EFFECT OF pH ON STRUCTURE AND STABILITY OF COLLAGEN-LIKE PEPTIDE: INSIGHT FROM MOLECULAR DYNAMICS SIMULATION

Abstract

Molecular dynamics simulations were carried out to investigate the effect of pH on structure and stability of collagen-like peptide. All simulations were performed using the consistent valence force field (CVFF) molecular mechanical force field and isothermal-isobaric ensemble (NPT). The initial geometries of the collagen-like peptide were from an X-ray crystallographic structure. Some analyses from the molecular dynamics trajectories have been completed. The results show that the diameter of collagen-like peptide increases and the volume swells obviously in basic environment; however, the size of peptide changes slightly in acidic environment. The stability of collagen-like peptide decreases in acid and basic environment comparing to neutral environment based on root mean square deviation (RMSD). The number of hydrogen bond formed by peptide has a tendency to decrease in both acidic and basic environment. The average of intra-molecular H-bond is minimal under basic condition, and the average of inter-molecular H-bond between amino acid residues and water molecules is minimal under acid condition. The radial distribution function (RDF) shows that side-chain oxygen atoms are easier to form hydrogen bonds with water than side-chain nitrogen atoms. The interaction of various amino acid residues with water is position dependent. Distance between two triple helices increases markedly under highly basic condition, but changes slightly under highly acidic condition.