Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study.
Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study.
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本质无序蛋白质结合的过渡路径动力学：模拟研究。
DOI：
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发表时间：
2019
影响因子：
4.4
通讯作者：
D. Makarov
中科院分区：
文献类型：
--
作者：
M. Ozmaian;D. Makarov
蛋白质和其他生物聚合物的结合是生命系统中普遍存在的过程。最近的单分子测量通过测量缔合过渡路径的性质，即，在蛋白质足够接近以相互作用的时间和最终复合物的形成之间的分子轨迹的短片段。解释这种测量需要足够的模型来描述实验观测的动态。在努力开发这样的模型，在这里，我们报告了两个相反的电荷，无序聚合物的关联动力学的模拟研究。我们通过监测单体间距离来模拟实验测量，我们将其视为“实验反应坐标”。“虽然分子质心之间的距离的动力学被发现是无记忆和扩散的，但实验反应坐标的动力学显示出显着的记忆，并且可以通过具有记忆内核的广义朗之万方程来描述。我们计算最常见的测量属性的过渡路径，过渡路径时间的分布，并表明，尽管非马尔可夫的基本动力学，它是很好地近似为一维扩散的平均力的潜力，提供了一个明显的值的扩散系数被使用。该表观值介于存储器内核的慢（低频）和快（高频）极限之间。我们进一步研究了如何平均过渡路径时间取决于离子强度，发现只有弱的依赖性，尽管强的静电吸引力之间的聚合物。
Association of proteins and other biopolymers is a ubiquitous process in living systems. Recent single-molecule measurements probe the dynamics of association in unprecedented detail by measuring the properties of association transition paths, i.e., short segments of molecular trajectories between the time the proteins are close enough to interact and the formation of the final complex. Interpretation of such measurements requires adequate models for describing the dynamics of experimental observables. In an effort to develop such models, here we report a simulation study of the association dynamics of two oppositely charged, disordered polymers. We mimic experimental measurements by monitoring intermonomer distances, which we treat as "experimental reaction coordinates." While the dynamics of the distance between the centers of mass of the molecules is found to be memoryless and diffusive, the dynamics of the experimental reaction coordinates displays significant memory and can be described by a generalized Langevin equation with a memory kernel. We compute the most commonly measured property of transition paths, the distribution of the transition path time, and show that, despite the non-Markovianity of the underlying dynamics, it is well approximated as one-dimensional diffusion in the potential of mean force provided that an apparent value of the diffusion coefficient is used. This apparent value is intermediate between the slow (low frequency) and fast (high frequency) limits of the memory kernel. We have further studied how the mean transition path time depends on the ionic strength and found only weak dependence despite strong electrostatic attraction between the polymers.
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影响因子：
62.1
作者：
Schreiber, G.;Haran, G.;Zhou, H-X
通讯作者：
Zhou, H-X
DOI：
10.1073/pnas.89.8.3338
发表时间：
1992-04-15
影响因子：
11.1
作者：
NORTHRUP, SH;ERICKSON, HP
通讯作者：
ERICKSON, HP
结构开关生物传感器：受自然的启发。
影响因子：
6.8
作者：
Vallée-Bélisle A;Plaxco KW
通讯作者：
Plaxco KW
影响因子：
4.4
作者：
Peng, B.;Muthukumar, M.
通讯作者：
Muthukumar, M.
DOI：
10.1021/jp903671p
发表时间：
2009-08-06
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Gopich IV;Szabo A
通讯作者：
Szabo A