A molecular dynamics analysis of ion pairs formed by lysine in collagen: implication for collagen function and stability

Abstract

With view to gain insight into the importance of lysine-ion pairs (K-ion pairs) in the stabilization of collagen like peptides, a detailed sequence analysis and molecular dynamics simulation studies have been carried out. Conventional G–P–O sequence based triplets has been chosen to model the collagen (host) and several possible ion pair consisting other amino acids viz. lysine, aspartic acid and glutamic acid have been introduced in the most stable collagen like sequence combinations (host–guest) consisting of K–G–D and K–G–E (guests). Molecular dynamic simulations have been carried out for 4 ns after 1 ns equilibration for all the host and host–guest systems. The results obtained from the MD analyses clearly brought out the nature of forces involved in the stabilization of triple helix.