Including Electronic Screening in Classical Force Field of Zinc Ion for Biomolecular Simulations

被引:9
作者
Del Frate, Gianluca [1 ,2 ]
Nikitin, Alexei [1 ,3 ]
机构
[1] Scuola Normale Super Pisa, Piazza Cavalieri 7, I-56126 Pisa, Italy
[2] IMT Sch Adv Studies Lucca, Piazza SFrancesco 19, I-55100 Lucca, Italy
[3] Russian Acad Sci, Engelhardt Inst Mol Biol, Moscow 119991, Russia
关键词
Force field; metal ions; metalloenzyme; molecular dynamics; COMBINING RULES; METAL-CATIONS; FREE-ENERGY; PARAMETERS; SOLVATION; EFFICIENT; PROTEINS;
D O I
10.1002/slct.201802864
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
We present a new force field for zinc ion to be used in classical Molecular Dynamics. Such model has been developed according to an optimization procedure by fitting experimental quantities taken from the literature. The metal ion electrostatic charge has been scaled by a factor 0.75, according to a recently proposed polarization model which considers the electronic screening effects due to the surrounding environment. Zinc interatomic interactions have been modeled by means of the Waldman-Hagler combination rule. It is demonstrated that the proposed force field for zinc is transferable from water solution to protein catalytic sites, offering in both the considered cases good performances in the reproduction of experimental quantities usually addressed in soft matter computer simulations.
引用
收藏
页码:12367 / 12370
页数:4
相关论文
共 27 条
[1]   Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations [J].
Ahlstrand, Emma ;
Hermansson, Kersti ;
Friedman, Ran .
JOURNAL OF PHYSICAL CHEMISTRY A, 2017, 121 (13) :2643-2654
[2]   Empirical force fields for biologically active divalent metal cations in water [J].
Babu, CS ;
Lim, C .
JOURNAL OF PHYSICAL CHEMISTRY A, 2006, 110 (02) :691-699
[3]   EFFICIENT ESTIMATION OF FREE-ENERGY DIFFERENCES FROM MONTE-CARLO DATA [J].
BENNETT, CH .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (02) :245-268
[4]   Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials.: The case of Zn2+, Ni2+, and Co2+ in aqueous solutions [J].
Chillemi, G ;
D'Angelo, P ;
Pavel, NV ;
Sanna, N ;
Barone, V .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2002, 124 (09) :1968-1976
[5]   A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [J].
Duan, Y ;
Wu, C ;
Chowdhury, S ;
Lee, MC ;
Xiong, GM ;
Zhang, W ;
Yang, R ;
Cieplak, P ;
Luo, R ;
Lee, T ;
Caldwell, J ;
Wang, JM ;
Kollman, P .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2003, 24 (16) :1999-2012
[6]   REFINED STRUCTURE OF HUMAN CARBONIC ANHYDRASE-II AT 2.0-A RESOLUTION [J].
ERIKSSON, AE ;
JONES, TA ;
LILJAS, A .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1988, 4 (04) :274-282
[7]   Force Field Parametrization of Metal Ions from Statistical Learning Techniques [J].
Fracchia, Francesco ;
Del Frate, Gianluca ;
Mancini, Giordano ;
Rocchia, Walter ;
Barone, Vincenzo .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2018, 14 (01) :255-273
[8]   GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation [J].
Hess, Berk ;
Kutzner, Carsten ;
van der Spoel, David ;
Lindahl, Erik .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (03) :435-447
[9]   Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions [J].
Jensen, Kasper P. ;
Jorgensen, William L. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2006, 2 (06) :1499-1509
[10]   COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER [J].
JORGENSEN, WL ;
CHANDRASEKHAR, J ;
MADURA, JD ;
IMPEY, RW ;
KLEIN, ML .
JOURNAL OF CHEMICAL PHYSICS, 1983, 79 (02) :926-935