Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
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DOI：
10.1016/j.jmb.2005.07.031
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发表时间：
2005-09-30
影响因子：
5.6
通讯作者：
Karplus, M
中科院分区：
文献类型：
--
作者：
Maragakis, P;Karplus, M
利用塑料网络模型(PNM)建立了基于开放构象和封闭构象两种晶体结构的大肠埃希菌腺苷酸激酶构象变化途径。在该模型中，与已知构象相对应的能量盆地以其最低的公共能量连接。这些结果被用来评价和分析这些盆地之间的最小能量路径。开放式到封闭式转变分析提供了与现有基于可用X射线结构的定义一致的铰链的识别。弹性能分布和C-α伪二面体变化提供了关于这些铰链的相似信息。该蛋白质和密切相关蛋白质的45个已发表结构的集合被证明总是在该途径的3.0埃以内，这对应于两个末端结构之间的构象变化，这两个末端结构之间的C-α原子根平均偏差为7.1埃。(C)2005爱思唯尔有限公司。保留所有权利。
The plastic network model (PNM) is used to generate a conformational change pathway for Escherichia coli adenylate kinase based on two crystal structures, namely that of an open and a closed conformer. In this model, the energy basins corresponding to known conformers are connected at their lowest common energies. The results are used to evaluate and analyze the minimal energy pathways between these basins. The, open to closed transition analysis provides an identification of hinges that is in agreement with the existing definitions based on the available X-ray structures. The elastic energy distribution and the C-alpha pseudo-dihedral variation provide similar information on these hinges. The ensemble of the 45 published structures for this protein and closely related proteins is shown to always be within 3.0 angstrom of the pathway, which corresponds to a conformational change between two end structures that differ by a C-alpha-atom root-meansquared deviation of 7.1 angstrom. (c) 2005 Elsevier Ltd. All rights reserved.