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2013 | 1 | 63-74
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A Stochastic Solver of the Generalized Born Model

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A stochastic generalized Born (GB) solver is presented which can give predictions of energies arbitrarily close to those that would be given by exact effective GB radii, and, unlike analytical GB solvers, these errors are Gaussian with estimates that can be easily obtained from the algorithm. This method was tested by computing the electrostatic solvation energies (ΔGsolv) and the electrostatic binding energies (ΔGbind) of a set of DNA-drug complexes, a set of protein-drug complexes, a set of protein-protein complexes, and a set of RNA-peptide complexes. Its predictions of ΔGsolv agree with those of the linearized Poisson-Boltzmann equation, but it does not predict ΔGbind well, although these predictions of ΔGbind may be marginally better than those of traditional analytical GB solvers. Apparently, the GB model itself must be improved before accurate estimates of ΔGbind can be obtained.
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  • N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon, Electrostatics of nanosystems: application tomicrotubules and the ribosome. Proc. Natl. Acad. Sci. USA 98(2001), 10037-10041.
  • D. Bashford and D. A. Case, Generalized Born models of macromolecular solvation effects. Ann. Rev. Phys. Chem.51(2000), 129-152.[Crossref]
  • I. Beá, M. G. Gotsev, P. M. Ivanov, C. Jaime, and P. A. Kollman, Chelate effect in cyclodextrin dimers: a computational(MD, MM/PBSA, and MM/GBSA) study, J. Org. Chem. 71(2006), 2056-2063.
  • H. M. Berman, T. N. Bhat, P. E. Bourne, Z. Feng, G. Gilliland, H. Weissig, and J. Westbrook, The protein data bankand the challenge of structural genomics. Nat. Struct. Mol. Biol. 7(2000), 957-959.[Crossref]
  • A. H. Boschitsch and M. O. Fenley, A fast and robust Poisson-Boltzmann solver based on adaptive Cartesian grids.J. Chem. Theory Comput. 7(2011), 1524-1540.[Crossref][WoS]
  • M. Bossy, N. Champagnat, S. Maire, and D. Talay, Probabilistic interpretation and random walk on spheres algorithmsfor the Poisson-Boltzmann equation in molecular dynamics. ESAIM, Math. Model. Numer. Anal. 44(2010),997-1048.[Crossref][WoS]
  • B. R. Brooks, C. L. Brooks III., A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels,S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera,T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable,H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus, CHARMM: The biomolecular simulation program. J.Comput. Chem. 30(2009), 1545-1614.
  • Q. Cai, J. Wang, H.-K. Zhao, and R. Luo, On removal of charge singularity in Poisson-Boltzmann equation. J. Chem.Phys. 130(2009), 145101.[Crossref][WoS]
  • M. L. Connolly, Solvent-accessible surfaces of proteins and nucleic acids. Science. 221(1983), 709.[PubMed]
  • W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W.Caldwell, and P. A. Kollman, A second generation force field for the simulation of proteins, nucleic acids, and organicmolecules. J. Am. Chem. Soc. 117(1995), 5179-5197.[Crossref]
  • T. J. Dolinsky, P. Czodrowski, H. Li, J. E. Nielsen, J. H. Jensen, G. Klebe, and N. A. Baker, Pdb2pqr: expanding andupgrading automated preparation of biomolecular structures for molecular simulations. Nucl. Acids Res. 35(2007),W522-W525.[WoS]
  • T. J. Dolinsky, J. E. Nielsen, J. A. McCammon, and N. A. Baker, Pdb2pqr: an automated pipeline for the setup ofPoisson-Boltzmann electrostatics calculations. Nucl. Acids Res. 32(2004), W665.
  • M. O. Fenley, M. Mascagni, J. McClain, A. R. J. Silalahi, and N. A. Simonov, Using correlated Monte Carlo samplingfor efficiently solving the linearized Poisson-Boltzmann equation over a broad range of salt concentration. J. Chem.Theory Comput. 6(2009), 300-314.[WoS]
  • F. Fogolari, P. Zuccato, G. Esposito, and P. Viglino, Biomolecular electrostatics with the linearized Poisson-Boltzmann equation. Biophys. J. 76(1999), 1-16.[PubMed]
  • W. Geng, S. Yu, and G. Wei, Treatment of charge singularities in implicit solvent models. J. Chem. Phys. 127(2007),114106.[Crossref]
  • S. Genheden and U. Ryde, How to obtain statistically converged MM/GBSA results. J. Comput. Chem. 31(2010),837-846.[WoS]
  • J. M. Hayes, V. T. Skamnaki, G. Archontis, C. Lamprakis, J. Sarrou, N. Bischler, A.-L. Skaltsounis, S. E. Zographos, andN. G. Oikonomakos, Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototypeindirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of watermolecules examined. Proteins: Struct. Funct. Bioinf. 79(2011), 703-719.
  • T. Hou, J. Wang, Y. Li, and W. Wang, Assessing the performance of the MM/PBSA and MM/GBSA methods. 1.the accuracy of binding free energy calculations based on molecular dynamics simulations. J. Chem. Inf. Model.51(2011), 69-82.[WoS]
  • W. Im, M. Feig, and C. L. Brooks III., An implicit membrane generalized Born theory for the study of structure,stability, and interactions of membrane proteins. Biophys. J. 85(2003), 2900-2918.[Crossref]
  • W. Im, M. S. Lee, and C. L. Brooks III., Generalized Born model with a simple smoothing function. J. Comput. Chem.24(2003), 1691-1702.
  • J. D. Jackson, Classical Electrodynamics, Third Edition, Wiley, New York, 1998.
  • M. S. Lee, M. Feig, F. R. Salsbury, and C. L. Brooks III., New analytic approximation to the standard molecularvolume definition and its application to generalized Born calculations. J. Comput. Chem. 24(2003), 1348-1356.
  • M. S. Lee, F. R. Salsbury, and C. L. Brooks III., Novel generalized Born methods. J. Chem. Phys. 116(2002), 10606.[Crossref]
  • H.-Y. Liu and X. Zou, Electrostatics of ligand binding: Parametrization of the generalized Born model and comparisonwith the Poisson-Boltzmann approach. J. Phys. Chem. B 110(2006), 9304-9313.
  • B. Z. Lu, Y. C. Zhou, M. J. Holst, and J. A. McCammon. Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications. Commun. Comput. Phys. 3(2008), 973-1009.
  • T. Mackoy, R. C. Harris, J. Johnson, M. Mascagni, and M. O. Fenley, Numerical optimization of a walk-on-spheressolver for the linear Poisson-Boltzmann equation. Commun. Comput. Phys. 13(2013) 195-206.
  • M. Mascagni and N. A. Simonov, Monte Carlo methods for calculating some physical properties of large molecules.SIAM J. Sci. Comput. 26(2005), 339.
  • C. J. Núñez-Agüero, C.-M. Escobar-Llanos, D. Díaz, C. Jaime, and R. Garduño-Juárez, Chiral discrimination ofibuprofen isomers in β-cyclodextrin inclusion complexes: experimental (NMR) and theoretical (MD, MM/GBSA)studies. Tetrahedron. 62(2006), 4162-4172.[Crossref]
  • A. Onufriev, D. Bashford, and D. A. Case, Modification of the generalized Born model suitable for macromolecules.J. Phys. Chem. B 104(2000), 3712-3720.
  • A. Onufriev, D. A. Case, and D. Bashford, Effective Born radii in the generalized Born approximation: The importanceof being perfect. J. Comput. Chem. 23(2002), 1297-1304.
  • X. Pang and H.-X. Zhou, Poisson-Boltzmann calculations: van der Waals or molecular surface? Commun. Comput.Phys. 13(2013), 1-12.[WoS]
  • S. Qin and H.-X. Zhou, Do electrostatic interactions destabilize protein-nucleic acid binding? Biopolymers. 86(2007),p. 112-118.[PubMed][Crossref][WoS]
  • G. Rastelli, A. Del Rio, G. Degliesposti, and M. Sgobba, Fast and accurate predictions of binding free energiesusing MM-PBSA and MM-GBSA. J. Comput. Chem. 31(2010), 797-810.
  • A. Rasulov, A. Karaivanova, and M. Mascagni, Quasirandom sequences in branching random walks. Monte CarloMethods Appl. 10(2004), 551-558.
  • N. A. Simonov, Monte Carlo methods for solving elliptic equations with boundary conditions containing the normalderivative. Doklady Mathematics. 74(2006), 656-659.[Crossref]
  • N. A. Simonov, M. Mascagni, and M. O. Fenley, Monte Carlo-based linear Poisson-Boltzmann approach makesaccurate salt-dependent solvation free energy predictions possible. J. Chem. Phys. 127(2007), 185105.[WoS][Crossref]
  • J. Srinivasan, M. W. Trevathan, P. Beroza, and D. A. Case, Application of a pairwise generalized Born model toproteins and nucleic acids: inclusion of salt effects. Theor. Chem. Acc. 101(1999), 426-434.[Crossref]
  • W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, Semianalytical treatment of solvation for molecularmechanics and dynamics. J. Am. Chem. Soc. 112(1990), 6127-6129.[Crossref]
  • L. Y. Zhang, E. Gallicchio, R. A. Friesner, and R. M. Levy, Solvent models for protein-ligand binding: Comparisonof implicit solvent Poisson and surface generalized Born models with explicit solvent simulations. J. Comput. Chem.22(2001), 591-607.
  • V. Zoete, M. B. Irving, and O. Michielin, MM-GBSA binding free energy decomposition and T cell receptor engineering.J. Mol. Recognit. 23(2010), 142-152.[WoS][Crossref]
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