Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Woo, Hyeonuk; Park, Sangjun; Choi, Yeol Kyo; Park, Tae‐Yong; Tanveer, Maham; Cao, Yiwei; Kern, Nathan R.; Lee, Jumin; Yeom, Min Sun; Croll, Tristan I.; Seok, Chaok; Im, Wonpil

doi:10.1021/acs.jpcb.0c04553

Cited by 249 publications

(230 citation statements)

References 67 publications

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“…Even less is known at the needed molecular level about the mechanism by which the FPs in the spearhead are involved in the fusion of the cell and virus membranes, despite the wealth of information that has recently accumulated from molecular dynamics (MD) simulations on SARS-CoV-2 models (e.g., see Refs. [24][25][26][27][28][29] ).…”

Section: Introductionmentioning

confidence: 99%

Ca²⁺-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Khelashvili

Plante

Doktorova

et al. 2020

Preprint

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Cell penetration after recognition of the SARS-CoV-2 virus by the ACE2 receptor, and the fusion of its viral envelope membrane with cellular membranes, are the early steps of infectivity. A region of the Spike protein (S) of the virus, identified as the “fusion peptide” (FP), is liberated at its N-terminal site by a specific cleavage occurring in concert with the interaction of the receptor binding domain of the Spike. Studies have shown that penetration is enhanced by the required binding of Ca2+ ions to the FPs of corona viruses, but the mechanisms of membrane insertion and destabilization remain unclear. We have predicted the preferred positions of Ca2+ binding to the SARS-CoV-2-FP, the role of Ca2+ ions in mediating peptide-membrane interactions, the preferred mode of insertion of the Ca2+-bound SARS-CoV-2-FP and consequent effects on the lipid bilayer from extensive atomistic molecular dynamics (MD) simulations and trajectory analyses. In a systematic sampling of the interactions of the Ca2+-bound peptide models with lipid membranes SARS-CoV-2-FP penetrated the bilayer and disrupted its organization only in two modes involving different structural domains. In one, the hydrophobic residues F833/I834 from the middle region of the peptide are inserted. In the other, more prevalent mode, the penetration involves residues L822/F823 from the LLF motif which is conserved in CoV-2-like viruses, and is achieved by the binding of Ca2+ ions to the D830/D839 and E819/D820 residue pairs. FP penetration is shown to modify the molecular organization in specific areas of the bilayer, and the extent of membrane binding of the SARS-CoV-2 FP is significantly reduced in the absence of Ca2+ ions. These findings provide novel mechanistic insights regarding the role of Ca2+ in mediating SARS-CoV-2 fusion and provide a detailed structural platform to aid the ongoing efforts in rational design of compounds to inhibit SARS-CoV-2 cell entry.STATEMENT OF SIGNIFICANCESARS-CoV-2, the cause of the COVID-19 pandemic, penetrates host cell membranes and uses viral-to-cellular membrane fusion to release its genetic material for replication. Experiments had identified a region termed “fusion peptide” (FP) in the Spike proteins of coronaviruses, as the spearhead in these initial processes, and suggested that Ca2+ is needed to support both functions. Absent structure and dynamics-based mechanistic information these FP functions could not be targeted for therapeutic interventions. We describe the development and determination of the missing information from analysis of extensive MD simulation trajectories, and propose specific Ca2+-dependent mechanisms of SARS-CoV-2-FP membrane insertion and destabilization. These results offer a structure-specific platform to aid the ongoing efforts to use this target for the discovery and/or of inhibitors.

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Section: Introductionmentioning

confidence: 99%

Ca²⁺-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Khelashvili

Plante

Doktorova

et al. 2020

Preprint

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“…Recent studies 20,21 have shown the ability of the SARS-CoV2 virus to utilize a highly glycosylated spike (S) protein to elude the host's immune system and bind to its target membrane receptor, ACE2, thus enabling entry into human cells. Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21][22][23][24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl .…”

Section: Resultsmentioning

confidence: 99%

Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry

Aguilar-Pineda

Albaghdadi

Jiang

et al. 2020

Preprint

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Emerging evidence suggests that males are more susceptible to severe infection by the SARS-CoV-2 virus than females. A variety of mechanisms may underlie the observed gender-related disparities including differences in sex hormones. However, the precise mechanisms by which female sex hormones may provide protection against SARS-CoV-2 infectivity remains unknown. Here we report new insights into the molecular basis of the interactions between the SARS-CoV-2 spike (S) protein and the human ACE2 receptor. We further observed that glycosylation of the ACE2 receptor enhances SARS-CoV-2 infectivity. Importantly estrogens can disrupt glycan-glycan interactions and glycan-protein interactions between the human ACE2 and the SARS-CoV2 thereby blocking its entry into cells. In a mouse model, estrogens reduced ACE2 glycosylation and thereby alveolar uptake of the SARS-CoV-2 spike protein. These results shed light on a putative mechanism whereby female sex hormones may provide protection from developing severe infection and could inform the development of future therapies against COVID-19.

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“…Epitopes that coincided with previously reported epitopes or had overlapping residues, were merged into one peptide which covers all reported and predicted epitopes and are shown in bold letters in Supplementary Table 1. To visualise the position of the compiled epitopes we used an optimised 3D model of the SARS-CoV-2 spike glycoprotein as a monomer (Supplementary figure 1) and in its trimeric conformation (Figure 2) (19). B cell epitopes reported in the literature are distributed in all domains of the spike glycoprotein similarly to epitopes predicted in this study (Supplementary figure 1A & B).…”

Section: Resultsmentioning

confidence: 99%

“…To provide a graphical representation of the epitopes, we used the structural model of the full-Length SARS-CoV-2 spike glycoprotein (ID: 6VSB_1_1_1) (18, 19). The 3D structures were built and analysed using PyMOL ® software (Schrödinger LLC.…”

Section: Methodsmentioning

confidence: 99%

Bioinformatic analysis of shared B and T cell epitopes amongst relevant coronaviruses to human health: Is there cross-protection?

Pacheco-Olvera

Remy-Hernández

Acevedo-Ochoa

et al. 2020

Preprint

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Within the last 30 years 3 coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2, have evolved and adapted to cause disease and spread amongst the human population. From the three, SARS-CoV-2 has spread world-wide and to July 2020 it has been responsible for more than 11 million confirmed cases and over half a million deaths. In the absence of an effective treatment or vaccine, social distancing has been the most effective measure to control the pandemic. However it has become evident that as the virus spreads the only tool that will allow us to fully control it is an effective vaccine. There are currently more than 150 vaccine candidates in different stages of development using a variety of viral antigens, with the S protein being the most targeted antigen. Although some new experimental evidence suggests cross-reacting responses between coronaviruses are present in the population, it remains unknown whether potential shared antigens between different coronaviruses could provide cross-protection. Given that coronaviruses are emerging pathogens and continue to represent a threat to global health, the development of a SARS-Cov-2 vaccine that could provide ‘universal’ protection against other coronaviruses should be pushed forward. Here we present a thorough review of reported B and T cell epitopes shared between SARS-CoV-2 and other relevant coronaviruses, in addition we used web-based tools to predict novel B and T cell epitopes that have not been reported before. Analysis of experimental evidence that is constantly emerging complemented with the findings of this study allow us support the hypothesis that cross-reactive responses, particularly those coming from T cells, might play a key role in controlling infection by SARS-CoV-2. We hope that with the evidence presented in this manuscript we provide arguments to encourage the study of cross-reactive responses in order to elucidate their role in immunity to SARS-CoV-2. Finally we expect our findings will aid targeted analysis of antigen-specific immune responses and guide future vaccine design aiming to develop a cross reactive effective vaccine against respiratory diseases caused by coronaviruses.

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Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Cited by 249 publications

References 67 publications

Ca²⁺-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Ca²⁺-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry

Bioinformatic analysis of shared B and T cell epitopes amongst relevant coronaviruses to human health: Is there cross-protection?

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Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Cited by 249 publications

References 67 publications

Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry

Bioinformatic analysis of shared B and T cell epitopes amongst relevant coronaviruses to human health: Is there cross-protection?

Contact Info

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Ca²⁺-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide

Ca²⁺-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide