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Biophysical characterization of SARS-CoV-2 spike protein - receptor interactions

SARS-CoV-2 刺突蛋白 - 受体相互作用的生物物理特征

基本信息

批准号：
10445350
负责人：
Wonpil Im
金额：
$ 22.63万
依托单位：
LEHIGH UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-06 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10445350
关键词：
2019-nCoV ACE2 Affinity Angiotensin Receptor Antiviral Therapy Binding Biological Assay Biophysical Process Biophysics CD209 gene COVID-19 COVID-19 complications COVID-19 pandemic Cell Surface Proteins Cell Surface Receptors Cell membrane Cells Cellular Membrane Cessation of life Clinical Research Clinical Trials Complex Country Data Detection Ebola virus Enzymes FDA approved Glycoproteins Human Immobilization Individual Kinetics Length Mechanics Mediating Membrane Membrane Fusion Membrane Proteins Modeling Mutation NRP1 gene Neuropilin-1 Pathway interactions Pharmaceutical Preparations Physiological Polysaccharides Positioning Attribute Protein Dynamics Proteins Reporting Research Research Personnel Route SARS-CoV-2 antiviral SARS-CoV-2 infection SARS-CoV-2 spike protein Serine Protease Spectrum Analysis Structural Models Structure Surface TMPRSS2 gene Techniques Testing Time Tropism Vaccines Viral Virion Virus Work base biophysical properties data modeling experience experimental study models and simulation molecular dynamics molecular modeling monomer novel pandemic disease particle protein activation protein structure protein structure prediction receptor receptor binding simulation single molecule tissue tropism tool uptake virus envelope

项目摘要

PROJECT SUMMARY/ABSTRACT The current pandemic of Coronavirus Disease-2019 (COVID-19) has had devastating impacts across the world. In order to enter human host cells, SARS-CoV-2, the virus causing COVID-19, uses its surface spike (S) protein to attach to host cell surface receptors. Besides the best-known receptor, ACE2, a number of cell surface proteins, including CD147, neuropilin-1 (NRP1) and DC-SIGN/L-SIGN, have been reported to bind to S protein and mediate SARS-CoV-2 entry. Consistently, our preliminary studies using single-molecule force spectroscopy show that CD147, NRP1 and L-SIGN can bind to the SARS-CoV-2 S protein with comparable affinities to those of ACE2. Therefore, the possible multiple receptor utilization could, at least partially, explain the broad tissue tropism and systemic complications of SARS-CoV-2 infection. However, it remains puzzling how the S protein can bind to these structurally diverse molecules with high affinity. In addition, our all-atom structural modeling data shows that most of the S protein surface is covered by glycans, and only when the S protein’s receptor binding domain (RBD) is in the “up position” can it bind to a receptor without glycan interference. Therefore, we hypothesize that limited regions on the S protein that are not covered by glycans, including the RBD in up position, as well as the S1/S2 junctional region, may be responsible for binding all the receptors. In the proposed work, we will systematically test the hypothesis using combined approaches of single-virus force spectroscopy, all- atom molecular modeling and simulation and pseudovirus internalization/entry assays. Moreover, since SARS- CoV-2 has two entry routes (direct viral-host membrane fusion or endocytic/macropinocytic internalization followed by endosomal entry), the exact entry pathways that these receptors mediate are not yet clear. The proposed research will determine whether every individual interaction is more prone to mediate direct viral-host membrane fusion or viral endocytic/macropinocytic internalization. Two specific aims will be pursued: 1) to characterize S protein interactions with host cell membrane receptors and 2) to determine the structural basis of S protein’s broad receptor recognition. The study will elucidate the structural and biophysical mechanisms behind S protein’s receptor recognition and utilization. Successful completion of this work will allow us to identify new targets for antiviral therapies to treat the systemic complications of COVID-19.

项目总结/摘要当前的2019冠状病毒病（COVID-19）大流行对全球产生了毁灭性影响。为了进入人类宿主细胞，引起COVID-19的病毒SARS-CoV-2使用其表面刺突（S）蛋白附着在宿主细胞表面受体上。除了最著名的受体ACE 2，一些细胞表面蛋白，包括CD 147、神经纤毛蛋白-1（NRP 1）和DC-SIGN/L-SIGN，已报道与S蛋白结合，介导SARS-CoV-2进入。因此，我们的初步研究，使用单分子力谱显示CD 147、NRP 1和L-SIGN可以与SARS-CoV-2S蛋白结合，其亲和力与那些 ACE 2的因此，可能的多受体利用可以，至少部分地，解释广泛的组织 SARS-CoV-2感染的嗜性和全身并发症。然而，令人困惑的是S蛋白如何能以高亲和力与这些结构多样的分子结合。此外，我们的全原子结构模型数据显示，S蛋白表面的大部分被聚糖覆盖，只有当S蛋白的受体结合结构域（RBD）处于“上方位置”，它可以在没有聚糖干扰的情况下与受体结合。所以我们假设S蛋白上未被聚糖覆盖的有限区域，包括位于上游位置的RBD，以及S1/S2连接区，可能负责结合所有受体。在拟议的工作中，我们将使用单病毒力谱的组合方法系统地测试假设，所有- 原子分子建模和模拟以及假病毒内化/进入测定。此外，自SARS以来- CoV-2有两种进入途径（直接病毒-宿主膜融合或内吞/巨胞饮内化随后进入内体），但这些受体介导的确切进入途径尚不清楚。的拟议的研究将确定是否每一个单独的相互作用更倾向于介导直接病毒-宿主膜融合或病毒内吞/巨胞饮内化。将追求两个具体目标：1）表征S蛋白与宿主细胞膜受体的相互作用，以及2）确定 S蛋白的广泛受体识别。这项研究将阐明背后的结构和生物物理机制 S蛋白的受体识别和利用。这项工作的成功完成将使我们能够确定新的抗病毒治疗的目标，以治疗COVID-19的全身性并发症。