Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides

Gunajyoti Das,Shilpi Mandal

doi:10.1155/2013/939865

Gunajyoti Das, Shilpi Mandal

Open Access

https://doi.org/10.1155/2013/939865

Copy DOI

Abstract

In this theoretical study, the role of the side chain moiety of C-terminal residue in influencing the structural and molecular properties of dipeptides is analyzed by considering a series of seven dipeptides. The C-terminal positions of the dipeptides are varied with seven different amino acid residues, namely. Val, Leu, Asp, Ser, Gln, His, and Pyl while their N-terminal positions are kept constant with Sec residues. Full geometry optimization and vibrational frequency calculations are carried out at B3LYP/6-311++G(d,p) level in gas and aqueous phase. The stereo-electronic effects of the side chain moieties of C-terminal residues are found to influence the values of Φ and Ω dihedrals, planarity of the peptide planes, and geometry around the C7 α-carbon atoms of the dipeptides. The gas phase intramolecular H-bond combinations of the dipeptides are similar to those in aqueous phase. The theoretical vibrational spectra of the dipeptides reflect the nature of intramolecular H-bonds existing in the dipeptide structures. Solvation effects of aqueous environment are evident on the geometrical parameters related to the amide planes, dipole moments, HOMOLUMO energy gaps as well as thermodynamic stability of the dipeptides.

Highlights

Twenty canonical amino acid residues adequately build up the proteins and enzymes necessary to support most of the cellular functions in all the three domains of life on earth
These dihedral angles do not deviate dramatically from their expected values in both phases, the extent of deviations observed in the values of the four dihedral angles obviously suggests that the geometry of the amide planes are not perfectly planar regardless of whether the systems are in gas phase or in strong polar solvents like water
The stereo-electronic effects of the varying –SC groups influence the values of φ, planarity of the peptide planes, and geometry around the C7 α-carbon atoms of the dipeptides while the solvation effects are evident on the values of bond lengths and bond angles of the amide planes

Summary

Introduction

Twenty canonical amino acid residues adequately build up the proteins and enzymes necessary to support most of the cellular functions in all the three domains of life on earth. Selenocysteine (Sec) and pyrrolysine (Pyl) are the two rarely occurring genetically encoded amino acids whose presence in the active sites of some enzymes enables them to sustain life in some extraordinarily unique ways [1,2,3,4,5,6,7]. Over the last few decades, small amino acid sequences like dior tripeptides have been used extensively as model systems in the experimental and theoretical studies concerning the structure of proteins and energetics of protein folding. It is realized that computational techniques are indispensable in elucidating atomic level structural information about biologically active molecules [9,10,11]

Methods

Results

Conclusion