New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

Structure - Tập 7 Số 3 - Trang R55-R60 - 1999
Tom Darden1,2, L. Perera3, Leping Li4, Lee G. Pedersen5
1National Institute of Environmental Health Science, Box 12233, MD-F008, RTP, NC 27709, USA E-mail:
2[email protected]
3Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599–3290, USA
4National Institute of Environmental Health Science, Box 12233, MD-F008, RTP, NC 27709, USA
5National Institute of Environmental Health Science, Box 12233, MD-F008, RTP, NC 27709, Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599–3290, USA

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Tài liệu tham khảo

Levitt, 1982, Computer simulation of DNA double-helix dynamics, Cold Spring Harbor Symp. Quant. Biol, 47, 251, 10.1101/SQB.1983.047.01.030

Seibel, 1985, A molecular dynamics simulation of double-helical B-DNA including counterions and water, Proc. Natl Acad. Sci. USA, 82, 6537, 10.1073/pnas.82.19.6537

Van Gunsteren, 1986, A molecular dynamics computer simulation of an eight-base-pair DNA fragment in aqueous solution: comparison with experimental two-dimensional NMR data, Annu. NY Acad. Sci, 482, 287, 10.1111/j.1749-6632.1986.tb20962.x

Miaskiewicz, 1993, Molecular dynamics of the hydrated d(CGCGAATTCGCG)2 dodecamer, J. Am. Chem. Soc, 115, 1526, 10.1021/ja00057a045

Steinbach, 1994, New spherical-cutoff methods for long range forces in macromolecular simulation, J. Comput. Chem, 15, 667, 10.1002/jcc.540150702

MacKerrell, 1997, Influence of magnesium ions on duplex DNA structural dynamic and solvation properties, J. Phys. Chem. B, 101, 646, 10.1021/jp9622795

Darden, 1993, Particle mesh Ewald-an NlogN method for Ewald sums in large systems, J. Chem. Phys, 98, 10089, 10.1063/1.464397

Essmann, 1995, A smooth particle mesh Ewald method, J. Chem. Phys, 103, 8577, 10.1063/1.470117

Cheatham, 1998, Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution, Theor. Chem. Accts, 99, 279, 10.1007/s002140050337

Sagui, 1999, Molecular dynamics of biomolecules: long-range electrostatic effects, Annu. Rev. Biophys. Biomed. Struct, 29, in press

Auffinger, 1998, Simulations of the molecular dynamics of nucleic acids, Curr. Opin. Struct. Biol, 8, 227, 10.1016/S0959-440X(98)80044-4

Greengard, 1988

Schmidt, 1991, Implementing the fast multipole method in 3 dimensions, J. Stat. Phys, 63, 1223, 10.1007/BF01030008

Pollock, 1996, Comments on P3M FMM and the Ewald method for large periodic Coulombic systems, Comput. Phys. Commun, 95, 93, 10.1016/0010-4655(96)00043-4

Figueirido, 1997, Large scale simulation of macromolecules in solution: combining the periodic fast multipole method with multiple time step integrators, J. Chem. Phys, 106, 9835, 10.1063/1.474115

Ewald, 1921, Die Berechnung optischer und elektrostatischer gitterpotentiale, Annals Phys, 64, 253, 10.1002/andp.19213690304

Ewald, 1979, A review of my papers on crystal optics 1912 to 1968, Acta Crystallogr. A, 35, 1, 10.1107/S0567739479000024

DeLeeuw, 1980, Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constant, Proc. R. Soc. Lond. A, 373, 27, 10.1098/rspa.1980.0135

Forester, 1991, Molecular dynamics studies of the behavior of water molecules and small ions in concentrated solutions of polymeric B-DNA, Mol. Phys, 72, 643, 10.1080/00268979100100481

Mohan, 1993, Molecular dynamics simulation of ions and water around triplex DNA, J. Phys. Chem, 97, 12984, 10.1021/j100151a055

Ten Eyck, 1973, Crystallographic fast Fourier transforms, Acta Crystallogr. A, 29, 183, 10.1107/S0567739473000458

Pearlman, 1995, 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, Comput. Phys. Chem, 91, 1

Darden, 1997, Long-range electrostatic effects in biomolecules, J. Chim. Phys. Physico-Chim. Biol, 94, 1346, 10.1051/jcp/1997941346

Deserno, 1998, How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines, J. Chem. Phys, 109, 7678, 10.1063/1.477414

Schreiber, 1992, Molecular dynamics studies of solvated polypeptides: why the cut-off scheme does not work, Chem. Phys, 168, 75, 10.1016/0301-0104(92)80111-8

Cheatham, 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, 10.1021/ja00119a045

Lee, 1995, Molecular dynamics simulation studies on a high-resolution Z-DNA crystal, J. Chem. Phys, 102, 3830, 10.1063/1.468564

York, 1995, Toward the accurate modeling of DNA – the importance of long-range electrostatics, J. Am. Chem. Soc, 117, 5001, 10.1021/ja00122a034

Lee, 1995, Accurate crystal molecular dynamics simulations using particle mesh Ewald-RNA dinucleotides – ApU and GpC, Chem. Phys. Letts, 243, 229, 10.1016/0009-2614(95)00845-U

Cheatham, 1996, Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution, J. Mol. Biol, 259, 434, 10.1006/jmbi.1996.0330

Young, 1998, Local dielectric environment of B-DNA in solution: results from a 14 ns molecular dynamics trajectory, J. Phys. Chem. B, 102, 7666, 10.1021/jp9823188

Young, 1997, 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, 59, 10.1021/ja960459m

Shui, 1998, The B-DNA dodecamer at high resolution reveals a spine of water on sodium, Biochemistry, 37, 8341, 10.1021/bi973073c

Young, 1998, Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn, J. Mol. Biol, 281, 675, 10.1006/jmbi.1998.1962

Simmerling, 1998, Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid, J. Am. Chem. Soc, 120, 7149, 10.1021/ja9727023

Srinivisan, 1998, Continuum solvent studies of DNA RNA and phosphoramide-DNA helices, J. Am. Chem. Soc, 120, 9401, 10.1021/ja981844+

Jayaram, 1998, Free energy analysis of the conformational preferences of A and B forms of DNA in solution, J. Am. Chem. Soc, 120, 10629, 10.1021/ja981307p

Cheatham, 1997, 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[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III), Structure, 5, 1297, 10.1016/S0969-2126(97)00282-7

Soliva, 1998, Molecular dynamics simulations in aqueous solution of triple helices containing d(GCC) trios, J. Am. Chem. Soc, 120, 11226, 10.1021/ja981121q

Beard, 1998, Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding tract of HIV-1 reverse transcriptase molecular nature of polymerase – nucleic acid interactions, J. Biol. Chem, 273, 30435, 10.1074/jbc.273.46.30435

Strahan, 1998, NMR structure refinement and dynamics of the K+-[d(G(3)T(4)G(3))]2 quadruplex via particle mesh Ewald molecular dynamics simulations, Biophys. J, 75, 968, 10.1016/S0006-3495(98)77585-X

Allen, 1998, A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA, EMBO J, 17, 5484, 10.1093/emboj/17.18.5484

Konerding, 1999, Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method, J. Biomol. NMR, in press

Li, 1997, Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm, Biochemistry, 36, 2132, 10.1021/bi962250r

Harvey, 1998, The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition, J. Comput. Chem, 19, 726, 10.1002/(SICI)1096-987X(199805)19:7<726::AID-JCC4>3.0.CO;2-S

Smith, 1996, Ewald artifacts in liquid state molecular dynamics simulations, J. Chem. Phys, 105, 4289, 10.1063/1.472246

Hunenberger, 1999, Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study, J. Chem. Phys, 110, 1856, 10.1063/1.477873

Hockney, 1981

Luty, 1994, A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems, Mol. Simul, 14, 11, 10.1080/08927029408022004

York, 1994, The fast Fourier–Poisson method for calculating Ewald sums, J. Chem. Phys, 101, 3298, 10.1063/1.467576

Huang, 1998, Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance, Science, 282, 1669, 10.1126/science.282.5394.1669

Ding, 1997, Protein–nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer, Biopolymers, 44, 125, 10.1002/(SICI)1097-0282(1997)44:2<125::AID-BIP2>3.0.CO;2-X

Esnouf, 1995, Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucloside inhibitors, Nat. Struct. Biol, 2, 303, 10.1038/nsb0495-303

Jacobo-Molina, 1993, Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-standed DNA at 3.0 Å resolution shows bent DNA, Proc. Natl Acad. Sci. USA, 90, 6320, 10.1073/pnas.90.13.6320