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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 |
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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.
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Received: 29 December 2020
Revised: 25 January 2021
Accepted manuscript online: 05 February 2021
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PACS:
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87.16.A-
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(Theory, modeling, and simulations)
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87.15.ap
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(Molecular dynamics simulation)
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87.14.E-
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(Proteins)
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87.18.Nq
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(Large-scale biological processes and integrative biophysics)
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| Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11974173 and 11934008) and the HPC Center of Nanjing University. |
Corresponding Authors:
Wenfei Li, Wei Wang
E-mail: wangwei@nju.edu.cn;wfli@nju.edu.cn
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Cite this article:
Wentao Zhu(祝文涛), Wenfei Li(李文飞), and Wei Wang(王炜) Modeling hydrogen exchange of proteins by a multiscale method 2021 Chin. Phys. B 30 078701
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