Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of yeast proteins, identify 1,505 likely to interact, and build structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. These complexes, which have as many as 5 subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function.

中文翻译：

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核心真核蛋白复合物的计算结构

蛋白质-蛋白质相互作用在生物学中起着至关重要的作用，但许多真核蛋白质复合物的结构尚不清楚，而且可能还有许多相互作用尚未确定。我们利用全蛋白质组氨基酸协同进化分析和基于深度学习的结构建模的进展，系统地识别和构建酿酒酵母核心真核蛋白复合物的准确模型蛋白质组。我们使用 RoseTTAFold 和 AlphaFold 的组合来筛选 830 万对酵母蛋白的配对多序列比对，确定 1,505 种可能相互作用，并为 106 个以前未识别的组件和 806 个尚未进行结构表征的组件建立结构模型。这些具有多达 5 个亚基的复合物在真核细胞的几乎所有关键过程中发挥作用，并提供对生物学功能的广泛见解。