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

• Published in: International journal of quantum chemistry Vol. 122; no. 21
• Main Authors: Botella, María, Ema, Ignacio, San Fabián, Jesús, García de la Vega, Jose Manuel
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 05-11-2022; Wiley Subscription Services, Inc
• Subjects: Amino acids; Asp dipeptide model; Chains; Chemistry; Conformational analysis; Constants; Density functional theory; Empirical analysis; Karplus equations; NMR; Nuclear magnetic resonance; Physical chemistry; Quantum physics; Residues; side‐chain conformation; Spin-spin coupling; spin–spin coupling constants; Statistical analysis
• ISSN: 0020-7608; 1097-461X
• DOI: 10.1002/qua.26979

The 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.
A computational protocol for the evaluation of the side‐chain torsional angle χ1 of amino acid residues is described. Extended Karplus equations and theoretical vicinal coupling constants are applied to Asp dipeptide model. Theoretical results of the χ1 values obtained with our computational protocol are successfully compared with those derived by nuclear magnetic resonance and X‐ray.