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Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations
Author(s) -
Yang Gang,
Zhu Rongxiu,
Zhou Lijun,
Liu Chengbu
Publication year - 2012
Publication title -
journal of mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 121
eISSN - 1096-9888
pISSN - 1076-5174
DOI - 10.1002/jms.3075
Subject(s) - chemistry , denticity , conformational isomerism , ab initio , affinities , density functional theory , glycine , molecule , crystallography , binding energy , amino acid , metal , stereochemistry , computational chemistry , ligand (biochemistry) , ion , crystal structure , organic chemistry , biochemistry , physics , receptor , nuclear physics
Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB III via only the hydroxyl group). The scaling factor of Zn(Gly) n structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number ( n ), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA) n binding affinities ( n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB III versus ZnA I (zwitterionic) relative energy differs by 41.9 kcal mol −1 at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol −1 ). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution. Copyright © 2012 John Wiley & Sons, Ltd.