Coarse-grained simulation of the translational and rotational diffusion of globular proteins by dissipative particle dynamics
文献类型：期刊论文
| 作者 | Wei JC(韦佳辰); LiuYW; Song F(宋凡)
|
| 刊名 | JOURNAL OF CHEMICAL PHYSICS
 |
| 出版日期 | 2020-12-01 |
| 卷号 | 153期号:23页码:234902 |
| DOI | 10.1115/1.4047627 |
| 英文摘要 | With simplified interactions and degrees of freedom, coarse-grained (CG) simulations have been successfully applied to study the translational and rotational diffusion of proteins in solution. However, in order to reach larger lengths and longer timescales, many CG simulations employ an oversimplified model for proteins or an implicit-solvent model in which the hydrodynamic interactions are ignored, and thus, the real kinetics are more or less unfaithful. In this work, we develop a CG model based on the dissipative particle dynamics (DPD) that can be universally applied to different types of proteins. The proteins are modeled as a group of rigid DPD beads without conformational changes. The fluids (including solvent and ions) are also modeled as DPD beads. The electrostatic interactions between charged species are explicitly considered by including charge distributions on DPD particles. Moreover, a surface friction between the protein and fluid beads is applied to control the slip boundary condition. With this model, we investigate the self-diffusion of a single globular protein in bulk solution. The translational and rotational diffusion coefficients of the protein can be tuned by the surface frictional constant to fit the predictions of the Stokes-Einstein (SE) relation. We find that both translational and rotational diffusion coefficients that meet with the prediction of the SE relation based on experimental results of the hydrodynamic radius are reached at almost the same frictional constant for different types of proteins. Such scaling behavior indicates that the model can be applied to simulate the translational and rotational diffusion together for various types of proteins. |
| 分类号 | 二类 |
| 语种 | 英语 |
| WOS记录号 | WOS:000599773400002 |
| 其他责任者 | 韦佳辰 |
| 源URL | [http://dspace.imech.ac.cn/handle/311007/85693]  |
| 专题 | 力学研究所_非线性力学国家重点实验室 |
| 推荐引用方式 GB/T 7714 | Wei JC,LiuYW,Song F. Coarse-grained simulation of the translational and rotational diffusion of globular proteins by dissipative particle dynamics[J]. JOURNAL OF CHEMICAL PHYSICS,2020,153(23):234902. |
| APA | 韦佳辰,LiuYW,&宋凡.(2020).Coarse-grained simulation of the translational and rotational diffusion of globular proteins by dissipative particle dynamics.JOURNAL OF CHEMICAL PHYSICS,153(23),234902. |
| MLA | 韦佳辰,et al."Coarse-grained simulation of the translational and rotational diffusion of globular proteins by dissipative particle dynamics".JOURNAL OF CHEMICAL PHYSICS 153.23(2020):234902. |
入库方式： OAI收割
来源：力学研究所
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