Roux B, Karplus M
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Biophys J. 1988 Mar;53(3):297-309. doi: 10.1016/S0006-3495(88)83107-2.
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.
通过对相对于平衡位置的原子运动进行振动分析，在简谐近似下研究了短杆菌肽 - A二聚体通道的动力学。该系统由一个经验势能函数表示，所有自由度（键长、键角和扭转角）都允许变化。计算了主链二面角phi和psi的热涨落、原子均方根位移以及不同酰胺平面之间的相关性。发现只有相邻的二面角psi i和phi i + 1高度相关，而不同的氢键结合酰胺平面之间只有弱相关性。振动频率相对较低（75 - 至175厘米-1）的模式对羰基摆动起主要作用。讨论了结构的一般柔韧性以及羰基摆动在离子传输机制中的作用。
