Structure and molecular dynamics simulation of archaeal prefoldin: The molecular mechanism for binding and recognition of nonnative substrate proteins
Structure and molecular dynamics simulation of archaeal prefoldin: The molecular mechanism for binding and recognition of nonnative substrate proteins
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DOI：
10.1016/j.jmb.2007.12.010
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发表时间：
2008-02-29
影响因子：
5.6
通讯作者：
Yohda, Masafumi
中科院分区：
文献类型：
--
作者：
Ohtaki, Akashi;Kida, Hiroshi;Yohda, Masafumi
前折叠蛋白(Prefoldin，PFD)是真核生物胞浆和古生菌中的一种异六聚体分子伴侣复合体，具有水母样结构，含有六个长长的卷曲触须。PFDs捕获蛋白质折叠中间体或未折叠的多肽，并将它们转移到第二类伴侣蛋白以促进折叠。虽然已经对与未折叠蛋白相互作用或与古生菌PFD伴侣蛋白合作的机制进行了详细的研究，但仍不清楚PFD是如何捕获未折叠蛋白的。在本研究中，我们测定了Horikoshii OT3PfD(PhPFD)在3.0埃分辨率下的X射线结构，并通过分子动力学(MD)模拟和突变分析研究了非本源底物蛋白结合和识别的分子机制。PhPFD有一个水母一样的结构，有六个长长的卷曲触须和一个大的中央空腔。每个亚基在结合未折叠底物蛋白的远端区域有疏水凹槽。在330K的分子动力学模拟中，每个盘绕的线圈都具有高度的灵活性，使其能够扩大其中央空腔并捕获各种标准蛋白质。PhPFD与未折叠胰岛素的对接MD模拟表明，β亚基基本上参与底物结合，而阿尔法亚单位调节中央空腔的形状和宽度。用氨基酸取代疏水沟槽中P亚基疏水残基的突变PhPFDs的分析表明，βIle107在形成疏水沟槽中起着关键作用。(C)2007 Elsevier Ltd.保留所有权利。
Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 angstrom resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various normative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the P subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.(C) 2007 Elsevier Ltd. All rights reserved.