Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics

被引:1
|
作者
Mapplebeck, Sarah [1 ,2 ]
Booth, Jonathan [1 ]
Shalashilin, Dmitrii [1 ]
机构
[1] Univ Leeds, Sch Chem, Leeds LS2 9JT, W Yorkshire, England
[2] Croda Europe Ltd, Cowick Hall, Goole DN14 9AA, East Yorkshire, England
来源
JOURNAL OF CHEMICAL PHYSICS | 2021年 / 155卷 / 08期
基金
英国工程与自然科学研究理事会;
关键词
TITIN IMMUNOGLOBULIN DOMAINS; FORCE SPECTROSCOPY; MONTE-CARLO; KINETICS; ADHESION;
D O I
10.1063/5.0059321
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We demonstrate how recently developed Boxed Molecular Dynamics (BXD) and kinetics [D. V. Shalashilin et al., J. Chem. Phys. 137, 165102 (2012)] can provide a kinetic description of protein pulling experiments, allowing for a connection to be made between experiment and the atomistic protein structure. BXD theory applied to atomic force microscopy unfolding is similar in spirit to the kinetic two-state model [A. Noy and R. W. Friddle, Methods 60, 142 (2013)] but with some differences. First, BXD uses a large number of boxes, and therefore, it is not a two-state model. Second, BXD rate coefficients are obtained from atomistic molecular dynamics simulations. BXD can describe the dependence of the pulling force on pulling speed. Similar to Shalashilin et al. [J. Chem. Phys. 137, 165102 (2012)], we show that BXD is able to model the experiment at a very long time scale up to seconds, which is way out of reach for standard molecular dynamics. Published under an exclusive license by AIP Publishing.
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收藏
页数:11
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