A study on the backbone/side-chain interaction in N-formyl-(L)serineamide

Abstract

The N-formyl-serineamide (For-Ser-NH2), a model diamide for the conformational behaviour of the protein backbone at serine residue, has been gradient optimized for selected conformations at the abinitio 3-21G level. Previous molecular mechanics ECEPP/2 calculations suggested that the optimal side-chain (χ1, χ2) and backbone [Formula: see text] conformations are strongly coupled, due to intramolecular H-bonding formed between the side-chain hydroxyl group and the amide moiety. Four different side-chain geometries (I–IV) were considered at each of the four backbone conformations (α, β, β′, γ) giving a total 16 different critical points on the coupled [Formula: see text] surface. The very fact that upon changing the [Formula: see text] values the global minimum of (χ1, χ2) surface was shifted indicated clearly that the two subspaces are strongly coupled. The present theoretical results were compared to experimental peptide and protein geometries taken from the Cambridge Structure Database and from the Brookhaven Protein Data Bank, respectively. Keywords: conformation of a serinediamide, backbone side-chain interactions, topological analysis of potential energy surfaces, abinitio calculations.