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Published on: October 7, 2021
Cargo Recognition Mechanisms of Yeast Myo2 Revealed by AlphaFold2-Powered Protein Complex Prediction
Yong Liu1,2,3, Lingxuan Li2,3, Cong Yu2,4,5
1SUSTech-HIT Joint PhD Program, Harbin Institute of Technology, Harbin 150001, China.
Abstract:
Myo2, a yeast class V myosin, transports a broad range of organelles and plays important roles in various cellular processes, including cell division in budding yeast. Despite the fact that several structures of Myo2/cargo adaptor complexes have been determined, the understanding of the versatile cargo-binding modes of Myo2 is still very limited, given the large number of cargo adaptors identified for Myo2. Here, we used ColabFold, an AlphaFold2-powered and easy-to-use tool, to predict the complex structures of Myo2-GTD and its several cargo adaptors. After benchmarking the prediction strategy with three Myo2/cargo adaptor complexes that have been determined previously, we successfully predicted the atomic structures of Myo2-GTD in complex with another three cargo adaptors, Vac17, Kar9 and Pea2, which were confirmed by our biochemical characterizations. By systematically comparing the interaction details of the six complexes of Myo2 and its cargo adaptors, we summarized the cargo-binding modes on the three conserved sites of Myo2-GTD, providing an overall picture of the versatile cargo-recognition mechanisms of Myo2. In addition, our study demonstrates an efficient and effective solution to study protein-protein interactions in the future via the AlphaFold2-powered prediction.
Insights
Yeast Myo2 myosin uses conserved binding sites to transport various cellular cargoes. This study used AlphaFold2 to predict and confirm Myo2-adaptor complex structures, revealing versatile cargo recognition mechanisms.
Area of Science:
- Molecular Biology
- Cell Biology
- Structural Biology
Background:
- Myo2, a yeast class V myosin, is crucial for organelle transport and cell division.
- Understanding Myo2's diverse cargo-binding mechanisms is limited despite identified adaptors.
- Previous structural studies have determined some Myo2/cargo adaptor complexes.
Purpose of the Study:
- To predict and characterize the complex structures of Myo2-GTD with its cargo adaptors using computational methods.
- To elucidate the versatile cargo-binding modes of Myo2.
- To provide an overall picture of Myo2's cargo-recognition mechanisms.
Main Methods:
- Utilized ColabFold, an AlphaFold2-based tool, for predicting protein complex structures.
- Benchmarked prediction strategy with three known Myo2/cargo adaptor complexes.
- Performed biochemical characterizations to confirm predicted structures.
Main Results:
- Successfully predicted atomic structures of Myo2-GTD in complex with Vac17, Kar9, and Pea2.
- Confirmed predictions through biochemical characterizations.
- Identified and compared interaction details across six Myo2-adaptor complexes.
Conclusions:
- Summarized cargo-binding modes on three conserved sites of Myo2-GTD.
- Provided insights into the versatile cargo-recognition mechanisms of Myo2.
- Demonstrated AlphaFold2 as an efficient tool for studying protein-protein interactions.
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