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Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

SYSNO ASEP	0351179
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins
Author(s)	Berka, K. (CZ) Laskowski, R. A. (GB) Hobza, P. (CZ) Vondrášek, Jiří (UOCHB-X)_{RID, ORCID}
Number of authors	4
Source Title	Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618 Roč. 6, č. 7 (2010), s. 2191-2203
Number of pages	13 s.
Language	eng - English
Country	US - United States
Keywords	protein structure ; DFT method ; force fields ; interaction energy
Subject RIV	CF - Physical ; Theoretical Chemistry
R&D Projects	GAP208/10/0725 GA ČR - Czech Science Foundation (CSF)
	LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
	AV0Z50520701 - BTO-N (2007-2013)
UT WOS	000279751500026
DOI	10.1021/ct100007y
Annotation	The interactions between amino acid side chains in proteins are generally considered to be the most important stabilizing factor controlling the precise arrangement of the polypeptide chain into a well-defined spatial structure. We used the RI-DFT-D method to calculate the full 20 × 20 matrix of interaction energies between all pairs of amino acid side chains. We find that all of the calculated interaction energies between selected pairs of amino acids are attractive in the gas phase with the exception of side chain pairs having the same total charge. We compared these data with those calculated by the parm03 and OPLS-AA/L force fields to investigate the reliability of simple methods in modeling biomolecules and their behavior. The force fields yield good overall interaction energies for our set but have problems in evaluation of some particular interactions which could be of principal importance for protein stability.
Workplace	Institute of Organic Chemistry and Biochemistry
Contact	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Year of Publishing	2011

Number of the records: 1