Molecular dynamics simulations to determine the optimal loop length in the helix-loop-helix motif.
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.
Liu
Hsuan-Liang
HL
Department of Chemical Engineering, National Taipei University of Technology, No. 1 Sec. 3 Chung-Hsiao E. Rd., Taipei 10643, Taiwan. f10894@ntut.edu.tw
Shu
Yann-Chi
YC
Wu
Yann-Huei
YH
D000595:Amino Acid Sequence; D003198:Computer Simulation; D018257:Helix-Loop-Helix Motifs; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D010446:Peptide Fragments