Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
Biophys J. 2021 Jul 20;120(14):2914-2926. doi: 10.1016/j.bpj.2021.02.041. Epub 2021 Mar 4.
Infection of human cells by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics simulations that take advantage of the highly mobile membrane mimetic model to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas, each for 300 ns. In 73% of the simulations, the FP reaches a stable, membrane-bound configuration, in which the peptide deeply penetrated into the membrane. Clustering of the results reveals three major membrane-binding modes (binding modes 1-3), in which binding mode 1 populates over half of the data points. Taking into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, the significant depth of penetration of the whole peptide, and the dense population of the respective cluster, we propose that the most deeply inserted membrane-bound form (binding mode 1) represents more closely the biologically relevant form. Analysis of FP-lipid interactions shows the involvement of specific residues, previously described as the "fusion-active core residues," in membrane binding. Taken together, the results shed light on a key step involved in SARS-CoV2 infection, with potential implications in designing novel inhibitors.
人类细胞被严重急性呼吸综合征冠状病毒 2 (SARS-CoV2) 感染依赖于其与特定受体的结合以及随后病毒和宿主细胞膜的融合。融合肽（FP）是刺突蛋白中的一个短肽段，在病毒最初穿透宿主细胞膜以及随后的两膜融合中起着核心作用。在这里，我们使用一系列分子动力学模拟，利用高度可移动的膜模拟模型，在原子水平上研究 SARS-CoV2 FP 与代表哺乳动物细胞膜的脂质双层的相互作用，并对肽的膜结合形式进行特征描述。通过改变 FP 相对于膜的初始定位和取向，生成了六个独立的系统，每个系统在五个独立的副本中进行了 300ns 的模拟。在 73%的模拟中，FP 达到了稳定的膜结合构象，在该构象中，肽深深地穿透了膜。对结果的聚类揭示了三种主要的膜结合模式（结合模式 1-3），其中结合模式 1占据了超过一半的数据点。考虑到病毒 FPs 之间的序列保守性以及确定 FP 中螺旋部分特定残基在膜结合中的作用的突变研究结果，整个肽的深度穿透以及各自聚类的密集分布，我们提出，最深入插入的膜结合形式（结合模式 1）更接近生物学上相关的形式。对 FP-脂质相互作用的分析表明，特定残基（先前被描述为“融合活性核心残基”）参与了膜结合。总之，这些结果揭示了 SARS-CoV2 感染过程中涉及的一个关键步骤，这可能对设计新型抑制剂具有重要意义。
