Structure of dipeptides having N-terminal selenocysteine residues: A DFT study in gas and aqueous phase

Abstract

Over the last few decades, dipeptides as well as their analogues have served as important model systems for the computational studies concerning the structure of protein and energetics of protein folding. Here, we present a density functional structural study on a set of seven dipeptides having N-terminal selenocysteine residues (the component in the C-terminus is varied with seven different combinations viz. Ala, Phe, Glu, Thr, Asn, Arg and Sec) in gas and simulated aqueous phase using a polarizable continuum model (PCM). The molecular geometries of the dipeptides are fully optimized at B3LYP/6-311++G(d,p) level and subsequent frequency calculations confirm them as true minima. The effects of solvation and identity of the varying C-terminal residue on the energetics, structural features of the peptide planes, values of the ψ and φ dihedrals, geometry around the α-carbon atoms and theoretically predicted vibrational spectra of the dipeptides are investigated. Two types of intramolecular H-bonds, namely N.H-N and O.H-C, are found to play important roles in influencing the planarity of the peptide planes and geometry around the α-carbon atoms of the dipeptides. The identity of the varying C-terminal residue influences the values of φ, planarity of the peptide planes and geometry around the C7 α-carbon atoms while the solvation effects are evident on the values of bond lengths and bond angles of the amide planes. © 2013 Springer-Verlag Berlin Heidelberg.