Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface
Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface
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DOI：
10.1021/acs.langmuir.2c01331
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发表时间：
2022-08-24
期刊：
影响因子：
3.9
通讯作者：
Zheng, Size
中科院分区：
文献类型：
--
作者：
Chen, Jing;Xu, Enze;Zheng, Size
了解生物分子的界面行为对生物材料和纳米生物传感技术的应用至关重要。在这项工作中，我们利用自动编码器为基础的图形聚类分析不连续分子动力学（DMD）模拟溶菌酶吸附在石墨烯表面。我们的高通量DMD模拟与G（o）over bar -样蛋白质-表面相互作用模型相结合，使得有可能以足够的精度在大的时间尺度上探索蛋白质吸附。图形自动编码器从接触图提取低维特征向量。然后对所提取的特征向量的序列进行聚类，从而将蛋白质分子结构在吸收过程中的演变分割为多个阶段。研究表明，残基-表面疏水相互作用和π-π堆积相互作用在五阶段吸附过程中起着关键作用。吸附后，溶菌酶的三级结构崩溃，二级结构也受到影响。通过基于自动编码器的图聚类获得的折叠阶段与蛋白质结构的详细分析一致。机器学习分析和有效的DMD模拟相结合，在这项工作中开发的可能是一个重要的工具，研究生物分子的界面行为。
Understanding the interfacial behaviors of biomolecules is crucial to applications in biomaterials and nanoparticle-based biosensing technologies. In this work, we utilized autoencoder-based graph clustering to analyze discontinuous molecular dynamics (DMD) simulations of lysozyme adsorption on a graphene surface. Our high-throughput DMD simulations integrated with a G (o) over bar -like protein-surface interaction model makes it possible to explore protein adsorption at a large temporal scale with sufficient accuracy. The graph autoencoder extracts a low dimensional feature vector from a contact map. The sequence of the extracted feature vectors is then clustered, and thus the evolution of the protein molecule structure in the absorption process is segmented into stages. Our study demonstrated that the residue-surface hydrophobic interactions and the pi-pi stacking interactions play key roles in the five-stage adsorption. Upon adsorption, the tertiary structure of lysozyme collapsed, and the secondary structure was also affected. The folding stages obtained by autoencoder-based graph clustering were consistent with detailed analyses of the protein structure. The combination of machine learning analysis and efficient DMD simulations developed in this work could be an important tool to study biomolecules' interfacial behaviors.