A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics

被引:18
作者
Masella, Michel [1 ]
Borgis, Daniel [2 ]
Cuniasse, Philippe [1 ]
机构
[1] Commissariat Energie Atom, Lab Chim Vivant, Serv Ingn Mol Prot, Inst Biol & Technol Saclay,Ctr Saclay, F-91191 Gif Sur Yvette, France
[2] Ecole Normale Super, UMR Pasteur, Dept Chim, F-75231 Paris 05, France
关键词
coarse grained; ion salvation; multiscale; polarizable force-field; MOLECULAR-DYNAMICS SIMULATIONS; PROTEIN-PROTEIN BINDING; LIQUID-STRUCTURE FORCES; PARTICLE-MESH EWALD; AQUEOUS-SOLUTION; FREE-ENERGIES; MEAN FORCE; BIOLOGICAL-SYSTEMS; AB-INITIO; ION-PAIRS;
D O I
10.1002/jcc.23237
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
A multiscale coarse-grained approach able to handle efficiently the solvation of microscopic solutes in extended chemical environment is described. That approach is able to compute readily and efficiently very long-range solute/solvent electrostatic microscopic interactions, up to the 1-m scale, by considering a reduced amount of computational resources. All the required parameters are assigned to reproduce available data concerning the solvation of single ions. Such a strategy makes it possible to reproduce with good accuracy the solvation properties concerning simple ion pairs in solution (in particular, the asymptotic behavior of the ion pair potentials of mean force). This new method represents an extension of the polarizable pseudoparticle solvent model, which has been recently improved to account for the main features of hydrophobic effects in liquid water (Masella et al., J. Comput. Chem. 2011, 32, 2664). This multiscale approach is well suited to be used for computing the impact of charge changes in free energy computations, in terms of both accuracy and efficiency. (c) 2013 Wiley Periodicals, Inc.
引用
收藏
页码:1112 / 1124
页数:13
相关论文
共 57 条
[1]   COMPUTER-SIMULATION STUDY OF THE MEAN FORCES BETWEEN FERROUS AND FERRIC IONS IN WATER [J].
BADER, JS ;
CHANDLER, D .
JOURNAL OF PHYSICAL CHEMISTRY, 1992, 96 (15) :6423-6427
[2]   Electrostatics of nanosystems: Application to microtubules and the ribosome [J].
Baker, NA ;
Sept, D ;
Joseph, S ;
Holst, MJ ;
McCammon, JA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (18) :10037-10041
[3]   Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly [J].
Barrault, Marie-Benedicte ;
Richet, Nicolas ;
Godard, Chloe ;
Murciano, Brice ;
Le Tallec, Benoit ;
Rousseau, Erwann ;
Legrand, Pierre ;
Charbonnier, Jean-Baptiste ;
Le Du, Marie-Helene ;
Guerois, Raphael ;
Ochsenbein, Francoise ;
Peyroche, Anne .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (17) :E1001-E1010
[4]   A semi-implicit solvent model for the simulation of peptides and proteins [J].
Basdevant, N ;
Borgis, D ;
Ha-Duong, T .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (08) :1015-1029
[5]   Particle-based implicit solvent model for biosimulations: Application to proteins and nucleic acids hydration [J].
Basdevant, Nathalie ;
Ha-Duong, Tap ;
Borgis, Daniel .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2006, 2 (06) :1646-1656
[6]   Generalized born models of macromolecular solvation effects [J].
Bashford, D ;
Case, DA .
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 2000, 51 :129-152
[7]   SOLVENT EFFECTS ON PROTEIN ASSOCIATION AND PROTEIN FOLDING [J].
BENNAIM, A .
BIOPOLYMERS, 1990, 29 (03) :567-596
[8]   SOLVENT EFFECT ON BINDING THERMODYNAMICS OF BIOPOLYMERS [J].
BENNAIM, A ;
TING, KL ;
JERNIGAN, RL .
BIOPOLYMERS, 1990, 29 (6-7) :901-919
[9]   SOLVENT-INDUCED FORCES IN PROTEIN FOLDING [J].
BENNAIM, A .
JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (17) :6893-6895
[10]   STRONG FORCES BETWEEN HYDROPHILIC MACROMOLECULES - IMPLICATIONS IN BIOLOGICAL-SYSTEMS [J].
BENNAIM, A .
JOURNAL OF CHEMICAL PHYSICS, 1990, 93 (11) :8196-8210