Bahar I, Erman B, Haliloglu T, Jernigan R L
Polymer Research Center and School of Engineering, Bogazici University, Istanbul, Turkey.
Biochemistry. 1997 Nov 4;36(44):13512-23. doi: 10.1021/bi971611f.
A low-resolution model is used together with recently developed knowledge-based potentials for exploring the dynamics of proteins. Configurations are generated using a Monte Carlo/Metropolis scheme combined with a singular value decomposition technique (SVD). The approach is shown to characterize the cooperative motions in good detail, at least 1 order of magnitude faster than atomic simulations. Trajectories are partitioned into modes, and the slowest ones are analyzed to elucidate the dominant mechanism of collective motions. Calculations performed for bacteriophage T4 lysozyme, a two-domain enzyme, demonstrate that the structural elements within each domain are subject to strongly coupled motions, whereas the motions of the two domains with respect to each other are strongly anticorrelated. This type of motion, evidenced by the synchronous fluctuations of the domain centroids by up to +/-4.0 A in opposite directions, is comparable to the movements observed by recent spin-labeling experiments in solution. The potential of mean force governing these fluctuations is shown to be anharmonic. The beta-sheet region at the N-terminal domain and the helix E in the C-terminal domain are identified as regions important for mediating cooperative motions and, in particular, for the opening and closing of the active-site cleft between the domains. Residues Leu66-Phe67 in the central helix C stop the propagation of correlated motions between the domains. There is a correlation between the groups involved in highly cooperative motions revealed by simulations and the highly protected regions during unfolding measured by pulsed H/D exchange and 2-D NMR.
一种低分辨率模型与最近开发的基于知识的势一起用于探索蛋白质的动力学。使用蒙特卡罗/梅特罗波利斯方案结合奇异值分解技术（SVD）生成构型。结果表明，该方法能够很好地详细描述协同运动，速度至少比原子模拟快1个数量级。轨迹被划分为模式，并对最慢的模式进行分析以阐明集体运动的主导机制。对噬菌体T4溶菌酶（一种双结构域酶）进行的计算表明，每个结构域内的结构元件都受到强耦合运动的影响，而两个结构域相对于彼此的运动则强烈反相关。这种运动类型，通过结构域质心在相反方向上高达±4.0 Å的同步波动得以证明，与最近在溶液中进行的自旋标记实验所观察到的运动相当。控制这些波动的平均力势被证明是非谐的。N端结构域的β折叠区域和C端结构域的螺旋E被确定为介导协同运动，特别是介导结构域之间活性位点裂隙的打开和关闭的重要区域。中央螺旋C中的Leu66 - Phe67残基阻止了结构域之间相关运动的传播。模拟揭示的高度协同运动中涉及的基团与脉冲H/D交换和二维NMR测量的解折叠过程中的高度保护区域之间存在相关性。
