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Molecular dynamics simulations to determine the optimal loop length in the helix-loop-helix motif
Hsuan-Liang Liu1, Yann-Chi Shu, Yann-Huei Wu
1Department of Chemical Engineering, National Taipei University of Technology, No. 1 Sec. 3 Chung-Hsiao E. Rd., Taipei 10643, Taiwan. f10894@ntut.edu.tw
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 alpha-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 alpha-helices.