Loop motions of triosephosphate isomerase observed with elastic networks
Loop motions of triosephosphate isomerase observed with elastic networks
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DOI：
10.1021/bi0518085
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发表时间：
2006-01-31
期刊：
影响因子：
2.9
通讯作者：
Doruker, P
中科院分区：
文献类型：
--
作者：
Kurkcuoglu, O;Jernigan, RL;Doruker, P
磷酸三糖异构酶的内部动力学已通过弹性网络（有或没有底物结合）进行了研究。最慢的运动模式涉及大域运动，但也涉及循环运动，符合晶体结构 8TIM 和 ITPH 之间观察到的变化。我们的计算证实，该循环的不同运动在几种计算出的最慢模式中很重要。我们已经证明，对该蛋白质系统的弹性网络计算可以通过几种不同的方式将结构功能部分的原子与结构其余部分的粗粒度（cg）表示结合起来。原子和混合 cg 模型的弹性网络模型中也可以看到类似的循环运动。通过组合酶的自由形式和复杂形式的四种最慢的运动模式，以 0.75-0.79 的重叠再现循环运动。
The internal dynamics of triosephosphate isomerase have been investigated with elastic networks, with and without a substrate bound. The slowest modes of motion involve large domain motions but also a loop motion that conforms to the changes observed between the crystal structures 8TIM and ITPH. Our computations confirm that the different motions of this loop are important in several of the computed slowest modes. We have shown that elastic network computations on this protein system can combine atoms for the functional parts of the structure with coarse-grained (cg) representations of the remainder of the structure in several different ways. Similar loop motions are seen with elastic network models for atomistic and mixed cg models. The loop motions are reproduced with an overlap of 0.75-0.79 by combining the four slowest modes of motion for the free and complex forms of the enzyme.