自组装肽生物材料:从自发和增强采样分子动力学模拟的见解

IF 6.1 Q2 CHEMISTRY, PHYSICAL Chemical physics reviews Pub Date : 2023-04-21 DOI:10.1063/5.0142302
Billy J. Williams-Noonan, Alexa Kamboukos, N. Todorova, I. Yarovsky
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引用次数: 2

摘要

肽自组装是肽分子聚集成低维(1D, 2D)或3D有序材料的过程,其潜在应用范围从药物输送到电子产品。由于相对简单的结构和易于调节其自组装过程以达到所需的材料性能,短肽是形成超分子组装体的特别好的候选者。纤维肽基纳米材料作为三维原子坐标的实验分辨率仍然具有挑战性。特别是对于表面介导的肽组装,通常不可能通过实验来解决多个构象不同的表面结合肽结构。由于复杂的相互作用以及自组装过程中涉及的多个时间和长度尺度的交换,肽自组装的机制仍然难以捉摸。肽在溶液中或由表面介导的自组装是由肽与水之间的特定相互作用、肽内部和/或肽聚集单元之间的竞争相互作用以及肽与溶剂分子之间的相互作用驱动的,后者是肽与溶剂分子之间的相互作用,以便吸附到近端表面上。计算方法已被证明有助于阐明肽自组装过程中形成的结构和驱动它的分子机制,因此在促进用于医疗或生物技术应用的功能肽基纳米材料的开发方面具有一定的范围。从这个角度来看,计算方法提供了对肽生物材料形成机制的分子见解,以及肽组装的全原子解析结构。综述了已建立的和最近出现的分子模拟方法,重点介绍了与肽组装相关的应用,包括全原子和粗粒度的“蛮力”分子动力学方法,以及增强的采样方法:保护伞采样,操纵和复制交换分子动力学,以及元动力学的变体。这些方法已被证明提供了尚未通过实验获得的全原子细节,以促进我们对肽自组装过程和生物材料形成的理解。这篇综述的范围包括总结了计算方法的现状,以及它们在应用于自组装肽生物材料方面的优势和局限性。
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Self-assembling peptide biomaterials: Insights from spontaneous and enhanced sampling molecular dynamics simulations
Peptide self-assembly is the process by which peptide molecules aggregate into low dimensional (1D, 2D) or 3D ordered materials with potential applications ranging from drug delivery to electronics. Short peptides are particularly good candidates for forming supramolecular assemblies due to the relatively simple structure and ease of modulating their self-assembly process to achieve required material properties. The experimental resolution of fibrous peptide-based nanomaterials as 3D atomic coordinates remains challenging. For surface-mediated peptide assembly in particular, it is typically not feasible to resolve multiple conformationally distinct surface bound peptide structures by experiment. The mechanisms of peptide self-assembly also remain elusive due to the interchange of complex interactions and multiple time and length scales involved in the self-assembly process. Peptide self-assembly in solution, or mediated by surfaces, is driven by specific interactions between the peptides and water, competing interactions within the peptide and/or between peptide aggregate units and, in the latter case, an interplay of the interactions between peptides and solvent molecules for adsorption onto a proximal surface. Computational methodologies have proven beneficial in elucidating the structures formed during peptide self-assembly and the molecular mechanisms driving it, and hence have scope in facilitating the development of functional peptide-based nanomaterials for medical or biotechnological applications. In this perspective, computational methods that have provided molecular insights into the mechanisms of formation of peptide biomaterials, and the all-atom-resolved structures of peptide assemblies are presented. Established and recently emerged molecular simulation approaches are reviewed with a focus on applications relevant to peptide assembly, including all-atom and coarse-grained “brute force” molecular dynamics methods as well as the enhanced sampling methodologies: umbrella sampling, steered and replica exchange molecular dynamics, and variants of metadynamics. These approaches have been shown to contribute all-atom details not yet available experimentally, to advance our understanding of peptide self-assembly processes and biomaterial formation. The scope of this review includes a summary of the current state of the computational methods, in terms of their strengths and limitations for application to self-assembling peptide biomaterials.
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