Helix Forming Tendency of Valine Substituted Poly-Alanine: A Molecular Dynamics Investigation

• Published in: The journal of physical chemistry. B Vol. 112; no. 30; pp. 9100 - 9104
• Main Authors: Raman, S. Sundar, Vijayaraj, R, Parthasarathi, R, Subramanian, V
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 31.07.2008
• Subjects: Alanine - chemistry; Algorithms; B: Biophysical Chemistry; Models, Molecular; Peptides - chemistry; Protein Structure, Secondary; Rotation; Temperature; Time Factors; Valine - chemistry
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp7119813

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 310 and α-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.