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

0351179 - ÚOCHB 2011 RIV US eng J - Journal Article
Berka, K. - Laskowski, R. A. - Hobza, P. - Vondrášek, Jiří
Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.
Journal of Chemical Theory and Computation. Roč. 6, č. 7 (2010), s. 2191-2203. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR GAP208/10/0725; GA MŠMT LC512
Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50520701
Keywords : protein structure * DFT method * force fields * interaction energy
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 5.138, year: 2010

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.
Permanent Link: http://hdl.handle.net/11104/0190986