Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment

Journal of Physical Chemistry B

Volumn 110, Issue 34, 2006, Pages 17240-17251

  Chocholoušová, Jana ^a   Feig, Michael ^a,b  

^a Michigan State University   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; DIELECTRIC DEVICES; ELECTROSTATICS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; PROTEINS; SOLVENTS;

COMPUTATIONAL COST; CONTINUUM DIELECTRIC ELECTROSTATICS; PROTEIN-DNA COMPLEX; SOLVENT SIMULATIONS;

DNA;

EID: 33748774659     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0627675     Document Type: Article

References (146)

1. Garvie, C. W.; Wolberger, C. Recognition of specific DNA sequences. Molecular Cell 2001, 8 (5), 937-946.
2. Schwabe, J. W. R. The role of water in protein DNA interactions. Curr. Opin. Struct. Biol. 1997, 7 (1), 126-134.
3. Janin, J. Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. Struct. Folding Design 1999, 7 (12), R277-R279.
4. Lane, A. N. Nmr-Studies of Dynamics in Nucleic-Acids. Prog. Nucl. Magn. Reson. Spectrosc. 1993, 25, 481-505.
5. 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 3-Dimensional Structures of Nucleic-Acids. Biophys. J. 1992, 63 (3), 751-759.
6. Hays, F. A.; Teegarden, A.; Jones, Z. J. R.; Harms, M.; Raup, D.; Watson, J.; Cavaliere, E.; Ho, P. S. How sequence defines structure: A crystallographic map of DNA structure and conformation. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (20), 7157-7162.
7. Williams, L. D. Between objectivity and whim: Nucleic acid structural biology. DNA Binders Relat. Subjects 2005, 253, 77-88.
8. Guzman, M. R.; Liquier, J.; Taillandier, E. Hydration and conformational transitions in DNA, RNA, and mixed DNA-RNA triplexes studied by gravimetry and FTIR spectroscopy. J. Biomol. Struct. Dyn. 2005, 23 (3), 331-339.
9. Andrashenko, V. V.; Kornilova, S. V.; Lapinos, L. E.; Hackl, E. V.; Galkin, V. L.; Grigoriev, D. N.; Blagoi, Y. P. IR-spectroscopic Studies of Divalent Metal Ion Effects on DNA Hydration. J. Mol. Struct. 1997, 408/409, 225-228.
10. Benevides, J. M.; Wang, A. H.-J.; Rich, A.; Kyogoku, Y.; Marel, G. A. van d.; Boom, J. H. v.; Thomas, G. J. The Raman Spectra of Single Crystals of r(GCG)d(CGC) and d(CCCCGGGG) as Model for A-DNA, their Structure Transitions in Aqueous Solution and Comparison with Double Helical Poly(dG)·Poly(dC). Biochemistry 1986, 25, 41-50.
11. Barkley, M. D.; Zimm, B. H. Theory of Twisting and Bending of Chain Macromolecules; Analysis of the Fluorescence Depolarization of DNA. J. Chem. Phys. 1979, 70, 2991-3007.
12. Häupl, T. Picosecond Fluorescence of Nucleic Acid Bases. Chem. Phys. Lett. 1997, 280, 520-524.
13. Cheatham, T. E.; Kollman, P. A. Molecular dynamics simulations of nucleic acids. Annu. Rev. Phys. Chem. 2000, 51, 435-471.
14. 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.; Cheatham, T. E., III Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
15. Cheatham, T. E. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 2004, 14 (3), 360-367.
16. Giudice, E.; Lavery, R. Simulations of nucleic acids and their complexes. Acc. Chem. Res. 2002, 35 (6), 350-357.
17. Beveridge, D. L.; Young, M. A.; Sprous, D. Modeling of DNA via Molecular Dynamics Simulation: Structure, Bending, and Conformational Transitions. In Molecular Modeling of Nucleic Acids; Leontis, N. B., Ed.; American Chemical Society: Washington, DC, 1997; pp 260-284.
18. Feig, M.; Pettitt, B. M. Experiment vs Force fields: DNA Conformation from Molecular Dynamics Simulations. J. Phys. Chem. B 1997, 101, 7361-7363.
19. Feig, M.; Pettitt, B. M. Structural Equilibrium of DNA Represented with Different Force Fields. Biophys. J. 1998, 75, 134-149.
20. Feig, M.; Pettitt, B. M. A Molecular Simulation Picture of DNA Hydration Around A- and B-DNA. Biopolymers (Nucleic Acid Sci.) 1998, 48, 199-209.
21. Norberg, J.; Nilsson, L. NMR Relaxation Times, Dynamics, and Hydration of a Nucleic Acid Fragment from Molecular Dynamics Simulations. J. Phys. Chem. 1995, 99, 14876-14884.
22. MacKerell, A. D., Jr.; Wiorkiewicz-Juczera, J.; Karplus, M. An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids. J. Am. Chem. Soc. 1995, 117, 11946-11975.
23. Banavali, N. K.; MacKerell, A. D. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol. 2002, 319, 141-160.
24. McConell, K. J.; Nirmala, R.; Young, M. A.; Ravishanker, G.; Beveridge, D. L. A Nanosecond Molecular Dynamics Trajectory for a B-DNA Double Helix: Evidence for Substates. J. Am. Chem. Soc. 1994, 116, 4461-4462.
25. 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. 1997, 73, 2313-2336.
26. Cheatham, T. E.; Kollman, P. A. Observation of the A-DNA to B-DNA Transition During Unrestrained Molecular Dynamics in Aqueous Solution. J. Mol. Biol. 1996, 259, 434-444.
27. Beveridge, D. L.; Maye, P. V.; Jayaram, B.; Ravishanker, G.; Mezei, M. Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Computer Simulation Studies. J. Biomol. Struct. Dyn. 1984, 2, 261-270.
28. Beveridge, D. L.; Swaminathan, S.; Ravishanker, G.; Withka, J. M.; Srinivasan, J.; Prevost, C.; Louise-May, S.; Langley, D. R.; DiCapua, F. M.; Bolton, P. H. Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers. In Water and Biological Macromolecules; Westhof, E., Ed.; CRC Press: Boca Raton, FL, 1993; pp 165-225.
29. Feig, M.; Pettitt, B. M. Crystallographic Water Sites from a Theoretical Perspective. Structure 1998, 6, 1351-1354.
30. Feig, M.; Pettitt, B. M. Modeling High-resolution Hydration Patterns in Correlation with DNA Sequence and Conformation. J. Mol. Biol. 1999, 286, 1075-1095.
31. Feig, M.; Pettitt, B. M. Sodium and Chlorine Ions as Part of the DNA Solvation Shell. Biophys. J. 1999, 77, 1769-1781.
32. Schneider, B.; Cohen, D. M.; Schleifer, L.; Srinivasan, A. R.; Olson, W. K.; Berman, H. M. A Systematic Method for Studying the Spatial Distribution of Water Molecules around Nucleic Acid Bases. Biophys. J. 1993, 65, 2291-2303.
33. Schneider, B.; Berman, H. M. Hydration of the DNA Bases is Local. Biophys. J. 1995, 69, 2661-2669.
34. Makarov, V.; Pettitt, B. M.; Feig, M. Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment Ace. Chem. Res. 2002, 35, 376-384.
35. Beveridge, D. L.; McConell, K. J.; Nirmala, R.; Young, M. A.; Vijayakumar, S.; Ravishanker, G. Recent Progress in Molecular Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent. ACS Symp. Ser. 1994, 568, 381-394.
36. Beveridge, D. L.; McConell, K. J.; Nirmala, R.; Young, M. A.; Vijayakumar, S.; Ravishanker, G. Molecular Dynamics Simulations of DNA and a Protein-DNA Complex Including Solvent. In Modelling of Biomolecular Structures and Mechanisms; Pullman, A., e.t al., Ed.; Kluwer Acade,oc Publishers: Dordrecht, The Netherlands, 1995; pp 409-423.
37. Tang, Y.; Nilsson, L. Interaction of Human SRY Protein with DNA: A Molecular Dynamics Study. Proteins 1998, 31, 417-433.
38. Tang, Y.; Nilsson, L. Molecular Dynamics Simulations of the Complex between Human U1A Protein and Hairpin II of U1 Small Nuclear RNA and of Free RNA in Solution. Biophys. J. 1999, 77, 1284-1305.
39. Kosztin, D.; Bishop, T. C.; Schulten, K. Binding of the Estrogen Receptor on DNA: The Role of Waters. Biophys. J. 1997, 73, 557-570.
40. Karplus, M. Molecular dynamics simulations of biomolecules. Acc. Chem. Res. 2002, 35, 321-323.
41. Makarov, V. A.; Feig, M.; Pettitt, B. M. Diffusion of Solvent around Biomolecular Solutes. A Molecular Dynamics Simulations Study. Biophys. J. 1998, 75, 150-158.
42. Leeuw, S. W. d.; Perram, J. W.; Smith, E. R. Simulation of Electrostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants. Proc. R. Soc., London A 1980, 373, 27-56.
43. Reed, M. S. C.; Flurchick, K. M. Investigation of Artifacts Due to Periodic Boundary Conditions. Comput. Phys. Commun. 1996, 95, 39-46.
44. Roux, B.; Simonson, T. Implicit Solvent Models. Biophys. Chem. 1999, 78, 1-20.
45. Honig, B.; Nicholls, A. Classical Electrostatics in Biology and Chemistry. Science 1995, 268, 1144-1149.
46. Baker, N.; Holst, M.; Wang, F. Adaptive Multilevel Finite Element Solution of the Poisson-Boltzmann Equation II. Refinement at Solvent-Accessible Surfaces in Biomolecular Systems. J. Comput. Chem. 2000, 21, 1343-1352.
47. Boschitsch, A. H.; Fenley, M. O.; Zhou, H.-X. Fast Boundary Element Method for the Linear Poisson-Boltzmann Equation. J. Phys. Chem. B 2002, 106, 2741-2754.
48. Holst, M.; Baker, N.; Wang, F. Adaptive Multilevel Finite Element Solution of the Poisson-Boltzmann Equation I. Algorithms and Examples. J. Comput. Chem. 2000, 21, 1319-1342.
49. Cortis, C. M.; Friesner, R. A. Numerical Solution of the Poisson-Boltzmann Equation Using Tetrahedral Finite-Element Meshes. J. Comput. Chem. 1997, 18, 1591-1608.
50. Warwicker, J.; Watson, H. C. Calculation of the Electric Potential in the Active Site Cleft due to α-Helix Dipoles. J. Mol. Biol. 1982, 157, 671-679.
51. Gilson, M. K.; Sharp, K. A.; Honig, B. H. Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment. J. Comput. Chem. 1987, 9, 327-335.
52. Prabhu, N. V.; Zhu, P. J.; Sharp, K. A. Implementation and testing of stable, fast implicit Solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. J. Comput. Chem. 2004, 25 (16), 2049-2064.
53. Lu, Q.; Luo, R. A Poisson-Boltzmann dynamics method with nonperiodic boundary condition. J. Chem. Phys. 2003, 119 (21), 11035-11047.
54. Luo, R.; David, L.; Gilson, M. K. Accelerated Poisson-Boltzmann Calculations for Static and Dynamic Systems. J. Comput. Chem. 2002, 23, 1244-1253.
55. Im, W.; Beglov, D.; Roux, B. Continuum Solvation Model: Computation of Electrostatic Forces from Numerical Solutions to the Poisson-Boltzmann Equation. Comput. Phys. Commun. 1998, 111, 59-75.
56. Bordner, A. J.; Huber, G. A. Boundary Element Solution of the Linear Poisson-Boltzmann Equation and a Multipole Method for the Rapid Calculation of Forces on Macromolecules in Solution. J. Comput. Chem. 2003, 24, 353-367.
57. Friedrichs, M.; Zhou, R. H.; Edinger, S. R.; Friesner, R. A. Poisson-Boltzmann analytical gradients for molecular modeling calculations. J. Phys. Chem. B 1999, 103, 3057-3061.
58. Sharp, K. Incorporating Solvent and Ion Screening into Molecular Dynamics Using the Finite-Difference Poisson-Boltzmann Method. J. Comput. Chem. 1991, 12, 454-468.
59. Fan, H.; Mark, A. E.; Zhu, J.; Honig, B. Comparative study of generalized Born models: Protein dynamics. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (19), 6760-6764.
60. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III New Analytical Approximation to the Standard Molecular Volume Definition And Its Application to Generalized Born Calculations. J. Comput. Chem. 2003, 24, 1348-1356.
61. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L., III Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures. J. Comput. Chem. 2004, 25, 265-284.
62. Im, W.; Lee, M. S.; Brooks, C. L., III Generalized Born model with a simple smoothing function. J. Comput. Chem. 2003, 24, 1691-1702.
63. Ghosh, A.; Rapp, C. S.; Friesner, R. A. Generalized Born Model Based on a Surface Integral Formulation. J. Phys. Chem. B 1998, 102, 10983-10990.
64. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
65. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii. J. Phys. Chem. A 1997, 101, 3005-3014.
66. Feig, M.; Brooks, C. L., III Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 2004, 14, 217-224.
67. Hawkins, G.; Cramer, C.; Truhlar, D. Pairwise descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 1995, 246, 122-129.
68. Onufriev, A.; Case, D. A.; Bashford, D. Effective Born Radii in the Generalized Born Approximation: The Importance of Being Perfect. J. Comput. Chem. 2002, 23, 1297-1304.
69. Scarsi, M.; Apostolakis, J.; Caflisch, A. Continuum electrostatic energies of macromolecules in aqueous solutions. J. Phys. Chem. A 1997, 101 (43), 8098-8106.
70. Bashford, D.; Case, D. A. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 2000, 51, 129-152.
71. Schaefer, M.; Froemmel, C. A Precise Analytical Method for Calculating the Electrostatic Energy of Macromolecules in Aqueous-Solution. J Mol. Biol. 1990, 216 (4), 1045-1066.
72. Dominy, B. N.; Brooks, C. L., III Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids. J. Phys. Chem. B 1999, 103, 3765-3773.
73. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III, Novel generalized Born methods. J. Chem. Phys. 2002, 116 (24), 10606-10614.
74. Lee, B.; Richards, F. M. Interpretation of Protein Structures-Estimation of Static Accessibility. J. Mol. Biol. 1971, 55, 379.
75. Richards, F. M. Areas, Volumes, Packing, and Protein-Structure Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176.
76. Nina, M.; Beglov, D.; Roux, B. Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations. J. Phys. Chem. 1997, 101, 5239-5248.
77. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988.
78. Zhu, J.; Shi, Y.; Liu, H. Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics. J. Phys. Chem. B 2002, 106, 4844-4853.
79. Swanson, J. M. J.; Adcock, S. A.; McCammon, J. A. Optimized radii for Poisson-Boltzmann calculations with the AMBER force field. J. Chem. Theory Comput. 2005, 1 (3), 484-493.
80. Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C. Investigation of salt bridge stability in a generalized born solvent model. J. Chem. Theory Comput. 2006, 2 (1), 115-127.
81. Banavali, N. K.; Roux, B. Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids. J. Phys. Chem. B 2002, 106, 11026-11035.
82. Rapp, C. S.; Friesner, R. A. Prediction of Loop Geometries Using a Generalized Born Model of Solvation Effects. Proteins 1999, 35, 173-183.
83. Calimet, N.; Schaefer, M.; Simonson, T. Protein Molecular Dynamics With the Generalized Born/ACE Solvent Model. Proteins 2001, 45, 144-158.
84. David, L.; Luo, R.; Gilson, M. K. Comparison of Generalized Born and Poisson Models: Energetics and Dynamics of HTV Protease. J. Comput. Chem. 2000, 21, 295-309.
85. Gallicchio, E.; Zhang, L. Y.; Levy, R. M. The SGB/NP Hydration Free Energy Model Based on the Surface Generalized Born Solvent Reaction Field and Novel Nonpolar Hydration Free Energy Estimators. J. Comput. Chem. 2002, 23, 517-529.
86. Liu, Y.; Beveridge, D. L. Exploratory Studies of Ab Initio Protein Structure Prediction; Multiple Copy Simulated Annealing AMBER Energy Functions, and a Generalized Born/Solvent Accessibility Solvation Model. Proteins 2002, 46, 128-146.
87. Xia, B.; Tsui, V.; Case, D. A.; Dyson, H. J.; Wright, P. E. Comparison of protein solution structures refined by molecular dynamics simulation in a vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 2002, 22, 317-331.
88. Zhang, L. Y.; Gallicchio, E.; Friesner, R. A.; Levy, R. M. Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent. Poisson and Surface Generalized Born Models with Explicit Solvent Simulations, J. Comput, Chem. 2001, 22, 591-607.
89. Tsui, V.; Case, D. A. Theory and Applications of the Generalized Born Solvation Model in Macromolecular Simulations. Biopolymers (Nucleic Acid Sci.) 2001, 56, 275-291.
90. Felts, A. K.; Gallicchio, E.; Wallqvist, A.; Levy, R. M. Distinguishing Native Conformations of Proteins From Decoys With an Effective Free Energy Estimator Based on the OPLS All-Atom Force Field and the Surface Generalized Born Solvent Model. Proteins 2002, 48, 404-422.
91. Nymeyer, H.; Garcia, A. E. Simulation of the folding equilibrium of a-helical peptides: A comparison of the generalized Born approximation with explicit solvent. Proc. Natl. Aacd, Sci. U.S.A. 2003, 100, 13934-13939.
92. Bursulaya, B. D.; Brooks, C. L., III Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models. J. Phys. Chem. B 2000, 104 (51), 12378-12383.
93. Tanizaki, S.; Feig, M. A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes. J. Chem. Phys. 2005, 122, 124706.
94. Scarsi, M.; Apostolakis, J.; Caflisch, A. Comparison of a GB solvation model with explicit solvent simulations: Potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane. J. Phys. Chem. B 1998, 102 (18), 3637-3641.
95. Tsui, V.; Case, D. A. Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Am. Chem. Soc. 2000, 122, 2489-2498.
96. Wang, L.; HIngerty, B. E.; Srinivasan, A. R.; Olson, W. K.; Broyde, S. Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions. Biophys. J. 2002, 83, 382-406.
97. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices. J. Am. Chem. Soc. 1998, 120, 9401-9409.
98. Zacharias, M.; Sklenar, H. Analysis of the Stability of Looped-Out and Stacked-In Conformations of an Adenine Bulge in DNA Using a Continuum Model for Solvent and Ions. Biophys. J. 1997, 73, 2990-3003.
99. Denisov, V. P.; Carlstrom, G.; Halle, B. Kinetics of DNA Hydration. J. Mol. Biol. 1997, 268, 118-136.
100. Forsyth, V. T.; Mahendrasingam, A.; Pigram, W. J.; Greenall, R. J.; Bellamy, K.; Fuller, W.; Mason, S. A. Neutron Fibre Diffraction Study of DNA Hydration. Int. J. Biol. Macromol. 1989, 11, 236-240.
101. Poltev, V. I.; Malenkov, G. G.; Gonzalez, E. J.; Teplukhin, A. V.; Rein, R.; Shibata, M.; Miller, J. H. Modeling DNA Hydration: Comparison of Calculated and Experimental Hydration Properties of Nucleic Acid Bases. J. Biomol. Struct. Dyn. 1996, 13, 717-725.
102. Tao, N. J.; Linsway, S. M.; Rupprecht, A. Structure of DNA Hydration Shells Studied by Raman Spectroscopy. Biopolymers 1989, 28, 1019-1030.
103. Chalikian, T. V.; Völker, J.; Srinivasan, A. R.; Olson, W. K.; Breslauer, K. J. The Hydration of Nucleic Acid Duplexes as Assessed by a Combination of Volumetric and Structural Techniques. Biopolymers 1999, 50, 459-471.
104. Ewald, P. P. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 1921, 64, 253-287.
105. Sagui, C.; Darden, T. A. Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.
106. Cheatham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations on Solvated Biomolecular Sys tems: The Particle Mesh Ewald Method. Leads to Stable Trajectories of DNA, RNA, and Proteins. J. Am. Chem. Soc. 1995, 117, 4193-4194.
107. Norberg, J.; Nilsson, L. On the truncation of long-range electrostatic interactions in DNA. Biophys. J. 2000, 79 (3), 1537-1553.
108. Shui, X.; McFail-Isom, L.; Hu, G. G.; Williams, L. D. The B-DNA Dodecamer at High Resolution Reveals a Spine of Water on Sodium. Biochemistry 1998, 37, 8341-8355.
109. Denisov, V. P.; Halle, B. Sequence-specific binding of counterions to B-DNA. Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (2), 629-633.
110. Anderson, C. F.; Record, M. T. Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu. Revi. Biophys. Biophys. Chem. 1990, 19, 423-465.
111. Manning, G. S. The Molecular Theory of Polyelectrolyte Solutions with Applications to the Electrostatic Properties of Polynucleotides. Q. Rev. Biophys. 1978, 11, 179-246.
112. Young, M. A.; Jayaram, B.; 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. 1997, 119, 59-69.
113. Ponomarev, S. Y.; Thayer, K. M.; Beveridge, D. L. Ion motions in molecular dynamics simulations on DNA. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (41), 14771-14775.
114. Cheatham, T. E.; Young, M. A. Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers 2000, 56 (4), 232-256.
115. Nishimura, Y.; Torigoe, C.; Tsuboi, M. Salt Induced B-A Transition of Poly(dG)·Poly(dC) and the Stabilization of A Form by its Methylation. Nucleic Acids Res. 1986, 14, 2737-2748.
116. Drew, H. R.; Wing, R. M.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R. E. Structure of a B-DNA Dodecamer: Conformation and Dynamics. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 2179-2183.
117. Drew, H. R.; Dickerson, R. E. Structure of a B-DNA Dodecamer. III. Geometry of Hydration. J. Mol. Biol. 1981, 151, 535-556.
118. MacKerell, A. D., Jr.; Banavali, N. K. All-Atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution. J. Comput. Chem. 2000, 21, 105-120.
119. Allen, M. D.; Yamasaki, K.; Ohme-Takagi, M.; Tateno, M.; Suzuki, M. A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. Embo J. 1998, 17 (18), 5484-5496.
120. Foloppe, N.; MacKerell, A. D., Jr. All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. J. Comput. Chem. 2000, 21, 86-104.
121. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, J. D.; Evanseck, M. J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586-3.616.
122. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400-1415.
123. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 2004, 126, 698-699.
124. Chocholousova, J.; Feig, M. Balancing an Accurate Representation of the Molecular Surface in Generalized Born Formalisms with Integrator Stability in Molecular Dynamics Simulations. J. Comput. Chem. 2006, 27, 719-729.
125. Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects. Theor. Chin. Acta 1999, 101, 426-434.
126. Tjandta, N.; Tate, S.; Ono, A.; Kainosho, M.; Bax, A. The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase. J. Am. Chem. Soc. 2000, 122 (26), 6190-6200.
127. Lu, X. J.; Olson, W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 2003, 31 (17), 5108-5121.
128. Pastor, R. W.; Brooks, B. R.; Szabo, A. An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms. Mol. Phys. 1988, 65 (6), 1409-1419.
129. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimisation, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
130. Feig, M.; Karanicolas, J.; Brooks, C. L., III MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology. J. Mol. Graph. Model. 2004, 22, 377-395.
131. Cheatham, T. E., III: ptraj - analysis module of AMBER.
132. Dickerson, R. E. DNA Bending: The Prevalence of Kinkiness and the Virtues of Normality. Nucleic Acids Res. 1998, 26, 1906-1926.
133. MacKerell, A. D., Jr.; Banavali, N. K. All-Atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution. J. Comput. Chem. 2000, 21, 105-120.
134. 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. 1983, 163, 129-146.
135. Giudice, E.; Varnai, P.; Lavery, R. Base pair opening within B-DNA: Free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res. 2003, 31, 1434-1443.
136. Pan, Y. P.; MacKerell, A. D. Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res. 2003, 31 (24), 7131-7140.
137. Pan, Y. P.; MacKerell, A. A conformational switch involving local base pair opening in duplex RNA. Biophys. J. 2004, 86 (1), 145A-145A.
138. van Aalten, D. M. F.; Erlanson, D. A.; Verdine, G. L.; Joshua-Tor, L. A structural snapshot of base-pair opening in DNA. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (21), 11809-11814.
139. Dornberger, U.; Leijon, M.; Fritzsche, H. High base pair opening rates in tracts of GC base pairs. J. Biol. Chem. 1999, 274 (11), 6957-6962.
140. Wang, Y.; Thomas, G. A.; Peticolas, W. L. A Duplex of the Oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) Forms an A to B Conformational Junction in Concentrated Salt Solutions. J. Biomol. Struct. Dyn. 1989, 6, 1177-1187.
141. Cheatham, T. E.; Crowley, M. F.; Fox, T.; Kollman, P. A. A Molecular Level Picture of the Stabilization of A-DNA in Mixed Ethanol-Water Solutions. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 9626-9630.
142. Cheatham, T. E.; Kollman, P. A. Insight into the Stabilization of A-DNA by Specific Ion Association: Spontaneous B-DNA to A-DNA Transitions Observed in Molecular Dynamics Simulations of d(ACCC-GCGGGT)$_2$ in the Presence of Hexaamminecobalt(III). Structure 1997, 15, 1297-1311.
143. Wahl, M. C.; Sundaralingam, M. Crystal Structures of A-DNA Duplexes. Biopolymers (Nucleic Acid Sci.) 1997, 44, 45-63.
144. Debye, P.; Huckel, E. The theory of electrolytes I. The lowering of the freezing point and related occurrences. Phys. Z. 1923, 24, 185-206.
145. Debye, P.; Huckel, E. The theory of the electrolyte II-The border law for electrical conductivity. Phys. Z. 1923, 24, 305-325.
146. Baucom, J.; Transue, T.; Fuentes-Cabrera, M.; Krahn, J. M.; Darden, T. A.; Sagui, C. Molecular dynamics simulations of the d(CCA-ACGTTGGX2) decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields. J. Chem. Phys. 2004, 121 (14), 6998-7008.