Role of aspartic acid in collagen structure and stability: A molecular dynamics investigation.
A molecular dynamics (MD) simulation study has been carried out to understand the stability of the triple helical collagen models. The calculations show that the presence of the aspartic acid residue in different positions leads to the local variation in the structure. Analyses of root-mean-square deviation (RMSD), radial distribution function (RDF), puckering effect, dihedral angle variation, hydrogen bond (H-bond), and conformational changes during molecular dynamics simulation reveal that the local perturbation in the sequences, increase in chain flexibility due to removal of five membered rings in the collagen by aspartic acid, change of intermolecular H-bonding pattern, and differences in the association of water are mainly influencing the nature of stabilization of collagen by aspartic acid.
Raman
S Sundar
SS
Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India.
Parthasarathi
R
R
Subramanian
V
V
Ramasami
T
T
D000595:Amino Acid Sequence; D001224:Aspartic Acid / Q000737:chemistry*; D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods*; D003094:Collagen / Q000737:chemistry*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D012984:Software; D013997:Time Factors
D010455:Peptides; D001224:Aspartic Acid; D003094:Collagen