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.

项目摘要/摘要当前的冠状病毒疾病大流行2019年（Covid-19）在世界各地产生了毁灭性的影响。为了进入人类宿主细胞，SARS-COV-2（导致COVID-19的病毒）使用其表面峰值蛋白附着在宿主细胞表面受体上。除了最著名的受体ACE2，许多细胞表面蛋白，据报道，包括CD147，Neuropilin-1（NRP1）和DC-SIGN/L-SIGN，已据报道与S蛋白结合和中介SARS-COV-2进入。一致地，我们使用单分子力光谱法的初步研究证明CD147，NRP1和L-SIGN可以与SARS-COV-2 S蛋白结合，与那些相当的亲和力结合 ace2。因此，可能的多个接收器使用情况至少可以部分解释宽组织 SARS-COV-2感染的向性和系统并发症。但是，仍然是S蛋白的难题可以与这些具有高亲和力的结构多样性分子结合。另外，我们的全原子结构建模数据表明，大多数S蛋白表面都被聚糖覆盖，并且仅在S蛋白接收器的接收器时才覆盖结合结构域（RBD）处于“向上位置”，它可以在没有聚糖干扰的情况下与受体结合。因此，我们假设在S蛋白上没有被聚糖覆盖的限制区域，包括RBD处于UP位置，以及S1/S2连接区域，也可能负责约束所有接收器。在拟议的工作中我们将使用单病毒力光谱法的联合方法系统地检验假设原子分子建模和仿真以及假病毒内在化/进入测定法。而且，由于sars- COV-2有两种进入路线（直接病毒宿主膜融合或内吞/大型细胞内在化其次是内体入口），这些接收器中介的确切进入途径尚不清楚。这拟议的研究将确定每个单独的互动是否更容易介导直接病毒宿主膜融合或病毒内吞/大型细胞内在化。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，2）确定 S蛋白的广泛受体识别。该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。成功完成这项工作将使我们能够确定新的抗病毒疗法的靶标治疗Covid-19的全身并发症。