Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation.
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
Raman
S Sundar
SS
Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India.
Vijayaraj
R
R
Parthasarathi
R
R
Subramanian
V
V
D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012399:Rotation; D013696:Temperature; D013997:Time Factors; D014633:Valine / Q000737:chemistry*
D010455:Peptides; D014633:Valine; D000409:Alanine