Yuan Chengqian, Li Shukun, Zou Qianli, Ren Ying, Yan Xuehai
State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
Phys Chem Chem Phys. 2017 Sep 13;19(35):23614-23631. doi: 10.1039/c7cp01923h.
Hierarchical self-assembly, abundant in biological systems, has been explored as an effective bottom-up method to fabricate highly ordered functional superstructures from elemental building units. Biomolecules, especially short peptides consisting of several amino acids, are a type of elegant building blocks due to their advantages of structural, mechanical, and functional diversity as well as high biocompatibility and biodegradability. The hierarchical self-assembly of peptides is a spontaneous process spanning multiple time and length scales under certain thermodynamics and kinetics conditions. Therefore, understanding the mechanisms of dynamic processes is crucial to directing the construction of complicated biomimetic systems with multiple functionalities. Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical self-assembly from the molecular level to the mesoscale. Herein, we provided an overview of the simulation hierarchies in the general field of peptide self-assembly modeling. In particular, we highlighted multiscale simulations for unraveling the mechanisms underlying the dynamic self-assembly process with an emphasis on weak intermolecular interactions in the process stages and the energies of different molecular alignments as well as the role of thermodynamic and kinetic factors at the microscopic level.
分层自组装在生物系统中广泛存在，已被探索为一种自下而上的有效方法，用于从基本构建单元制造高度有序的功能超结构。生物分子，尤其是由几个氨基酸组成的短肽，是一类出色的构建模块，因其具有结构、机械和功能多样性以及高生物相容性和生物降解性等优点。肽的分层自组装是在特定热力学和动力学条件下跨越多个时间和长度尺度的自发过程。因此，理解动态过程的机制对于指导构建具有多种功能的复杂仿生系统至关重要。结合并系统地连接多个层次的多尺度分子模拟可以提供从分子水平到中尺度的分层自组装的演化和动力学的见解。在此，我们概述了肽自组装建模一般领域中的模拟层次。特别是，我们强调了用于揭示动态自组装过程潜在机制的多尺度模拟，重点关注过程阶段中的弱分子间相互作用、不同分子排列的能量以及微观层面热力学和动力学因素的作用。
