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Wang J, Wang X, Chu Y, Li C, Li X, Meng X, Fang Y, No KT, Mao J, Zeng X. Exploring the Conformational Ensembles of Protein-Protein Complex with Transformer-Based Generative Model. J Chem Theory Comput 2024; 20:4469-4480. [PMID: 38816696 DOI: 10.1021/acs.jctc.4c00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Protein-protein interactions are the basis of many protein functions, and understanding the contact and conformational changes of protein-protein interactions is crucial for linking the protein structure to biological function. Although difficult to detect experimentally, molecular dynamics (MD) simulations are widely used to study the conformational ensembles and dynamics of protein-protein complexes, but there are significant limitations in sampling efficiency and computational costs. In this study, a generative neural network was trained on protein-protein complex conformations obtained from molecular simulations to directly generate novel conformations with physical realism. We demonstrated the use of a deep learning model based on the transformer architecture to explore the conformational ensembles of protein-protein complexes through MD simulations. The results showed that the learned latent space can be used to generate unsampled conformations of protein-protein complexes for obtaining new conformations complementing pre-existing ones, which can be used as an exploratory tool for the analysis and enhancement of molecular simulations of protein-protein complexes.
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Affiliation(s)
- Jianmin Wang
- The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Korea
| | - Xun Wang
- School of Computer Science and Technology, China University of Petroleum, Qingdao, Shandong 266580, P. R. China
- High Performance Computer Research Center, University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yanyi Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Chunyan Li
- School of Informatics, Yunnan Normal University, Kunming, Yunnan 650500, P. R. China
| | - Xue Li
- School of Computer Science and Technology, China University of Petroleum, Qingdao, Shandong 266580, P. R. China
| | - Xiangyu Meng
- School of Computer Science and Technology, China University of Petroleum, Qingdao, Shandong 266580, P. R. China
| | - Yitian Fang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Korea
| | - Jiashun Mao
- School of Medical Information and Engineering, Southwest Medical University, Luzhou, Sichuan 646000, P. R. China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
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Hall D, Basu G, Ito N. Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday. Biophys Rev 2023; 14:1211-1222. [PMID: 36620377 PMCID: PMC9809522 DOI: 10.1007/s12551-022-01039-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
- Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Gautam Basu
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VII-M, Kolkata, 700054 India
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-Ku, Tokyo, 113-8510 Japan
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