. 124 (2002) 13680-13681
73. Nguyen B., Hamelberg D., Bailly C., Colson P., Stanek J., Brun R., Neidle S., and Wilson W.D. Characterization of a novel DNA minor-groove complex. Biophys. J. 86 (2004) 1028-1041
74. Tanious F.A., Hamelberg D., Bailly C., Czarny A., Boykin D.W., and Wilson W.D. DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives. J. Am. Chem. Soc. 126 (2004) 143-153
75. Fang Y.-Y., Ray B.D., Claussen C.A., Lipkowitz K.B., and Long E.C. Ni(II)-Arg-Gly-His-DNA interactions: investigation into the basis for minor groove binding and recognition. J. Am. Chem. Soc. 126 (2004) 5403-5412
76. Srinivasan J., Cheatham III T.E., Cieplak P., Kollman P.A., and Case D.A. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate helices. J. Am. Chem. Soc. 120 (1998) 9401-9409
77. Spackova N., Cheatham III T.E., Ryjacek F., Lankas F., van Meervelt L., Hobza P., and Sponer J. Molecular dynamics simulations and thermodynamic analysis of DNA-drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution. J. Am. Chem. Soc. 125 (2003) 1759-1769
78. Wellenzohn B., Loferer M.J., Trieb M., Rauch C., Winger R.H., Mayer E., and Liedl K.R. Hydration of hydroxypyrrole influences binding of ImHpPyPy-beta-Dp polyamide to DNA. J. Am. Chem. Soc. 125 (2003) 1088-1095
79. Nguyen D.H., Dieckmann T., Colvin M.E., and Fink W.H. Dynamics studies of a malachite green-RNA complex revealing the origin of the red-shift and energetic contributions of stacking interactions. J. Phys. Chem. B 108 (2004) 1279-1286
80. Gouda H., Kuntz I.D., Case D.A., and Kollman P.A. Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 68 (2003) 16-34
81. Swanson J.M.J., Henchman R.H., and McCammon J.A. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 86 (2004) 67-74
82. Rueda M., Kalko S.G., Javier Luque F., and Orozco M. The structure and dynamics of DNA in the gas phase. J. Am. Chem. Soc. 125 (2003) 8007-8014
83. Wong K.-Y., and Pettitt B.M. Orientation of DNA on a surface from simulation. Biopolymers 73 (2004) 570-578
84. Barnett R.N., Cleveland C.L., Joy A., Landman U., and Schuster G.B. Charge migration in DNA: ion-gated transport. Science 294 (2001) 567-571
85. Lewis J.P., Pikus J., Cheatham III T.E., Starikov E.B., Wang H., Tomfohr J., and Sankey O.F. A comparison of electronic states in periodic and aperiodic poly(dA)-poly(dT) DNA. Phys. Status Solidi (b) 233 (2002) 90-100
86. Lewis J.P., Cheatham III T.E., Wang H., Starikov E.B., and Sankey O.F. Dynamically amorphous character of electronic states in poly(dA)-poly(dT) DNA. J. Phys. Chem. B 107 (2003) 2581-2587
87. Bouvier B., Dognon J.P., Lavery R., Markovitsi D., Millie P., Onidas D., and Zakrzewska K. Influence of conformational dynamics on the exciton states of DNA oligomers. J. Phys. Chem. B 107 (2003) 13512-13522
88. Stefl R., Cheatham III T.E., Spackova N., Fadrna E., Berger I., Koca J., and Sponer J. Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamical analysis of the substates. Biophys. J. 85 (2003) 1787-1804
89. Avino A., Cubero E., Gonzalez C., Eritja R., and Orozco M. Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives. J. Am. Chem. Soc. 125 (2003) 16127-16138
90. Cubero E., Abrescia N.G.A., Subirana J.A., Javier Luque F., and Orozco M. Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex. J. Am. Chem. Soc. 125 (2003) 14603-14612
91. Wu M., Yan S., Patel D.J., Geacintov N.E., and Broyde S. Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability. Nucleic Acids Res. 30 (2002) 3422-3432
92. Yan S.X., Wu M., Patel D.J., Geacintov N.E., and Broyde S. Simulating structural and thermodynamic properties of carcinogen-damaged DNA. Biophys. J. 84 (2003) 2137-2148
93. Perlow R.A., and Broyde S. Extending the understanding of mutagenicity: structural insights into primer-extension past a benzo[a]pyrene diol epoxide-DNA adduct. J. Mol. Biol. 327 (2003) 797-818
94. Yan S.X., Wu M., Buterin T., Naegeli H., Geacintov N.E., and Broyde S. Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts. Biochemistry 42 (2003) 2339-2354
95. Sarzynska J., Nilsson L., and Kulinski T. Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations. Biophys. J. 85 (2003) 3445-3459
96. Kang X., Schafer R.H., and Kuntz I.D. Calculation of ligand-nucleic acid binding free energies with the generalized-Born model in DOCK. Biopolymers 73 (2004) 192-204
97. Banavali N.K., and Roux B. Atomic radii for continuum electrostatics calculations on nucleic acids. J. Phys. Chem. B 106 (2002) 11026-11035
98. Zakrzewska K. DNA deformation energetics and protein binding. Biopolymers 70 (2003) 414-423
99. Hall K.B., and Williams D.J. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations. RNA 10 (2004) 34-47
100. Sorin E.J., Engelhardt M.A., Herschlag D., and Pande V.S. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J. Mol. Biol. 317 (2002) 493-506
101. Sorin E.J., Rhee Y.M., Nakatani B.J., and Pande V.S. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys. J. 85 (2003) 790-803
102. Villescas-Diaz G., and Zacharias M. Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis. Biophys. J. 85 (2003) 416-425
103. De Castro L.F., and Zacharias M. DAPI binding to the DNA minor groove: a continuum solvent analysis. J. Mol. Recogn. 15 (2002) 209-220
104. Malliavin T.E., Gau J., Snoussi K., and Leroy J.L. Stability of the I-motif structure is related to the interactions between phosphodiester backbones. Biophys. J. 84 (2003) 3838-3847
105. Tsui V., and Case D.A. Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Am. Chem. Soc. 122 (2000) 2489-2498
106. Tsui V., and Case D.A. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopol. Nucleic Acid Sci. 56 (2001) 275-291
107. Cui G., and Simmerling C. Conformational heterogeneity observed in simulations of a pyrene-substituted DNA. J. Am. Chem. Soc. 124 (2002) 12154-12164
108. Cheng X., Hornak V., and Simmerling C. Improved conformational sampling through an efficient combination of mean-field simulation approaches. J. Phys. Chem. B 108 (2004) 426-437
109. Cheatham III T.E., and Brooks B.R. Recent advances in molecular dynamics simulation towards the reliable representation of biomolecules in solution. Theor. Chem. Acc. 99 (1998) 279-288
110. Hunenberger P.H., and McCammon J.A. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys. Chem. 78 (1999) 69-88
111. Weber W., Hunenberger P.H., and McCammon J.A. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J. Phys. Chem. B 104 (2000) 3668-3675
112. Kastenholz M.A., and Hunenberger P.H. Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice sums. J. Phys. Chem. B 108 (2004) 774-788
113. Mazur A.K. Titration in silico of reversible B↔A transitions in DNA. J. Am. Chem. Soc. 125 (2003) 7849-7859
114. Patra M., Karttunen M., Hyvonen M.T., Falck E., and Vattulainen I. Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions. J. Phys. Chem. B 108 (2004) 4485-4494
115. Patra M., and Karttunen M. Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties. J. Comput. Chem. 25 (2004) 678-689
116. + binding in the minor groove of DNA. J. Am. Chem. Soc. 126 (2004) in press
117. Darden T., Pearlman D., and Pedersen L.G. Ionic charging free energies: spherical versus periodic boundary conditions. J. Chem. Phys. 109 (1998) 10921-10935
118. Petrov A.S., Pack G.R., and Lamm G. Calculations of magnesium-nucleic acid site binding in solution. J. Phys. Chem. B 108 (2004) 6072-6081
119. 2 in the presence of hexaammine cobalt(III). Structure 5 (1997) 1297-1311
120. Cheatham III T.E., Crowley M.F., Fox T., and Kollman P.A. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc. Natl Acad. Sci. 94 (1997) 9626-9630
121. 2: major groove binding by one spermine molecule delays the A→B transition. J. Biomol. Struct. Dyn. 21 (2004) 469-487
122. 2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol. 10 (2003) 551-561
123. 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol. 335 (2004) 555-571
124. Cheatham III T.E., and Kollman P.A. Molecular dynamics simulations highlight the structural differences in DNA:DNA, RNA:RNA and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119 (1997) 4805-4825
125. Korolev N., Lyubartsev A.P., Laaksonen A., and Nordenskiold L. A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations. Nucleic Acids Res. 31 (2003) 5971-5981
126. Korolev N., Lyubartsev A.P., Laaksonen A., and Nordenskiold L. Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure. Biopolymers 73 (2004) 542-555
127. Pan Y.P., and MacKerell Jr. A.D. Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res. 31 (2003) 7131-7140
128. Reblova K., Spackova N., Sponer J.E., Koca J., and Sponer J. Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res. 31 (2003) 6942-6952
129. Reblova K., Spackova N., Stefl R., Csaszar K., Koca J., Leontis N.B., and Sponer J. Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys. J. 84 (2003) 3564-3582
130. * and TAR-aptamer. Nucleic Acids Res. 31 (2003) 4275-4284
131. Aci S., Ramstein J., and Genest D. Base pairing at the stem-loop junction in the SL1 kissing complex of HIV-1 RNA: a thermodynamic study probed by molecular dynamics simulation. J. Biomol. Struct. Dyn. 21 (2004) 833-839
132. Fadrna E., Spackova N., Stefl R., Koca J., Cheatham III T.E., and Sponer J. Molecular dynamics simulations of guanine quadruplex loops: advances and force field limitations. Biophys. J. 87 (2004) 227-242
133. Tung C.-S., Joseph S., and Sanbonmatsu K.Y. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nat. Struct. Biol. 9 (2002) 750-755
134. Sanbonmatsu K.Y., and Joseph S. Understanding discrimination by the ribosome: stability testing and goove measurement of codon-anticodon pairs. J. Mol. Biol. 328 (2003) 33-47