Searching conformational analysis of Asp residues through theoretical 3J vicinal coupling constants and Karplus equations

Abstract

AbstractThe dependence of the vicinal spin–spin coupling constants on the torsion side chain angle χ1 through the Karplus equations is considered for the study of the structure of Asp amino acid residues. Experimental and theoretical, obtained with density functional theory methods, vicinal coupling constants combined with extended Karplus equations, which include six coefficients, are applied to a dipeptide model of the amino acid Asp. To find out the empirical χ1 angles of the side chain, a statistical analysis procedure is developed to compute the rmsd values and find the χ1 as the minimum of those values. The χ1 values obtained in this work for nine Asp residues of the flavodoxin protein Desulfovibrio vulgaris are successfully compared with those derived by nuclear magnetic resonance and X‐rays.