Structural and molecular properties of dipeptides containing N-terminal selenomethionine: a theoretical study

Abstract

Although the genetic code encodes only 22 amino acids during protein bio-synthesis, there are more than 140 natural amino acids whose incorporation into the protein structures is vital for proper functioning of the chemical and bio-chemical machineries associated with living beings. Among these, selenium-containing amino acids are of special interest for amino acid biochemistry. During the last few decades, the structure–function relationships of proteins are being best pursued by considering amino acids, dipeptides as well as their analogs as model systems. By performing this theoretical study it is intended to investigate the influence of functional group/groups present in side chain moieties of the varying C-terminal residues on the molecular and structural features of a set of seven dipeptides, constructed by conserving selenomethionine at their N-terminal positions while the C-terminal ends are varied with one of the following amino acid residues—Val, Trp, Glu, Cys, Tyr, Arg, and Sec. Geometry optimization and vibrational frequency calculations were carried out in gas and aqueous phase using B3LYP/6-311++G(d,p) level of theory. The results furnished by this DFT study provide a good account of the role of the C-terminal residue’s identity in determining the structural features of the amide planes, values of the ψ and ф dihedrals, geometry about the α-carbon atoms, theoretical IR spectra and the number and type of intramolecular H-bond interactions existing in the dipeptides. In aqueous phase, the dipeptide geometries exhibit larger values of total dipole moments, greater HOMO–LUMO energy gaps and enhanced thermodynamic stability than those in gas phase.