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Development of non-standard arginine residue parameters for use with the AMBER force fields
University of Gothenburg, Gothenburg, Sweden.
Örebro University, School of Science and Technology.ORCID iD: 0000-0003-3315-8835
University of Gothenburg, Gothenburg, Sweden.
2013 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 584, p. 188-194Article in journal (Refereed) Published
Abstract [en]

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. (c) 2013 Elsevier B.V. All rights reserved.

Place, publisher, year, edition, pages
2013. Vol. 584, p. 188-194
National Category
Theoretical Chemistry
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:oru:diva-32344DOI: 10.1016/j.cplett.2013.08.071ISI: 000324860000035Scopus ID: 2-s2.0-84884814598OAI: oai:DiVA.org:oru-32344DiVA, id: diva2:663630
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Funder
Swedish Research CouncilAvailable from: 2013-11-12 Created: 2013-11-12 Last updated: 2018-05-21Bibliographically approved

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Strid, Åke

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