纳米孔壁面作用对蛋白质过孔影响的粗粒化分子动力学模拟

doi:10.19596/j.cnki.1001-246x.7982

计算物理 ›› 2020, Vol. 37 ›› Issue (1): 63-68.DOI: 10.19596/j.cnki.1001-246x.7982

纳米孔壁面作用对蛋白质过孔影响的粗粒化分子动力学模拟

史晓蕊, 刘振宇, 吴慧英

上海交通大学机械与动力工程学院, 上海 200240

收稿日期:2018-10-10 修回日期:2018-11-12 出版日期:2020-01-25 发布日期:2020-01-25
通讯作者: 吴慧英,E-mail:whysrj@sjtu.edu.cn
作者简介:史晓蕊(1993-),女,硕士研究生,主要从事分子动力学模拟研究
基金资助:
国家自然科学基金（51536005，51820105009，51676124）及上海市国际科技合作基金（18160743900）资助项目

Coarse-grained MD Simulation of Nanopore Interaction Influence on Protein Translocation

SHI Xiaorui, LIU Zhenyu, WU Huiying

School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

Received:2018-10-10 Revised:2018-11-12 Online:2020-01-25 Published:2020-01-25

摘要/Abstract

摘要： 基于粗粒化分子动力学方法模拟电驱动蛋白质过孔过程，研究纳米孔-水/纳米孔-蛋白质相互作用对电泳迁移率的影响；用操控式分子动力学模拟分析蛋白质在不同相互作用下过孔摩擦系数和摩擦阻力.研究发现：蛋白质黏附纳米孔壁面对其过孔特性影响并不明显，而纳米孔-水相互作用对蛋白质过孔电泳迁移率和摩擦系数影响较大.随纳米孔-水相互作用增强，纳米孔壁面与蛋白质附近水分子运动差异显现，蛋白质过孔摩擦阻力显著增大，过孔摩擦系数随之增大，进而影响蛋白质过孔电泳迁移率.所得结果可为纳米孔材料设计提供理论指导.

关键词: 纳米孔, 蛋白质, 分子动力学模拟, 相互作用

Abstract: Effect of nanopore-water/nanopore-protein interaction on electrophoresis mobility of protein translocation is studied with coarse-grained molecular dynamics simulation. With steer molecular dynamics, friction coefficient and friction of protein under different interactions are analyzed. It shows that protein adhesion to nanopore wall has weak effect on protein translocation through a nanopore, while nanopore-water interaction has significant effect on electrophoretic mobility and friction coefficient. The increase of interaction between nanopore and water increases difference between movement of water molecules near nanopore wall and protein, which leads to increase of friction coefficient of protein translocation. As a result, mobility electrophoresis of protein through nanopore is affected. It provides a theoretical guidance for the design of nanopore materials.

Key words: nanopore, protein, molecular dynamics, interaction

中图分类号:

O647

史晓蕊, 刘振宇, 吴慧英. 纳米孔壁面作用对蛋白质过孔影响的粗粒化分子动力学模拟[J]. 计算物理, 2020, 37(1): 63-68.

SHI Xiaorui, LIU Zhenyu, WU Huiying. Coarse-grained MD Simulation of Nanopore Interaction Influence on Protein Translocation[J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2020, 37(1): 63-68.

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纳米孔壁面作用对蛋白质过孔影响的粗粒化分子动力学模拟

Coarse-grained MD Simulation of Nanopore Interaction Influence on Protein Translocation

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