Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface
Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface
复制标题
生物分子界面行为的不连续分子动力学模拟：Ovispirin-1 在石墨烯表面吸附的研究
DOI：
10.1021/acs.jctc.0c01172
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发表时间：
2021
影响因子：
5.5
通讯作者：
Wei, Tao
中科院分区：
文献类型：
--
作者：
Zheng, Size;Sajib, Md Symon;Wei, Yong;Wei, Tao
对生物分子界面行为的基本了解，如微观尺度上的蛋白质吸附，对于在生物材料、纳米医学和基于纳米颗粒的生物传感技术中的广泛应用至关重要。同时达到计算效率和精度的目标对原子和分子尺度的模拟研究都是一个重大挑战。在这项工作中，我们开发了一种独特的、准确的、高通量的模拟方法，该方法将非连续分子动力学(DMD)模拟与类GO蛋白质-表面相互作用模型相结合，不仅有效地求解了动力学，而且在原子尺度上精确地描述了蛋白质分子内和分子间相互作用，在粗粒度尺度上精确地描述了蛋白质-表面相互作用。利用我们的模拟方法和自行开发的软件，我们对α-螺旋Ovispirin-1多肽在石墨烯表面的吸附进行了系统的研究，重点研究了表面疏水相互作用和π-π堆积对蛋白质吸附的影响。我们的DMD模拟与全原子分子动力学模拟一致，表明由于蛋白质-表面强烈的相互作用，单一的Ovispirin-1肽躺在平坦的石墨烯表面，具有随机的二级结构。在主体环境中疏水残基的强烈相互作用的驱动下，形成了具有内部疏水核心的多肽聚集体。然而，在吸附后，疏水的石墨烯表面会通过变性单个多肽结构来破坏疏水核心，导致聚集体结构解体，进而使Ovispirin-1多肽的二级结构随机化。
Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Go-like protein–surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein–surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π–π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein–surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide’s secondary structures.