Estimation of the binding free energy of doubly charged cations to amino acid functional groups by means of modern force fields.
Abstract
Purification of water from heavy metal ions is an urgent environmental problem. An actively studied method for this is the binding of metal ions by means of proteins that can be isolated from easily accessible plant materials. Carboxyl, thiolate groups of amino acid residues are capable of complexing with metal cations, which leads to the removal of pollutants from water. Methods of computational chemistry are actively used for research, in particular classical molecular dynamics modeling. The work evaluates the correctness of reproducing binding free energies of a number of doubly charged metal cations with functional groups of amino acids. A set of modern potential models of cations is used, which correctly reproduces the characteristics of cations in aqueous solution. Comparisons are made with experimentally measured stability constants of modeled complexes or their structural analogues. Calculations of free energies are performed by the method of alchemical transformation. It is shown that despite the validity of the potential models used, the binding free energies to functional groups of amino acids are generally poorly reproduced: moderately underestimated for the thiolate and amino groups, extremely overestimated for the carboxylate group, and incorrect for imidazole. Thus, it is shown that the classical molecular dynamics modeling method should be used with caution for calculation of the energy characteristics of metal binding by amino acids and proteins.
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References
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