Multiscale, Multiresolution Coarse-Grained Model via a Hybrid Approach: Solvation, Structure, and Self-Assembly of Aromatic Tripeptides
Multiscale, Multiresolution Coarse-Grained Model via a Hybrid Approach: Solvation, Structure, and Self-Assembly of Aromatic Tripeptides
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基于混合方法的多尺度、多分辨率粗粒模型：芳香族三肽的溶剂化、结构和自组装
DOI：
10.1021/acs.jctc.3c00458
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发表时间：
2023-11-06
影响因子：
5.5
通讯作者：
Dutt，Meenakshi
中科院分区：
文献类型：
--
作者：
Hooten，Mason;Banerjee，Akash;Dutt，Meenakshi
利用计算技术，已经观察到短芳香肽组装成不同的纳米结构，包括纤维、管和囊泡。然而，计算研究采用了自顶向下的粗粒度（CG）模型，这些模型无法以与分子的全原子（AA）表示一致的方式捕获聚合体中肽的组装以及构象、包装和组织。在本研究中，采用基于结构和力的混合方法，利用AA轨迹的参考数据建立了自下而上的三苯丙氨酸CG力场。这种方法遵循一种灵活的方法，用所选的CG表示近似底层AA表示的化学复杂性。开发了两个具有不同芳香侧链表示的CG模型。第一个使用简单的单颗表示法，而第二个使用三颗表示法来更准确地表示环的平面度。单头模型产生纳米棒，而三头模型产生纳米球。不同的化学基团在纳米结构组装中的作用被确定，以及空间效应对组装内肽的包装的重要性。
Short aromatic peptides have been observed to assemble into diverse nanostructures, including fibers, tubes, and vesicles, using computational techniques. However, the computational studies have employed top-down coarse-grained (CG) models, which are unable to capture the assembly along with the conformation, packing, and organization of the peptides within the aggregates in a manner that is consistent with the all atom (AA) representation of the molecules. In this study, a hybrid structure- and force-based approach is adapted to develop a bottom-up CG force field of triphenylalanine using reference data from AA trajectories. This approach follows a flexible methodology to approximate the chemical complexity of the underlying AA representation with the chosen CG representation. Two CG models are developed with distinct representations of the aromatic side chains. The first uses a simple single-bead representation, while the second uses a three-bead representation to more accurately represent the planarity of the ring. The one-bead model yields nanorods, while the three-bead model results in nanospheres. The role of different chemical groups in the assembly of nanostructures is identified, along with the importance of steric effects on the packing of the peptides within assemblies.