Modeling hydrogen exchange of proteins by a multiscale method

doi:10.1088/1674-1056/abe377

中国物理B ›› 2021, Vol. 30 ›› Issue (7): 78701-078701.doi: 10.1088/1674-1056/abe377

Modeling hydrogen exchange of proteins by a multiscale method

Wentao Zhu(祝文涛), Wenfei Li(李文飞)^†, and Wei Wang(王炜)^‡

School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

收稿日期:2020-12-29 修回日期:2021-01-25 接受日期:2021-02-05 出版日期:2021-06-22 发布日期:2021-06-24
通讯作者: Wenfei Li, Wei Wang E-mail:wangwei@nju.edu.cn;wfli@nju.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11974173 and 11934008) and the HPC Center of Nanjing University.

Modeling hydrogen exchange of proteins by a multiscale method

Wentao Zhu(祝文涛), Wenfei Li(李文飞)^†, and Wei Wang(王炜)^‡

School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

Received:2020-12-29 Revised:2021-01-25 Accepted:2021-02-05 Online:2021-06-22 Published:2021-06-24
Contact: Wenfei Li, Wei Wang E-mail:wangwei@nju.edu.cn;wfli@nju.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11974173 and 11934008) and the HPC Center of Nanjing University.

摘要/Abstract

摘要： We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments. By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm, we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations. We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy. These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.

关键词: coarse-grained model, hydrogen exchange, multiscale method, proteins, integrative molecular simulations

Abstract: We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments. By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm, we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations. We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy. These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.

Key words: coarse-grained model, hydrogen exchange, multiscale method, proteins, integrative molecular simulations

中图分类号: (Theory, modeling, and simulations)

87.16.A-

87.15.ap (Molecular dynamics simulation) 87.14.E- (Proteins) 87.18.Nq (Large-scale biological processes and integrative biophysics)

Wentao Zhu(祝文涛), Wenfei Li(李文飞), and Wei Wang(王炜). Modeling hydrogen exchange of proteins by a multiscale method[J]. 中国物理B, 2021, 30(7): 78701-078701.

Wentao Zhu(祝文涛), Wenfei Li(李文飞), and Wei Wang(王炜). Modeling hydrogen exchange of proteins by a multiscale method[J]. Chin. Phys. B, 2021, 30(7): 78701-078701.

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Modeling hydrogen exchange of proteins by a multiscale method

Modeling hydrogen exchange of proteins by a multiscale method

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