The normal modes of the gramicidin-A dimer channel.
The normal modes of the gramicidin-A dimer channel.
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DOI：
10.1016/s0006-3495(88)83107-2
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发表时间：
1988-03
影响因子：
3.4
通讯作者：
B. Roux;M. Karplus
中科院分区：
文献类型：
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作者：
B. Roux;M. Karplus
通过原子运动相对于平衡位置的振动分析，在谐波近似下研究了gramicidin-A二聚体通道的动力学。该系统由经验势能函数表示，所有自由度（键长、键角和扭角）都允许变化。计算了主二面角phi和psi的热波动、原子均方根位移以及不同酰胺面之间的相关性。发现只有相邻的二面体psi i和phi i+1是强相关的，而不同的氢键酰胺平面只有弱相关。相对较低的振动频率（75 ~ 175 cm-1）对羰基振动起主导作用。讨论了结构的一般柔韧性和羰基振动在离子传递机制中的作用。
The dynamics of the gramicidin-A dimer channel is studied in the harmonic approximation by a vibrational analysis of the atomic motions relative to their equilibrium positions. The system is represented by an empirical potential energy function, and all degrees of freedom (bonds lengths, bond angles, and torsional angles) are allowed to vary. The thermal fluctuations in the backbone dihedral angles phi and psi, atomic root mean square displacements, and the correlations between the different amide planes are computed. It is found that only adjacent dihedral psi i and phi i+1 are strongly correlated, while different hydrogen-bonded amide planes are only weakly correlated. Modes with relatively low vibrational frequencies (75–175 cm-1) make the dominant contributions to the carbonyl librations. The general flexibility of the structure and the role of carbonyl librations in the ion transport mechanism are discussed.