Dipeptides containing N-terminal threonine residues: quantum chemical structural studies on nonionic, zwitterionic and water-clustered systems

Abstract

Despite having a surprisingly limited number of functional groups, the amino acid side-chain moieties serve as important determinants for protein folding and functional diversity of proteins. The current study was aimed at investigating the influence of the side-chain moiety of C-terminal residue on the structural and molecular properties of threonine-containing dipeptides, modeled by conserving threonine at their N-terminal positions and varying the C-terminal components with seven different combinations, viz. Val, Phe, Asp, Cys, Ser, His and Sec. Gas- and aqueous-phase B3LYP/6-311++G(d,p) level calculations on nonionic, zwitterionic and water-clustered forms of the dipeptides provide valuable insights regarding the influence of the C-terminal residues 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 as well as the number and type of intramolecular H-bond interactions existing in the dipeptides. The results furnished in this investigation are in good agreement with the earlier theoretical and experimental observations and reveal that B3LYP hybrid functional in combination with 6-311++G(d,p) basis set performs well in describing the electronic and vibrational spectroscopic properties of biologically relevant molecules. The zwitterions of the dipeptides are not stable in gas phase; after geometry optimization, they are converted to the nonionic forms.