Tirado-Rives J, Jorgensen W L
Department of Chemistry, Yale University, New Haven, Connecticut 06511.
Biochemistry. 1991 Apr 23;30(16):3864-71. doi: 10.1021/bi00230a009.
Molecular dynamics simulations of the S-peptide analogue AETAAAKFLREHMDS have been conducted in aqueous solution for 300 ps at 278 K and for 500 ps in two different runs at 358 K. The results show agreement with experimental observations in that at low temperature, 5 degrees C, the helix is stable, while unfolding is observed at 85 degrees C. In the low-temperature simulation a solvent-separated ion pair was formed between Glu-2 and Arg-10, and the side chain of His-12 reoriented toward the C-terminal end of the alpha-helix. Detailed analyses of the unfolding pathways at high temperature have also revealed that the formation or disappearance of main-chain helical hydrogen bonds occurs frequently through an alpha in equilibrium with 3(10) in equilibrium with no hydrogen bond sequence.
对S肽类似物AETAAAKFLREHMDS进行了分子动力学模拟，在278 K的水溶液中进行了300 ps的模拟，并在358 K下分两次进行了500 ps的模拟。结果与实验观察结果一致，即在低温（5℃）下，螺旋结构稳定，而在85℃时观察到解折叠。在低温模拟中，Glu-2和Arg-10之间形成了溶剂分隔的离子对，His-12的侧链重新定向至α螺旋的C末端。对高温下解折叠途径的详细分析还表明，主链螺旋氢键的形成或消失经常通过与3(10)处于平衡且无氢键序列的α状态来实现。
