A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices.
A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices.
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螺旋传播的微观视图：丙氨酸螺旋中 N 端和 C 端螺旋的生长。
DOI：
10.1006/jmbi.1996.0339
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发表时间：
1996
影响因子：
5.6
通讯作者：
Brooks3rd,CL
中科院分区：
文献类型：
--
作者：
Young,WS;Brooks3rd,CL
采用分子动力学模拟方法，对Ace-（Ala）n-NMe（n =（4，5，10，15））在水中的C端和N端小螺旋传播过程进行了自由能模拟.从由此产生的自由能表面，计算作为一个功能的终端的双二面角，长度和末端效应在螺旋传播中的作用进行了探讨。一个充满活力的分析的螺旋，形成和部分形成，是用来开发一个分子的合理化所观察到的趋势，螺旋稳定性。我们发现，微观螺旋传播参数变化显着取决于末端和螺旋长度的末端氢键形成。一个模型，认为传播的螺旋从任何一端作为统计独立的收益Zimm-Braggs参数在0.5至1.5的范围内，取决于螺旋长度。螺旋传播的机制的分析表明，310-螺旋在螺旋形成中起作用，但它的人口应该是低的螺旋状态，这些模型肽。
Molecular dynamics simulations with umbrella sampling are used to perform free energy simulations of C-terminal and N-terminal helix propagation in small helices of Ace-(Ala)n-NMe, withn= (4,5,10,15), in water. From the resulting free energy surfaces, computed as a function of the terminal ψ dihedral angle, the roles of length and end effects in helix propagation are explored. An energetic analysis of the helices, both formed and partially formed, is used to develop a molecular rationalization for the observed trends in helix stability. We find that the microscopic helix propagation parameters vary significantly depending on the end and ψ length of the helix in which the terminal hydrogen bond is forming. A model which considers propagation of the helices from either end as statistically independent yields Zimm-Braggsparameters in the range of 0.5 to 1.5, depending on helical length. Analysis of the mechanism of helix propagation suggests that 310-helix plays a role in helix formation but its population should be low in the helical state of these model peptides.