Repository: Freie Universit├Ąt Berlin, Math Department

Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

Pluharova, E. and Baer, M. and Mundy, Ch. and Schmidt, B. and Jungwirth, P. (2014) Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics. J. Phys. Chem. Lett., 5 (13). pp. 2235-2240.

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Official URL: http://dx.doi.org/10.1021/jz500976m

Abstract

Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water.

Item Type:Article
Subjects:Physical Sciences > Chemistry > Physical Chemistry
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group
ID Code:1420
Deposited By: BioComp Admin
Deposited On:12 Jun 2014 06:21
Last Modified:03 Jul 2014 08:09

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