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Cited by 0SARS-CoV-2 and COVID-19 ResearchProtein Structure and DynamicsAnimal Virus Infections Studies

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Structural dynamics and allosteric communication of a SARS-like bat coronavirus spike glycoprotein

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Balogun, Toheeb A., Kearns, Fiona L., Calvó-Tusell, Carla, Tse, Alexandra L., Acreman, Cory M., Casalino, Lorenzo, Lasso, Gorka, Miller, Emily Happy, Chandran, Kartik, McLellan, Jason S., Amaro, Rommie E.·2026·Biophysical Journal
DOI 10.1016/j.bpj.2026.04.023PMC PMC13507448

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Abstract

Abstract SARS-like bat coronaviruses (CoVs) pose ongoing public health risks due to their zoonotic potential, making it important to understand the molecular pathways driving their evolution. We recently showed that SHC014-CoV can infect human cell lines in an ACE2-dependent manner after acquiring two spike ectodomain mutations (F294L and A835D). However, how the wild-type (WT) SHC014 spike differs dynamically from these mutants remains unclear. Here, we built fully glycosylated ectodomain models of WT and three mutants (F294L, A835D, and the double mutant, DM) and performed triplicate 1-μs all-atom molecular dynamics (MD) simulations for each variant. The two mutations exhibit epistasis, altering structural rearrangements relative to WT. Notably, the DM receptor binding domain (RBD) begins sampling the open conformation in our conventional MD. At the atomic level, the DM spike mitigates the dense negative packing introduced by A835D through a salt-bridge network, while F294L disrupts π-mediated interactions, together enhancing RBD opening propensity—critical for viral entry. Increased flexibility of the subdomain-2 “620-loop” further modulates DM RBD openness. Dynamical network analysis identified three allosteric communication pathways. In WT and F294L, “Pathway 1” forms the baseline route linking the 620-loop to the RBD, whereas in A835D and DM it extends to the FPPR, reshaping long-range communication. “Pathway 2” is conserved across variants but is most prominent in WT and F294L. “Pathway 3” appears only in A835D and DM, compensating for reduced communication along Pathway 2. Overall, this work provides an atomistic perspective on SHC014 molecular adaptation during host-to-host transmission and highlights mechanistic features that may inform future therapeutic and pandemic-preparedness efforts. Statement of Significance Bat coronaviruses are an important source of future pandemic threats, but we still know little about how small genetic changes help them infect humans. In this study, we used detailed computer simulations to watch how tiny mutations in a bat coronavirus spike protein change its motion and shape. We found that two specific mutations work together to make the spike more likely to open—a step required for the virus to enter human cells. By revealing how these molecular changes increase infection potential, our work helps improve understanding of coronavirus evolution and may guide strategies to prepare for future outbreaks.

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Metadata

Authors
Balogun, T. A., Kearns, F. L., Calvó-Tusell, C., Tse, A. L., Acreman, C. M., Casalino, L., Lasso, G., Miller, E. H., Chandran, K., McLellan, J. S., & Amaro, R. E.
Affiliations
  • University of California San Diego (US)
  • Albert Einstein College of Medicine (US)
  • The University of Texas at Austin (US)
Corresponding author
Amaro, Rommie E.
ORCID
Venue
Biophysical Journal
Publisher
Elsevier BV
Published
2026-08
Volume
125
Issue
16
Pages
4420-4436
ISSN
0006-3495 (ISSN-L)
DOI
10.1016/j.bpj.2026.04.023
PMC
PMC13507448
OpenAlex
W4417346604
Cited by
0
References
2
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Biophysical Journal (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
Funders
  • National Science Foundation
  • National Institutes of Health
  • The Welch Foundation
  • Thermo Fisher Scientific Inc
  • Shurl and Kay Curci Foundation
  • AG Leventis Foundation
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords
spike protein, receptor binding domain, allosteric communication, epistasis, double mutants, salt bridge network, structural dynamics, glycosylation, host-to-host transmission, zoonotic potential
MeSH terms
Protein Domains, Allosteric Regulation, Animals, Chiroptera, Humans, Mutation, Molecular Dynamics Simulation, Spike Glycoprotein, Coronavirus

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