Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology.
Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology.
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DOI：
10.1021/acs.jpcb.2c07015
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发表时间：
2022-11-17
影响因子：
3.3
通讯作者：
Liang, Jie
中科院分区：
文献类型：
--
作者：
Manuchehrfar, Farid;Li, Huiyu;Ma, Ao;Liang, Jie
势垒跨越过程中反应坐标的动力学是理解蛋白质等复杂系统中激活过程的关键。克拉默斯的物理直觉的默认假设是一个扩散过程。然而，在天然复杂分子中的势垒跨越的动力学在很大程度上是未探索的。在这里，我们调查的丙氨酸二肽异构化，最简单的复杂系统，具有大量的非反应坐标，可以作为一个足够的热浴进料能量到反应坐标的过渡动力学。我们沿着时间轴分离构象，构造反应的动态概率面。我们量化它的拓扑结构和旋转通量使用持久的同源性和微分形式。我们的结果揭示了组态-时间空间中的一个强反应涡旋区域，那里是最高几率峰和过渡态系综的位置。这个反应区域包含强烈的旋转通量：大多数反应轨迹在两个最重要的反应坐标的子空间中围绕这个区域旋转多次。此外，旋转通量是由沿着等离子体表面的协同运动和正交势垒交叉引起的。总的来说，我们的研究结果提供了第一次瞥见反应性涡流区域，其特征是自然发生的激活过程的障碍交叉的非扩散动力学。
Dynamics of reaction coordinates during barrier-crossing are key to understand activated processes in complex systems such as proteins. The default assumption from Kramers’ physical intuition is that of a diffusion process. However, the dynamics of barrier-crossing in natural complex molecules are largely unexplored. Here we investigate the transition dynamics of alanine-dipeptide isomerization, the simplest complex system with a large number of non-reaction coordinates that can serve as an adequate thermal bath feeding energy into the reaction coordinates. We separate conformations along the time axis and construct the dynamic probability surface of reaction. We quantify its topological structure and rotational flux using persistent homology and differential form. Our results uncovered a region with strong reactive vortex in the configuration-time space, where the highest probability peak and the transition state ensemble are located. This reactive region contains strong rotational fluxes: Most reactive trajectories swirl multiple times around this region in the subspace of the two most-important reaction coordinates. Furthermore, the rotational fluxes result from cooperative movement along the isocommitter surfaces and orthogonal barrier-crossing. Overall, our findings offer a first glimpse into the reactive vortex regions that characterize the non-diffusive dynamics of barrier-crossing of a naturally occurring activation process.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
DOI：
10.1021/acs.jpcb.1c00904
发表时间：
2021-05-13
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Manuchehrfar F;Li H;Tian W;Ma A;Liang J
通讯作者：
Liang J
影响因子：
4.4
作者：
Collins, Peter;Ezra, Gregory S.;Wiggins, Stephen
通讯作者：
Wiggins, Stephen
DOI：
10.1073/pnas.100127697
发表时间：
2000-05-23
影响因子：
11.1
作者：
Bolhuis, PG;Dellago, C;Chandler, D
通讯作者：
Chandler, D
影响因子：
4.4
作者：
CHANDLER, D
通讯作者：
CHANDLER, D