Show simple item record

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

dc.contributor.authorCheatham, Thomas E.
dc.contributor.authorBrooks, Bernard R.
dc.contributor.authorKollman, Peter A.
dc.date.accessioned2020-01-13T15:14:57Z
dc.date.available2020-01-13T15:14:57Z
dc.date.issued2001-07
dc.identifier.citationCheatham, Thomas E.; Brooks, Bernard R.; Kollman, Peter A. (2001). "Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation." Current Protocols in Nucleic Acid Chemistry 5(1): 7.9.1-7.9.21.
dc.identifier.issn1934-9270
dc.identifier.issn1934-9289
dc.identifier.urihttps://hdl.handle.net/2027.42/152997
dc.description.abstractThis unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all‐atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics.
dc.publisherWiley Periodicals, Inc.
dc.publisherOxford University Press
dc.titleMolecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.subject.hlbtoplevelEngineering
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152997/1/cpnc0709.pdf
dc.identifier.doi10.1002/0471142700.nc0709s05
dc.identifier.sourceCurrent Protocols in Nucleic Acid Chemistry
dc.identifier.citedreferenceSharp, K.A. and Honig, B. 1990. Electrostatic interactions in macromolecules: Theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19: 301 ‐ 332.
dc.identifier.citedreferenceSpolar, R.S. and Record, M.T. 1994. Coupling of local folding to site‐specific binding of proteins to DNA. Science 263: 777 ‐ 784.
dc.identifier.citedreferenceSprous, D., Young, M.A., and Beveridge, D.L. 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‐B transition. J. Phys. Chem. B. 102: 4658 ‐ 4667.
dc.identifier.citedreferenceSridharan, S., Nicholls, A., and Sharp, K.A. 1995. A rapid method for calculating derivatives of solvent accessible surface areas of molecules. J. Comp. Chem. 16: 1038 ‐ 1044.
dc.identifier.citedreferenceSteinbach, P.J. and Brooks, B.R. 1994. New spherical‐cutoff methods for long‐range forces in macromolecular simulation. J. Comp. Chem. 15: 667 ‐ 683.
dc.identifier.citedreferenceStill, W.C., Tempczyk, A., Hawley, R.C., and Hendrickson, T. 1990. Semi analytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112: 6127 ‐ 6128.
dc.identifier.citedreferenceTapia, O. and Velazquez, I. 1997. Molecular dynamics simulations of DNA with protein’s consistent GROMOS force field and the role of counterions’ symmetry. J. Am. Chem. Soc. 119: 5934 ‐ 5938.
dc.identifier.citedreferenceTironi, I.G., Sperb, R., Smith, P.E., and van Gunsteren, W.F. 1995. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102: 5451 ‐ 5459.
dc.identifier.citedreferenceTironi, I.G., Luty, B.A., and van Gunsteren, W.F. 1997. Space‐time correlated reaction field: A stochastic dynamical approach to the dielectric continuum. J. Chem. Phys. 106: 6068 ‐ 6075.
dc.identifier.citedreferenceToukmaji, A.Y. and Board, J.A.J. 1996. Ewald summation techniques in perspective: A survey. Comp. Phys. Comm. 95: 73 ‐ 92.
dc.identifier.citedreferenceTuckerman, M., Berne, B.J., and Martyna, G.J. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97: 1990 ‐ 2001.
dc.identifier.citedreferenceValleau, J.P. and Whittington, S.G. 1977. A guide to Monte Carlo for statistical mechanics: 1. Highways. In Statistical Mechanics A: A Modern Theoretical Chemistry,Vol. 5‐6 ( B.J. Berne, ed.),pp. 137 ‐ 167. Plenum Press, New York.
dc.identifier.citedreferencevan Gunsteren, W.F., Berendsen, H.J.C., and Rullman, J.A.C. 1978. Inclusion of a reaction field in molecular dynamics: Application to liquid water. Faraday Disc. 66: 58 ‐ 70.
dc.identifier.citedreferencevon Kitzing, E. and Diekmann, S. 1987. Molecular mechanics calculations of dA 12 ‐dT 12 and the curved molecule d(GCTCGAAAAA) 4 ‐d(TTTTTCGAGC) 4. Eur. Biophys. J. 15: 13 ‐ 26.
dc.identifier.citedreferenceWarshel, A. and Aqvist, J. 1991. Electrostatic energy and macromolecular function. Annu. Rev. Biophys. Biophys. Chem. 20: 267 ‐ 298.
dc.identifier.citedreferenceWarshel, A. and Levitt, M. 1976. Theoretical studies of enzyme reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103: 227 ‐ 249.
dc.identifier.citedreferenceWarshel, A. and Russell, S.T. 1984. Calculation of electrostatic interactions in biological systems and in solution. Quart. Rev. Biophys. 17: 283 ‐ 422.
dc.identifier.citedreferenceWeber, W., Hunenberger, P.H., and McCammon, J.A. 2000. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. J. Phys. Chem. B. 104: 3668 ‐ 3675.
dc.identifier.citedreferenceWesson, L. and Eisenberg, D. 1992. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Prot. Sci. 1: 227 ‐ 235.
dc.identifier.citedreferenceWilliams, R.L., Vila, J., Perrot, G., and Scheraga, H.A. 1992. Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor. Proteins 14: 110 ‐ 119.
dc.identifier.citedreferenceYork, D. and Yang, W. 1994. The fast Fourier Poisson method for calculating Ewald sums. J. Chem. Phys. 101: 3298 ‐ 3300.
dc.identifier.citedreferenceZacharias, M. and Sklenar, H. 1997. 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. 73: 2990 ‐ 3003.
dc.identifier.citedreferenceZauhar, R.J. 1991. The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations. J. Comp. Chem. 12: 575 ‐ 583.
dc.identifier.citedreferenceZhurkin, V.B., Ulyanov, N.B., Gorin, A.A., and Jernigan, R.L. 1991. Static and statistical bending of DNA evaluated by Monte Carlo calculations. Proc. Natl. Acad. Sci. U.S.A. 88: 7046 ‐ 7050.
dc.identifier.citedreferenceAllen, M.P. and Tildesley, D.J. 1987. Computer Simulation of Liquids. Oxford University Press Oxford.
dc.identifier.citedreferenceAqvist, J. 1990. Ion‐water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94: 8021 ‐ 8024.
dc.identifier.citedreferenceAuffinger, P. and Beveridge, B.L. 1995. A simple test for evaluating the truncation effects in simulations of systems involving charged groups. Chem. Phys. Lett. 234: 413 ‐ 415.
dc.identifier.citedreferenceBader, J.S. and Chandler, D. 1992. Computer simulation study of the mean forces between ferrous and ferric ions in water. J. Phys. Chem. 96: 6423 ‐ 6427.
dc.identifier.citedreferenceBashford, D. and Case, D.A. 2000. Generalized Born models of molecular solvation effects. Annu. Rev. Phys. Chem. 51: 129 ‐ 152.
dc.identifier.citedreferenceBashford, D. and Karplus, M. 1990. pKa’s of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochem. 29: 10219 ‐ 10225.
dc.identifier.citedreferenceBeglov, D. and Roux, B. 1994. Finite representation of in infinite bulk system: Solvent boundary potential for computer simulations. J. Chem. Phys. 100: 9050 ‐ 9063.
dc.identifier.citedreferenceBerendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., and Haak, J.R. 1984. Molecular dynamics with coupling to an external bath. J. Comp. Phys. 81: 3684 ‐ 3690.
dc.identifier.citedreferenceBerendsen, H.J.C., Grigera, J.R., and Straatsma, T.P. 1987. The missing term in effective pair potentials. J. Phys. Chem. 91: 6269 ‐ 6274.
dc.identifier.citedreferenceBerkowitz, M.L. and McCammon, J.A. 1982. Molecular dynamics with stochastic boundary conditions. Chem. Phys. Lett. 90: 215 ‐ 217.
dc.identifier.citedreferenceBeveridge, D.L., Swaminathan, S., Ravishanker, G., Withka, J.M., Srinivasan, J., Prevost, C., Louise‐May, S., Langley, D.R., DiCapua, F.M., and Bolton, P.H. 1993. Molecular dynamics simulations on the hydration,structure and motions of DNA oligomers. In Water and Biological Molecules ( E. Westhof, ed.)pp. 165 ‐ 225. Macmillan Press, New York.
dc.identifier.citedreferenceBiesiadecki, J.J. and Skeel, R.D. 1993. Dangers of multiple time step methods. J. Comp. Phys. 109: 318 ‐ 328.
dc.identifier.citedreferenceBogusz, S., Cheatham, T.E. III, and Brooks, B.R. 1998. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential. J. Chem. Phys. 108: 7070 ‐ 7084.
dc.identifier.citedreferenceBoresch, S. and Steinhauser, O. 1997. Presumed versus real artifacts of the Ewald summation technique: The importance of dielectric boundary conditions. Ber. Bunsenges. Phys. Chem. 101: 1019 ‐ 1029.
dc.identifier.citedreferenceBorn, M. 1920. Volumen der Hydratationswärme der Ione. Z. Phys. Chem. 1: 45 ‐ 48.
dc.identifier.citedreferenceBrooks, C.L., Brunger, A., and Karplus, M. 1985. Active site dynamics in protein molecules: A stochastic boundary‐molecular dynamics approach. Biopolymers 24: 843 ‐ 865.
dc.identifier.citedreferenceBrooks, C.L. III., Karplus, M., and Pettitt, B.M. 1988. Proteins. A theoretical perspective of dynamics, structure, and thermodynamics. In Advances in Chemical Physics,Vol. 71 ( I. Prigogine, and S.A. Rice, eds.) John Wiley & Sons New York.
dc.identifier.citedreferenceChallacombe, M., White, C., and Head‐Gordon, M. 1997. Periodic boundary conditions and the fast multipole method. J. Chem. Phys. 107: 10131 ‐ 10140.
dc.identifier.citedreferenceCheatham, T.E. III. and Kollman, P.A. 1998. Molecular dynamics simulation of nucleic acids in solution: How sensitive are the results to small perturbations in the force field and environment. In Structure,Motion,Interactions and Expression of Biological Macromolecules ( M. Sarma and R. Sarma, eds.)pp. 99 ‐ 116. Adenine Press, Schenectady, New York.
dc.identifier.citedreferenceCheatham, T.E. III. and Kollman, P.A. 2000. Molecular dynamics simulation of nucleic acids. Annu. Rev. Phys. Chem. 51: 435 ‐ 471.
dc.identifier.citedreferenceCheatham, T.E. III., Miller, J.L., Fox, T., Darden, T.A., and Kollman, P.A. 1995. 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: 4193 ‐ 4194.
dc.identifier.citedreferenceCheatham, T.E. III., Crowley, M.F., Fox, T., and Kollman, P.A. 1997. A molecular level picture of the stabilization of A‐DNA in mixed ethanol‐water solutions. Proc. Natl. Acad. Sci. U.S.A. 94: 9626 ‐ 9630.
dc.identifier.citedreferenceCheng, Y.‐K. and Pettitt, B.M. 1992. Hoogsteen versus reverse‐Hoogsteen base pairing in DNA triplex helices. J. Am. Chem. Soc. 114: 4465 ‐ 4474.
dc.identifier.citedreferenceCheng, Y.‐K. and Pettitt, B.M. 1995. Solvent effects on model d(CG‐G) 7 and d(TA‐T) 7 DNA triplex helices. Biopolymers 35: 457 ‐ 473.
dc.identifier.citedreferenceCramer, C.J. and Truhlar, D.G. 1995. Continuum solvation models: Classical and quantum mechanical implementations. In Reviews in Computational Chemistry,Vol. 6 ( K.D. Lipkowitz and D.B. Boyd, eds.)pp. 1 ‐ 72. VCH, New York.
dc.identifier.citedreferenceDaggett, V., Kollman, P.A., and Kuntz, I.D. 1991. Molecular dynamics simulations of small peptides: Dependence on dielectric model and pH. Biopolymers 31: 285 ‐ 304.
dc.identifier.citedreferenceDang, L.X. and Pettitt, B.M. 1987. Chloride ion pairs in water. J. Am. Chem. Soc. 109: 5531 ‐ 5532.
dc.identifier.citedreferenceDarden, T.A., York, D.M., and Pedersen, L.G. 1993. Particle mesh Ewald: An N log( N ) method for Ewald sums in large systems. J. Chem. Phys. 98: 10089 ‐ 10092.
dc.identifier.citedreferenceDarden, T.A., Pedersen, L.G., Toukmaji, A.Y., Crowley, M.F., and Cheatham, T.E. III. 1997. Eighth SIAM conference on parallel processing for scientific computing, Minneapolis, Minn. Society for Industrial and Applied Mathematics, Philadelphia.
dc.identifier.citedreferenceDavis, M.E. and McCammon, J.A. 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90: 509 ‐ 521.
dc.identifier.citedreferenceDeLeeuw, S.W., Perram, J.M., and Smith, E.R. 1980. Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants. Proc. R. Soc. Lond. A373: 27 ‐ 56.
dc.identifier.citedreferenceDill, K.A. 1990. Dominant forces in protein folding. Biochemistry 29: 7133 ‐ 7155.
dc.identifier.citedreferenceDing, H.Q., Karasawa, N., and Goddard, W.A. 1992. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 97: 4309 ‐ 4315.
dc.identifier.citedreferenceDrew, H.R. and Dickerson, R.E. 1981. Structure of a B‐DNA dodecamer. III. Geometry of hydration. J. Mol. Biol. 151: 535 ‐ 556.
dc.identifier.citedreferenceEisenberg, D. and McLachlan, A.D. 1986. Solvation energy in protein folding and binding. Nature 319: 199 ‐ 203.
dc.identifier.citedreferenceEssex, J.W. and Jorgensen, W.L. 1995. An empirical boundary potential for water droplet simulations. J. Comp. Chem. 16, 951 ‐ 972.
dc.identifier.citedreferenceEssmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., and Pedersen, L.G. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577 ‐ 8593.
dc.identifier.citedreferenceEwald, P. 1921. Investigations of crystals by means of Roentgen rays. Ann. Phys. (Leipzig) 64: 253 ‐ 264.
dc.identifier.citedreferenceFeller, S.E., Zhang, Y., Pastor, W., and Brooks, B.R. 1995. Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 103: 4613 ‐ 4621.
dc.identifier.citedreferenceFeller, S.E., Pastor, R.W., Rojnuckarin, A., Bogusz, S., and Brooks, B.R. 1996. Effect of electrostatic force truncation on interfacial and transport properties of water. J. Phys. Chem. 100: 17011 ‐ 17020.
dc.identifier.citedreferenceFigueirido, F., Del Buono, G.S., and Levy, R.M. 1997. On finite‐size corrections to the free energy of ionic hydration. J. Phys. Chem. 101: 5622 ‐ 5623.
dc.identifier.citedreferenceFlatters, D., Zakrzewska, K., and Lavery, R. 1997. Internal coordinate modeling of DNA: Force field comparisons. J. Comp. Chem. 18: 1043 ‐ 1055.
dc.identifier.citedreferenceFox, T. and Kollman, P.A. 1996. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the X‐ray structure “maintained.” Proteins 25: 315 ‐ 334.
dc.identifier.citedreferenceFraczkiewicz, R. and Braun, W. 1998. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comp. Chem. 19: 319 ‐ 333.
dc.identifier.citedreferenceFriedman, H. 1975. Image approximation to the reaction field. Mol. Phys. 29: 1533 ‐ 1543.
dc.identifier.citedreferenceFriedman, R.A. and Honig, B. 1992. The electrostatic contribution to DNA base‐stacking interactions. Biopolymers 32: 145 ‐ 159.
dc.identifier.citedreferenceFriedman, R.A. and Honig, B. 1995. A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys. J. 69: 1528 ‐ 1535.
dc.identifier.citedreferenceFritsch, V., Ravishanker, G., Beveridge, D.L., and Westhof, E. 1993. Molecular dynamics simulations of poly(dA)‐poly(dT): Comparisons between implicit and explicit solvent representations. Biopolymers 33: 1537 ‐ 1552.
dc.identifier.citedreferenceGilson, M.K. 1995. Theory of electrostatic interactions in macromolecules. Curr. Opin. Struct. Biol. 5: 216 ‐ 223.
dc.identifier.citedreferenceGilson, M.K. and Honig, B. 1991. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Comp. Aided Mol. Des. 5: 5 ‐ 20.
dc.identifier.citedreferenceGilson, M.K., Sharp, K.A., and Honig, B.H. 1987. Calculating the electrostatic potential of molecules in solution: Method and error assessment. J. Comp. Chem. 9: 327 ‐ 335.
dc.identifier.citedreferenceGilson, M.K., Davis, M.E., Luty, B.A., and McCammon, J.A. 1993. Computation of electrostatic forces on solvated molecules using the Poisson‐Boltzmann equation. J. Phys. Chem. 97: 3591 ‐ 3600.
dc.identifier.citedreferenceGreengard, L. 1988. The Rapid Evaluation of Potential Fields in Particle Systems. MIT Press, Cambridge, Mass.
dc.identifier.citedreferenceGreengard, L. 1994. Fast algorithms for classical physics. Science 265: 909 ‐ 914.
dc.identifier.citedreferenceGreengard, L. and Rokhlin, V. 1989. On the evaluation of electrostatic interactions in molecular modeling. Chem. Scrip. 29A: 139 ‐ 144.
dc.identifier.citedreferenceHarvey, S.C. 1989. Treatment of electrostatic effects in macromolecular modeling. Proteins 5: 78 ‐ 92.
dc.identifier.citedreferenceHawkins, G.D., Lynch, G.C., Giesen, D.J., Rossi, I., Storer, J.W., Liotard, D.A., Cramer, C.J., and Thular, D.G. 1996. AMSOL (QCPE Bull. 16,11), Minnesota, Minn.
dc.identifier.citedreferenceHawkins, G.D., Cramer, C.J., and Truhlar, D.G. 1997. Parameterized model for aqueous free energies of solvation using geometry‐dependent atomic surface tensions with implicit electrostatics. J. Phys. Chem. B. 101: 7147 ‐ 7157.
dc.identifier.citedreferenceHingerty, B.E., Ritchie, R.H., Ferrell, T.L., and Turner, J.E. 1985. Dielectric effects in biopolymers: The theory of ionic saturation revisited. Biopolymers 24: 427 ‐ 439.
dc.identifier.citedreferenceHockney, R.W. and Eastwood, J.W. 1981. Computer simulation using particles. McGraw‐Hill, New York.
dc.identifier.citedreferenceHoover, W.G. 1985. Canonical dynamics: Equilibrium phase distributions. Phys. Rev. A. 31: 1695 ‐ 1697.
dc.identifier.citedreferenceHummer, G., Soumpasis, D.M., and Neumann, M. 1993. Computer simulations do not support Cl‐Cl pairing in aqueous NaCl solution. Mol. Phys. 81: 1155 ‐ 1163.
dc.identifier.citedreferenceHummer, G., Pratt, L.R., and Garcia, A. 1997. Ion sizes and finite‐size corrections for ionic‐solvation free energies. J. Chem. Phys. 107: 9275 ‐ 9277.
dc.identifier.citedreferenceJayaram, B. and Beveridge, D.L. 1996. Modeling DNA in aqueous solutions: Theoretical and computer simulation studies on the ion atmosphere of DNA. Annu. Rev. Biophys. Biomol. Struct. 25: 367 ‐ 394.
dc.identifier.citedreferenceJorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., and Klein, M.L. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79: 926 ‐ 935.
dc.identifier.citedreferenceKang, Y.K., Nemethy, G., and Scheraga, H.A. 1988. Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model. J. Chem. Phys. 79: 926 ‐ 935.
dc.identifier.citedreferenceKing, G. and Warshel, A. 1989. A surface constrained all‐atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91: 3647 ‐ 3661.
dc.identifier.citedreferenceKirkwood, J.G. 1939. The dielectric polarization of liquids. J. Chem. Phys. 7: 911 ‐ 919.
dc.identifier.citedreferenceLebrun, A. and Lavery, R. 1996. Modelling extreme stretching of DNA. Nucl. Acids Res. 24: 2260 ‐ 2267.
dc.identifier.citedreferenceLebrun, A., Shakked, Z., and Lavery, R. 1997. Local DNA stretching mimics the distortion caused by TATA box‐binding protein. Proc. Natl. Acad. Sci. U.S.A. 94: 2993 ‐ 2998.
dc.identifier.citedreferenceLee, F.S., Chu, Z.T., and Warshel, A. 1993. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the Polaris and Enzymix programs. J. Comp. Chem. 14: 161 ‐ 185.
dc.identifier.citedreferenceLeGrand, S.M. and Merz, K.M. 1993. Rapid approximation to molecular surface area via the use of boolean logic and look‐up tables. J. Comp. Chem. 14: 349 ‐ 352.
dc.identifier.citedreferenceLevitt, M. 1983. Computer simulation of DNA double‐helix dynamics.Cold Spring Harbor. Symp. Quant. Biol. 47: 251 ‐ 262.
dc.identifier.citedreferenceLevitt, M., Hirshberg, M., Sharon, R., and Daggett, V. 1995. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp. Phys. Comm. 91: 215 ‐ 231.
dc.identifier.citedreferenceLuo, R., Moult, J., and Gilson, M.K. 1997. Dielectric screening treatment of electrostatic solvation. J. Phys. Chem. B. 101: 11226 ‐ 11236.
dc.identifier.citedreferenceLuty, B.A., Tironi, I.G., and van Gunsteren, W.F. 1995. Lattice‐sum methods for calculating electrostatic interactions in molecular simulations. J. Chem. Phys. 103: 3014 ‐ 3021.
dc.identifier.citedreferenceMacKerell, A.D. Jr. 1997. Influence of magnesium ions on duplex DNA structural,dynamic, and solvation properties. J. Phys. Chem. B101: 646 ‐ 650.
dc.identifier.citedreferenceMacKerell, A.D. Jr. and Banavali, N. 2000. All‐atom empirical force field for nucleic acids. 2. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comp. Chem. 21: 105 ‐ 120.
dc.identifier.citedreferenceMacKerell, A.D. Jr., Wiorkiewicz‐Kuczera, J., and Karplus, M. 1995. An all‐atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117: 11946 ‐ 11975.
dc.identifier.citedreferenceMadura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., and McCammon, J.A. 1995. Electrostatics and diffusion of molecules in solution—Simulations with the University of Houston brownian dynamics program. Comp. Phys. Comm. 91: 57 ‐ 95.
dc.identifier.citedreferenceManning, G.S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 2: 159 ‐ 246.
dc.identifier.citedreferenceMcConnell, K.J., Nirmala, R., Young, M.A., Ravishanker, G., and Beveridge, D.L. 1994. A nanosecond molecular dynamics trajectory for a B DNA double helix ‐ Evidence for substates. J. Am. Chem. Soc. 116: 4461 ‐ 4462.
dc.identifier.citedreferenceMisra, V.K. and Honig, B. 1996. The electrostatic contribution to the B to Z transition of DNA. Biochem. 35: 1115 ‐ 1124.
dc.identifier.citedreferenceMisra, V.K., Sharp, K.A., Friedman, R.A., and Honig, B. 1994. Salt effects on ligand‐DNA binding. Minor groove binding antibiotics. J. Mol. Biol. 238: 245 ‐ 263.
dc.identifier.citedreferenceMohanty, D., Elber, R., Thirumalai, D., Beglov, D., and Roux, B. 1997. Kinetics of protein folding: Computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272: 423 ‐ 442.
dc.identifier.citedreferenceNeumann, M. 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Mol. Phys. 50: 841 ‐ 858.
dc.identifier.citedreferenceNorberg, J. and Nilsson, L. 1995. NMR relaxation times,dynamics, and hydration of a nucleic acid fragment from molecular dynamics simulations. J. Phys. Chem. 99: 14876 ‐ 14884.
dc.identifier.citedreferenceNorberg, J. and Nilsson, L. 1996. Glass transition in DNA from molecular dynamics simulations. Proc. Natl. Acad. Sci. U.S.A. 93: 10173 ‐ 10176.
dc.identifier.citedreferenceNorberto de Souza, O. and Ornstein, R.L. 1997. Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle‐mesh Ewald method. Biophys. J. 72: 2395 ‐ 2397.
dc.identifier.citedreferenceNose, S. 1984. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52: 255 ‐ 268.
dc.identifier.citedreferenceOnsager, L. 1936. Electric moments of molecules in liquids. J. Am. Chem. Soc. 58: 1486 ‐ 1493.
dc.identifier.citedreferenceOoi, I., Oobatake, M., Nemethy, G., and Scheraga, H.A. 1987. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. U.S.A. 84: 3086 ‐ 3090.
dc.identifier.citedreferencePapazyan, A. and Warshel, A. 1997. Continuum and dipole‐lattice models of solvation. J. Phys. Chem. B 101: 11254 ‐ 11264.
dc.identifier.citedreferencePetersen, H.G. 1995. Accuracy and efficiency of the particle mesh Ewald method. J. Chem. Phys. 103: 3668 ‐ 3679.
dc.identifier.citedreferencePollock, E.L. and Glosli, J. 1996. Comments on P3M, PMM, and the Ewald method for large periodic Coulombic systems. Comp. Phys. Comm. 95: 93 ‐ 110.
dc.identifier.citedreferenceRamstein, J. and Lavery, R. 1988. Energetic coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. U.S.A. 85: 7231 ‐ 7235.
dc.identifier.citedreferenceRoberts, J.E. and Schnitker, J. 1995. Boundary conditions in simulations of aqueous ionic solutions: A systematic study. J. Phys. Chem. 99: 1322 ‐ 1331.
dc.identifier.citedreferenceRyckaert, J.P., Ciccotti, G., and Berendsen, H.J.C. 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.
dc.identifier.citedreferenceSarai, A., Mazur, J., Nussinov, R., and Jernigan, R.L. 1988. Origin of DNA helical structure and its sequence dependence. Biochemistry 27: 8498 ‐ 8502.
dc.identifier.citedreferenceSchiffer, C.A., Caldwell, J.W., Kollman, P.A., and Stroud, R.M. 1993. Protein structure prediction with a combined solvation free energy‐molecular mechanics force field. Mol. Sim. 10: 121 ‐ 149.
dc.identifier.citedreferenceSchmidt, K.E. and Lee, M.A. 1997. Multipole Ewald sums for the fast multipole method. J. Stat. Phys. 89: 411 ‐ 424.
dc.identifier.citedreferenceSchreiber, H. and Steinhauser, O. 1992a. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 31: 5856 ‐ 5860.
dc.identifier.citedreferenceSchreiber, H. and Steinhauser, O. 1992b. Taming cutoff induced artifacts in molecular dynamics studies of polypeptides. The reaction field method. J. Mol. Biol. 228: 909 ‐ 923.
dc.identifier.citedreferenceSeibel, G.L., Singh, U.C., and Kollman, P.A. 1985. A molecular dynamics simulation of double‐helical B‐DNA including counterions and water. Proc. Nat. Acad. Sci. U.S.A. 82: 6537 ‐ 6540.
dc.identifier.citedreferenceSharp, K.A. 1991. Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson‐Boltzmann approach. J. Comp. Chem. 12: 454 ‐ 468.
dc.identifier.citedreferenceAlden, C.J. and Kim, S.‐H. 1979. Solvent‐accessible surfaces of nucleic acids. J. Mol. Biol. 132: 411 ‐ 434.
dc.identifier.citedreferenceSingh, U.C., Weiner, S.C., and Kollman, P.A. 1985. Molecular dynamics simulations of d(C‐G‐C‐G‐A)‐d(T‐C‐G‐C‐G) with and without “hydrated” counterions. Proc. Natl. Acad. Sci. U.S.A. 82: 755 ‐ 759.
dc.identifier.citedreferenceSmith, P.E. and Pettitt, B.M. 1991. Peptides in ionic solution—A comparison of the Ewald and switching function techniques. J. Chem. Phys. 95: 8430 ‐ 8441.
dc.identifier.citedreferenceSmith, P.E. and Pettitt, B.M. 1996. Ewald artifacts in liquid state molecular dynamics simulations. J. Chem. Phys. 105: 4289 ‐ 4293.
dc.identifier.citedreferenceSmith, P.E., Blatt, H.D., and Pettitt, B.M. 1997. On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution. J. Phys. Chem. 101B: 3886 ‐ 3890.
dc.identifier.citedreferenceSolvason, D., Kolafa, J., Petersen, H.G., and Perram, J.W. 1995. A rigorous comparison of the Ewald method and the fast multipole method in two dimensions. Comp. Phys. Comm. 87: 307 ‐ 318.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.