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Development of non-standard arginine residue parameters for use with the AMBER force fields

Journal article
Authors Min Wu
A. Strid
Leif A Eriksson
Published in Chemical Physics Letters
Volume 584
Pages 188-194
ISSN 0009-2614
Publication year 2013
Published at Department of Chemistry and Molecular Biology
Pages 188-194
Language en
Links dx.doi.org/10.1016/j.cplett.2013.08...
Keywords CONFORMATIONAL ENERGIES, ELECTRON-TRANSFER, AMINO-ACIDS, RESP MODEL, RADICALS, CATALYSIS, CHARGES, WELL
Subject categories Chemical Sciences, Molecular biology

Abstract

Amino acid radicals are often involved as intermediates in biological processes, but are difficult to capture by experiment. Computational modeling can be employed to study the features of the species involved. The neutral arginyl radical has previously been detected experimentally using ECD and ETD spectroscopy. Protonation of the radical can occur on the guanidinium carbon, depending on the peptide structure and protein environment. Accurate force fields are essential for reproducing the conformational and dynamic behavior of these intermediates. New AMBER ff99 parameters for the arginyl radical and hydrogenated arginyl side chains are presented based on ab initio quantum chemical calculations.

Page Manager: Webmaster|Last update: 9/11/2012
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