Switching Spike Plasticity Shapes ACE2 Engagement Across SARS-CoV-2 Variants.

Sarah Stainer¹ Rong Zhu¹ Manuel Reithofer² Gerhard Stadlmayr² Katharina Stadlbauer² Panchika Prangkio³ Christoph Rippel¹ Markus Hahn¹ Aniko Eva Kasztner² Stefanie Stohl² Petr Bednar^4,5,6 Daniel Ruzek^4,5,7 David Glück⁸ Robert Tampé⁸ Gordana Wozniak-Knopp² Yoo Jin Oh¹ Miriam Klausberger² Peter Hinterdorfer¹

Affiliations 8 institutions

Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
Department of Biotechnology and Food Science, Institute of Molecular Biotechnology, BOKU University, Vienna, Austria.
Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
Veterinary Research Institute, Brno, Czech Republic.
Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.
Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany.

PMID42671377 DOI10.1002/advs.77290 Year2026 Journal Advanced science (Weinheim, Baden-Wurttemberg, Germany) Adv Sci (Weinh) Languageeng Publication statusActive

Active Last checked 2026-10-09 03:30:37 Source: NCBI PubMed

Abstract

Conformational plasticity allows class I viral fusion proteins, including the SARS-CoV-2 spike, to undergo major structural rearrangements that support receptor binding and membrane fusion, making them key vaccine and antiviral targets. Using high-speed atomic force microscopy (AFM) and single-molecule force spectroscopy, we analyzed the ancestral and nine spike variants and found an evolutionary trend from increased flexibility in early strains to greater rigidification beginning with Delta, fluctuating plasticity in Omicron sublineages, and pronounced compaction in JN.1. Delta favored multivalent ACE2 engagement through its three receptor-binding domains, whereas later Omicron variants shifted toward predominantly single-site interactions. This change was compensated by stronger RBD-ACE2 bond stability. Overall, spike evolution appears to balance openness and compaction to regulate receptor accessibility, mobility, and immune escape while preserving or enhancing entry efficiency. These single-molecule measurements define functional constraints on viral adaptation and may inform prediction of future variants and design of improved countermeasures.

Supporting text Virus Host Location

atomic force microscopy 1 biophysics 2 evolution 65 force spectroscopy 1 glycosylation 24 mass spectrometry 4 protein engineering 3 protein purification 1 severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) 1 virology 12

Evidence records

4 total

Functional Mechanism

4 records · 2 evidence types

Evidence type Receptor Usage

2 records

OVE12089 Receptor Usage

Key finding

The SARS-CoV-2 Delta variant spike favors multivalent engagement of ACE2 via its three RBDs.

Virus

Host

Location

Supporting text

Delta favored multivalent ACE2 engagement through its three receptor-binding domains

Method: high-speed atomic force microscopy (AFM) | single-molecule force spectroscopy
Receptors: ACE2

OVE12090 Receptor Usage

Key finding

Later Omicron variants of SARS-CoV-2 predominantly use single-site ACE2 interactions, compensated by stronger RBD–ACE2 bond stability.

Virus

Host

Location

Supporting text

whereas later Omicron variants shifted toward predominantly single-site interactions. This change was compensated by stronger RBD-ACE2 bond stability.

Method: high-speed atomic force microscopy (AFM) | single-molecule force spectroscopy
Receptors: ACE2

Evidence type Molecular Adaptation

2 records

OVE12091 Molecular Adaptation

Key finding

Later Omicron variants compensate a shift to predominantly single-site ACE2 engagement by increasing the stability of the RBD–ACE2 bond.

Virus

Host

Location

Supporting text

Later Omicron variants shifted toward predominantly single-site interactions. This change was compensated by stronger RBD-ACE2 bond stability.

Genes or proteins: spike | RBD
Receptors: ACE2
Mechanism types: receptor binding | host entry | transmission fitness | immune escape

OVE12092 Molecular Adaptation

Key finding

Spike conformational plasticity evolved from flexible early strains to rigidified Delta, fluctuating in Omicron, and compact JN.1, balancing receptor accessibility, mobility, and immune escape while maintaining entry efficiency.

Virus

Host

Location

Supporting text

we analyzed the ancestral and nine spike variants and found an evolutionary trend from increased flexibility in early strains to greater rigidification beginning with Delta, fluctuating plasticity in Omicron sublineages, and pronounced compaction in JN.1. ... Overall, spike evolution appears to balance openness and compaction to regulate receptor accessibility, mobility, and immune escape while preserving or enhancing entry efficiency.

Genes or proteins: spike
Receptors: ACE2
Mechanism types: receptor binding | host entry | immune escape | transmission fitness | host-range expansion

References

68 references

Reference network

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Evidence overview

Evidence 4

Categories 1

Types 2

Virus 1

Host 0

Country 0

Evidence categories

Linked entities

Viruses

Hosts

No standardized host entity.

Locations

Publication metadata

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Volume / Issue / Pages: - / - / e77290
ISSN: 2198-3844
Journal country: Germany
DOI: 10.1002/advs.77290