Abstract
Theoretical relationships between the vicinal spin–spin coupling constants (SSCCs) and the χ1 torsion angles have been studied to predict the conformations of protein side chains. An efficient computational procedure is developed to obtain the conformation of dipeptides through theoretical and experimental SSCCs, Karplus equations, and quantum chemistry methods, and it is applied to three aliphatic hydrophobic residues (Val, Leu, and Ile). Three models are proposed: unimodal-static, trimodal-static-stepped, and trimodal-static-trigonal, where the most important factors are incorporated (coupled nuclei, nature and orientation of the substituents, and local geometric properties). Our results are validated by comparison with NMR and X-ray empirical data described in the literature, obtaining successful results on the 29 residues considered. Using out trimodal residue treatment, it is possible to detect and resolve residues with a simple conformation and those with two or three staggered conformers. In four residues, a deeper analysis explains that they do not have a unique conformation and that the population of each conformation plays an important role.
Highlights
The properties of the amino acid (AA) side chain in proteins are key determinants of protein function, and for the understanding of life
AA side chains allow for many different types of intramolecular and intermolecular interactions, which are modulated by the dynamics of the side chains.[6,7]
The flexibility and dynamics of AAs, number of conformations that appear per residue, and the frequencies of these conformational changes play an important role in biological properties
Summary
The properties of the amino acid (AA) side chain in proteins are key determinants of protein function, and for the understanding of life. AA side chains allow for many different types of intramolecular and intermolecular interactions, which are modulated by the dynamics of the side chains.[6,7] The flexibility and dynamics of AAs, number of conformations that appear per residue, and the frequencies of these conformational changes play an important role in biological properties
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