Modeling AAA+ ring complexes from monomeric structures
Modeling AAA+ ring complexes from monomeric structures
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DOI：
10.1016/j.jsb.2006.04.011
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发表时间：
2006-10-01
影响因子：
3
通讯作者：
Lupas, Andrei N.
中科院分区：
文献类型：
--
作者：
Diemand, Alexander V.;Lupas, Andrei N.
AAA+ 蛋白质形成大的环形复合物，充当大分子的能量依赖性解折叠酶。该超家族中蛋白质的许多晶体结构已被确定，但大多数为单体或非生理寡聚形式。因此，从单体坐标组装环形复合物引起了相当大的兴趣。我们从实验确定的低聚物中提取了与单体距中心轴的距离、单体相对方向和界面分子接触相关的复杂形成的结构特征，并在 iMolTalk 服务器中实现了基于 Rosetta-Dock 的半自动建模程序 (http://protevo.eb.tuebingen.mpg.de/iMolTalk)。作为此过程的示例，我们在此介绍 Apaf-1、MalT 和 ClpB 的模型。我们表明，最近基于 EM 的凋亡体模型与 AAA+ 复合物的保守结构特征不兼容，并且 ClpB 的 D1 和 D2 环很可能被一个亚基偏移，这与 ClpA 提出的结构一致。 (c) 2006 Elsevier Inc. 保留所有权利。
AAA+ proteins form large, ring-shaped complexes, which act as energy-dependent unfoldases of macromolecules. Many crystal structures of proteins in this superfamily have been determined, but mostly in monomeric or non-physiological oligomeric forms. The assembly of ring-shaped complexes from monomer coordinates is, therefore, of considerable interest. We have extracted structural features of complex formation relating to the distance of monomers from the central axis, their relative orientation and the molecular contacts at their interfaces from experimentally determined oligomers and have implemented a semi-automated modeling procedure based on Rosetta-Dock into the iMolTalk server (http://protevo.eb.tuebingen.mpg.de/iMolTalk). As examples of this procedure, we present here models of Apaf-1, MalT and ClpB. We show that the recent EM-based model of the apoptosome is not compatible with the conserved structural features of AAA+ complexes and that the D1 and D2 rings of ClpB are most likely offset by one subunit, in agreement with the structure proposed for ClpA. (c) 2006 Elsevier Inc. All rights reserved.