Biomedical Research

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Studies on Molecular Dynamics Simulation and Solvent Stability analysis of Collagen Mimetic Peptide GFO with Cyclodextrin ? An Insilico analysis for Tissue Engineering.

Collagen mimetic peptides (CMPs) and collagen-like proteins (CLPs) that mimic either structural or functional characteristics of natural collagens have many applications to engineering collagen-like materials for potential biomedical use. Molecular modeling studies on collagen and collagen-like peptides suggest that triple-helical stability can vary along the amino acid chain. GFO is collagen-like peptide constructed using building script (BuScr) triple helix builder, whose stability is calculated in same scripting software and the Tm is found to be 30.74 OC.The stabilized GFO peptide is docked with α- cyclodextrin using auto dock 4.01v freeware and found atom-atom interaction with amino acids like Phe 11, Gly7 respectively. The estimated free energy of binding is calculated using auto dock was found to be as -8.26 kcal/Mol with Inhibition Constant, Ki = 880.75 nM at 298.15K. The interaction and negative binding shows there is stability between the docked complex, this study is conducted experimentally to confirm the same process in a wet lab.To the docked complex, solvent is added in two ways either for the whole complex else to specific docked region using specific options protocol available in Accelrys’ Discovery Studio 2.1v.Cascade dynamics studies are carried out for two different solvated complex with ensembles NVT and NPT, the changes in energy are observed only in the production stage for both complexes. Finally, the trajectory path is generated using principle component analysis(PCA) for the complex shows a small unit of changes in total energy at 302.526K.This computational study is correlated with experimental study shows, the stability of the Peptide complex in solvent environment.

Author(s): Lavanya Gunamalai, Chellam Jaynthy