Abstract:The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze S in situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular domain unexpect… Show more
“…(23,37,38) To this end, we have performed MD simulations of fully glycosylated spike protein of SARS-COV-2 in both open and closed states. Analysis of dynamics for 1 μs trajectories showed a tilting motion in the stalk region, which was also demonstrated with experimental cryo-ET images (29,30) and suggested to aid the virus with screening the host cells for receptor proteins (Figure 2A). Glycan motions were characterized by RMSF ( Figures 2B and S3), which showed higher values for stalk glycans demonstrating the high shielding potential of this normally solvent-exposed region.…”
The ongoing pandemic caused by coronavirus SARS-COV-2 continues to rage with devastating consequences on human health and global economy. The spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all current antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein, we performed microsecond-long MD simulation in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the spike trimer. Role of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis, where the high betweenness centrality of glycans at the apex revealed their importance and function in the glycan shield. Microdomains of glycans were identified featuring a high degree of intra-communication in these microdomains. An antibody overlap analysis revealed the glycan microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Overall, the results of this study provide detailed understanding of the spike glycan shield, which may be utilized for therapeutic efforts against this crisis.
“…(23,37,38) To this end, we have performed MD simulations of fully glycosylated spike protein of SARS-COV-2 in both open and closed states. Analysis of dynamics for 1 μs trajectories showed a tilting motion in the stalk region, which was also demonstrated with experimental cryo-ET images (29,30) and suggested to aid the virus with screening the host cells for receptor proteins (Figure 2A). Glycan motions were characterized by RMSF ( Figures 2B and S3), which showed higher values for stalk glycans demonstrating the high shielding potential of this normally solvent-exposed region.…”
The ongoing pandemic caused by coronavirus SARS-COV-2 continues to rage with devastating consequences on human health and global economy. The spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all current antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein, we performed microsecond-long MD simulation in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the spike trimer. Role of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis, where the high betweenness centrality of glycans at the apex revealed their importance and function in the glycan shield. Microdomains of glycans were identified featuring a high degree of intra-communication in these microdomains. An antibody overlap analysis revealed the glycan microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Overall, the results of this study provide detailed understanding of the spike glycan shield, which may be utilized for therapeutic efforts against this crisis.
“…Large dynamical variations thus seems to be a feature of these extracellular glycoproteins. The RBD rocking motion and S conformational variability have been proposed as mechanisms for immune evasion and efficient receptor search in the host cell (43,44) but the similar rocking motion of ACE2 we observed also suggests a mechanical aspect to ACE2-S interaction. The process of S conformational transition upon binding to the receptor and cell fusion remains elusive, but ACE2's intrinsic flexibility could promote a large swinging motion of the ACE2-S1 complex, providing a mechanical force for the approximation of the two membranes and shedding of S1 towards fusion of the S2 domains into the receptor cell (Figure 7b).…”
The COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics.Statement of SignificanceAs the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.
“…The cleavage sites present near S1/S2 and S2′ participate in the viral entry and modulate host range and cell tropism. The structure of SARS-CoV-2 spike protein was analysed in situ by combing cryo-electron tomography, sub-tomogram averaging and molecular dynamics simulations ( Turoňová et al, 2020 ). Molecular dynamics simulations of the spike proteins reveal the conformational alterations in the protein required for the mechanistic function.…”
Section: Coronavirusmentioning
confidence: 99%
“…Molecular dynamics simulations of the spike proteins reveal the conformational alterations in the protein required for the mechanistic function. The SARS-CoV-2 spike protein contains three hinge regions that provide the S1 A and S1 B domains orientational freedom that allows them to scan the host cell surface for potential receptors ( Turoňová et al, 2020 ). Fig.…”
A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. In this review, we discuss structural features of HCoV spike proteins and recognition of host proteins and carbohydrate receptors.
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