Molecular Dynamics Simulations to Determine the Optimal Loop Length in the Helix-loop-helix Motif

Abstract

In this study, 100 ps molecular dynamics simulations were conducted to determine the optimal length of the Gly loop in the helix-loop-helix motif. The results revealed that the length of the loop significantly affected the stability of the two a-helices. In addition, the optimal loop length to maintain the highest helicity of the target peptide was found to be the one corresponding to 7 Gly residues. Longer loop length resulted in structural destabilization due to the entropic effect, while shorter loop length was not suitable to achieve intrachain packing of the two α-helices.

Key words:

• Molecular dynamics
• Helix-loop-helix
• Helicity
• α-helices