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Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters
Author(s) -
Gresh Nohad,
El Hage Krystel,
Perahia David,
Piquemal JeanPhilip,
Berthomieu Catherine,
Berthomieu Dorothée
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23724
Subject(s) - bimetallic strip , chemistry , polarizability , molecular dynamics , molecule , computational chemistry , ligand (biochemistry) , binding energy , ab initio , crystallography , chemical physics , metal , atomic physics , physics , biochemistry , receptor , organic chemistry
The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn‐superoxide dismutase (SOD) has been inferred from high‐resolution X‐ray crystallography. Long‐duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second‐generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn‐SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short‐duration MD simulations of 296 waters solvating Cu/Zn‐SOD. Six representative geometries are selected and energy‐minimized. Single‐point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest‐energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments (2.7–3.0 Debye), equal and larger than the one computed by SIBFA in ice‐like arrangements (2.7 D).