Molecular dynamic simulation studies on the effect of one residue chain staggering on the structure and stability of heterotrimeric collagen-like peptides with interruption

A systematic molecular dynamics (MD) simulation has been carried out on collagen-like peptides with different combinations of interruptions in the GlyXAAYAA repeats. Although experimental studies have been carried out to elucidate the structural consequences of homotrimeric collagen-like peptides, this is the first report on the structural effect on the heterotrimeric models with G4G and G1G breaks present simultaneously in the constituent chains with difference in one residue chain staggering. The results reveal that the axial registry of the interrupted region changes significantly from that of conventional triple helical peptide without interruption. Further, results from MD simulations show the formation of a kink in the interrupted region of the triple-helical peptides. The conformational analysis reveals that the interruption in the GlyXAAYAA pattern in these peptides induces beta-strand conformation in triple helical peptides. The conventional hydrogen bonds in the interrupted triad are affected and new nonconventional H-bonds are formed in the triple helical structure, and as a result interrupted region becomes locally fragile. MM-PBSA calculations on the different systems clearly suggest that the binding affinity varies marginally due to one residue staggering. However, it is found from the structural parameters that hydrogen-bonding pattern differs significantly due to the difference in the staggering of chains. (c) 2012 Wiley Periodicals, Inc. Biopolymers 97:847863, 2012.