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Theoretical DFT karplus equations: Amino acid side‐chain torsion angle χ 1
Author(s) -
García De La Vega J. M.,
San Fabián J.,
CrespoOtero R.,
Suardíaz R.,
Pérez C.
Publication year - 2012
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.24030
Subject(s) - dihedral angle , desulfovibrio vulgaris , fourier transform , density functional theory , chemistry , root mean square , flavodoxin , computational chemistry , physics , mathematical analysis , mathematics , quantum mechanics , molecule , hydrogen bond , ferredoxin , organic chemistry , biology , bacteria , genetics , enzyme , biochemistry
Abstract Theoretical Karplus equations for determining the conformation in proteins is applied to phenylalanine and tyrosine residues of Desulfovibrio vulgaris flavodoxin using density functional theory (DFT) calculations. The accuracy of different Karplus equations is evaluated showing that S 2 Fourier coefficient is not negligible and C 1 adopts positive values for some couplings. These two points should be considered in future empirical parameterizations. The dihedral angles χ 1 calculated in this study using the full set of Fourier coefficients present a root mean square deviation of 6° against those obtained from X‐ray structures. © 2012 Wiley Periodicals, Inc.