Theoretical DFT karplus equations: Amino acid side-chain torsion angle χ1

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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 S2 Fourier coefficient is not negligible and C1 adopts positive values for some couplings. These two points should be considered in future empirical parameterizations. The dihedral angles χ1 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.

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