无模板预测新型单域跨膜蛋白折叠和组装的 AlphaFold2。

Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2.

机构信息

Department of Chemistry, Vanderbilt University, Nashville, Tennessee.

Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.

出版信息

Biophys J. 2023 Jun 6;122(11):2041-2052. doi: 10.1016/j.bpj.2022.11.011. Epub 2022 Nov 9.

Abstract

AlphaFold2 (AF2) has revolutionized the field of protein structural prediction. Here, we test its ability to predict the tertiary and quaternary structure of a previously undescribed scaffold with new folds and unusual architecture, the monotopic membrane protein caveolin-1 (CAV1). CAV1 assembles into a disc-shaped oligomer composed of 11 symmetrically arranged protomers, each assuming an identical new fold, and contains the largest parallel β-barrel known to exist in nature. Remarkably, AF2 predicts both the fold of the protomers and the interfaces between them. It also assembles between seven and 15 copies of CAV1 into disc-shaped complexes. However, the predicted multimers are energetically strained, especially the parallel β-barrel. These findings highlight the ability of AF2 to correctly predict new protein folds and oligomeric assemblies at a granular level while missing some elements of higher-order complexes, thus positing a new direction for the continued development of deep-learning protein structure prediction approaches.

摘要

AlphaFold2 (AF2) 彻底改变了蛋白质结构预测领域。在这里,我们测试了它预测具有新折叠和不常见结构的以前未描述支架的三级和四级结构的能力,该支架是单跨膜蛋白窖蛋白-1 (CAV1)。CAV1 组装成由 11 个对称排列的原聚体组成的盘状寡聚体,每个原聚体采用相同的新折叠,并且包含自然界中已知存在的最大平行 β-桶。值得注意的是,AF2 预测了原聚体的折叠和它们之间的界面。它还将 7 到 15 个 CAV1 拷贝组装成盘状复合物。然而,预测的多聚体在能量上是紧张的,特别是平行的β-桶。这些发现强调了 AF2 在颗粒水平上正确预测新蛋白质折叠和寡聚体组装的能力,同时错过了一些高级复合物的元素,从而为深度学习蛋白质结构预测方法的持续发展提出了一个新的方向。

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