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Functional assessment of “in vivo” and “in silico” mutations in the guanine binding site of RNase T 1 : A DFT study
Author(s) -
Mig Pierre,
Loverix Stefan,
Steyaert Jan,
Geerlings Paul
Publication year - 2004
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.20114
Subject(s) - in silico , cooperativity , rnase p , mutant , guanine , density functional theory , in vivo , chemistry , mutation , side chain , binding energy , binding site , rnase h , biophysics , crystallography , stereochemistry , computational chemistry , biochemistry , genetics , biology , rna , nucleotide , gene , physics , organic chemistry , nuclear physics , polymer
Experimentally, the functional assessment of amino acid side chains in proteins is carried out by comparing parameters such as binding constants for the wild‐type protein and a mutant protein in which the considered side chain is deleted. In the present study, we apply a density functional theory (DFT) methodology to obtain changes in binding energy upon mutations in the enzyme ribonuclease T 1 . Mutant structures were either taken directly from crystallographic data (“in vivo”) allowing for conformational changes upon mutation, or derived from the wild‐type (“in silico”). Excluding entropic contributions, the computed interaction energy changes upon mutation in vivo correlate qualitatively well with experimental binding free energy changes. In contrast, the in silico approach does not perform as well, especially for residues that contribute largely to binding. Subsequently, we assessed the applicability of the in vivo approach by analyzing the functional cooperativity between pairs of side chains. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004