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. 2022 Nov 3;5(1):1170.
doi: 10.1038/s42003-022-04138-6.

SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact

Yui Tik Pang #  1 , Atanu Acharya #  1   2 , Diane L Lynch  1 , Anna Pavlova  1 , James C Gumbart  3
Affiliations

SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact

Yui Tik Pang et al. Commun Biol. .

Abstract

The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a "down" (closed) to an "up" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody's epitope is continuously exposed, explaining its high efficacy.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. S protein of SARS-CoV-2.
a The trimeric S protein in the all-down state, colored by protomer. Glycans are shown as red spheres. b Top view of the S protein in the one-up state. Important domains of the spike are highlighted, including the N-terminal domain (NTD, 14–306), the receptor binding domains (RBD, 336–518), the heptad repeat 1 (HR1, 908–986), and the central helix (CH, 987–1035). c, d The two collective variables defined to describe the opening of RBD-A include: c the center-of-mass distance d between RBD-A (336–518, pink) and SD1-B (531–592, lime), and d the dihedral angle ϕ formed by the center of mass of the domains RBD-A (336–518, pink), SD1-A (531–592, purple), SD2-A (593–677, ice blue), and NTD-A (27–307, cyan). RBD-A in both the down (solid pink) and up (transparent pink) states are shown.
Fig. 2
Fig. 2. PMFs describing the opening of RBD-A.
a, b The 2D PMFs of the a glycosylated and b un-glycosylated systems along two collective variables, d and ϕ, defined to describe the opening of RBD-A (Fig. 1c, d). The location of the down- (6XR8) and up-state (6VYB) cryo-EM structures are indicated in a with a "+'' and "x'' sign, respectively. The black dotted line shows the MEP for each system. c The free energies are projected onto d and plotted as 1D PMFs. See also Supplementary Data 1.
Fig. 3
Fig. 3. Kinetics of S-protein opening and closing.
a Transitions between RBD-down, up, and bound states are shown with their associated rates. b–d Fraction of S proteins in each state (up, down, and ACE2-bound) under different conditions, namely b with no glycans, c with no glycans and an assumed increase in the free energy of binding of RBD to ACE2 of 0.35 kcal/mol, and d with no glycans and an increase in binding free energy of 2.03 kcal/mol. e Bound-state fraction at equilibrium for the three conditions in (b–d).
Fig. 4
Fig. 4. Hydrogen bond and contact analysis reveals the different interaction patterns with and without glycans.
a, b Along the MEPs as indicated by the path parameter λ (see Fig. S2), the number of hydrogen bonds formed between the opening RBD-A and the rest of the spike are counted and classified by domain for the a glycosylated and the b un-glycosylated systems. The locations of the down- and up-state energy wells are shown with white backgrounds while other regions are shaded in grey. c, d The average number of contacts for the glycosylated system formed between the glycans at c N122 and d N165 and the neighboring β-strand from NTD-B (165–172) and RBD-A (353–360), which would otherwise form hydrogen bonds with each other if not separated by the glycans. e Snapshot from the REUS simulation showing the glycans at N165 and N122 disrupting hydrogen bond formation between RBD-A and NTD-B, destabilizing the up state compared to the un-glycosylated system.
Fig. 5
Fig. 5. Glycan-protein interactions.
Representative locations of S-protein glycans at N165, N234, and N343 in S-protein a down and b up states extracted from the REUS trajectories. c Surface representation of RBD residues in (above) down and (below) up states that make contact with glycans at N165 (green) and N343 (orange). The cross-hatch pattern indicates contacts with both glycans. The up and down states of the S protein were selected from the MEP.
Fig. 6
Fig. 6. Epitope analysis for selected antibodies.
a Exposed area on antibody epitopes (AbASA) in the presence of protein and glycans. b Surface area of epitopes covered by glycans along the MEP quantified by subtracting the two AbASA values calculated with and without glycans. All accessible surface area calculations were performed using a 7-Å probe.
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References

    1. Hu B, Guo H, Zhou P, Shi Z-L. Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol. 2020;19:141–154. - PMC - PubMed
    1. Liu Y, Wang K, Massoud TF, Paulmurugan R. SARS-CoV-2 Vaccine Development: An Overview and Perspectives. ACS Pharmacol. Transl. Sci. 2020;3:844–858. - PMC - PubMed
    1. Taylor PC, et al. Neutralizing monoclonal antibodies for treatment of COVID-19. Nat. Rev. Immunol. 2021;21:382–393. - PMC - PubMed
    1. Owen DR, et al. An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19. Science. 2021;374:1586–1593. - PubMed
    1. Bowen JE, et al. Omicron spike function and neutralizing activity elicited by a comprehensive panel of vaccines. Science. 2022;377:890–894. - PMC - PubMed

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