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学者姓名：杨嵩
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Abstract ：
Proteins are inherently dynamic molecules, and their conformational transitions among various states are essential for numerous biological processes, which are often modulated by their interactions with surrounding environments. Although molecular dynamics (MD) simulations are widely used to investigate these transitions, all-atom (AA) methods are often limited by short time scales and high computational costs, and coarse-grained (CG) implicit-solvent Go-like models are usually incapable of studying the interactions between proteins and their environments. Here, we present an approach called Multiple-basin Go-Martini, which combines the recent Go-Martini model with an exponential mixing scheme to facilitate the simulation of spontaneous protein conformational transitions in explicit environments. We demonstrate the versatility of our method through five diverse case studies: GlnBP, Arc, Hinge, SemiSWEET, and TRAAK, representing ligand-binding proteins, fold-switching proteins, de novo designed proteins, transporters, and mechanosensitive ion channels, respectively. Multiple-basin Go-Martini offers a new computational tool for investigating protein conformational transitions, identifying key intermediate states, and elucidating essential interactions between proteins and their environments, particularly protein-membrane interactions. In addition, this approach can efficiently generate thermodynamically meaningful data sets of protein conformational space, which may enhance deep learning-based models for predicting protein conformation distributions.
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| GB/T 7714 | Yang, Song , Song, Chen . Multiple-Basin Go-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins [J]. | JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 2025 , 21 (10) : 5304-5321 . |
| MLA | Yang, Song 等. "Multiple-Basin Go-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins" . | JOURNAL OF CHEMICAL THEORY AND COMPUTATION 21 . 10 (2025) : 5304-5321 . |
| APA | Yang, Song , Song, Chen . Multiple-Basin Go-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins . | JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 2025 , 21 (10) , 5304-5321 . |
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Abstract ：
The Sec translocon is vital for guiding membrane protein insertion into lipid bilayers. The insertion and folding processes of membrane proteins are poorly understood. Here, we report cryo-electron microscopy structures of multi-spanning membrane proteins inserting through the SecY channel, the Sec translocon in prokaryotes. The high-resolution structures illustrate how bulky amino acids pass the narrow channel restriction. Comparison of different translocation states reveals that the cytoplasmic and extracellular cavities of the channel create distinct environments for promoting the unfolding and folding of transmembrane segments (TMs), respectively. Released substrate TMs are either flexible or stabilized by an unexpected hydrophilic groove between TM3 and TM4 of SecY. Disruption of the groove causes global defects in the folding of the membrane proteome. These findings demonstrate that beyond its role as a passive protein-conducting channel, the SecY translocon actively serves as a chaperone, employing multiple mechanisms to promote membrane protein insertion and folding.
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| GB/T 7714 | Ou, Xiaomin , Ma, Chengying , Sun, Dongjie et al. SecY translocon chaperones protein folding during membrane protein insertion [J]. | CELL , 2025 , 188 (7) . |
| MLA | Ou, Xiaomin et al. "SecY translocon chaperones protein folding during membrane protein insertion" . | CELL 188 . 7 (2025) . |
| APA | Ou, Xiaomin , Ma, Chengying , Sun, Dongjie , Xu, Jinkun , Wang, Yang , Wu, Xiaofei et al. SecY translocon chaperones protein folding during membrane protein insertion . | CELL , 2025 , 188 (7) . |
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