MOLECULAR DYNAMICS SIMULATION STUDY ON THE EFFECT OF WATER ON THE THERMAL STABILITY OF COLLAGEN POLYPEPTIDE

Molecular dynamics simulations were carried out to investigate the effect of water oil the thermal stability of a collagen polypeptide with 79 amino acid residues. All the simulations were performed Using the Consistent Valence Force Field (CVFF) molecular mechanical force field and isothermal-isobaric ensemble (NPT). The theoretical parameters, root mean square deviation (RMSD) and root mean square fluctuation (RMSF) were Used to evaluate the structural stability and flexibility of the collagen polypeptide, respectively. The initial geometries of the collagen polypeptide were from an x-ray crystallographic structure. The results obtained indicate that the presence of water is beneficial to keeping the crystal structure of collagen polypeptide. But water favors the flexibility of backbone atoms and amino acid residues owing to the formation of water-polypeptide hydrogen bonds. Therefore, the triple helix structure of polypeptide is easier to collapse in the presence of water with rising temperature compared with that without water. Dehydration leads to a remarkable increase of inter-chain and intra-chain hydrogen bonds, so that the collagen polypeptide chains are more tightly combined with each other. As a result, the configurations of dehydrated collagen polypeptide depart from the initial configuration, and collagen polypeptide possesses less flexibility and higher thermal stability.