Abhishek Moll of the Max Planck Institute for Material Structure and Dynamics (MPSD) in Hamburg and his colleagues investigated the structural dynamics of the protein shell called the capsid that surrounds the virus’s genetic material.
Specifically, we investigated the behavior of the capsid of bacteriophage MS2 under dehydration conditions. MS2 is shaped by an icosahedron, 20 triangular surfaces that form a spherical, single-stranded RNA virus that infects bacteria. Escherichia coliis widely used as a model system in virology. The experiments were performed on the SPB/SFX instrument at the European XFEL.
Capsid design is important for protecting the viral genome and helping the virus interact with host cells. However, viruses often face environments that compromise their structural integrity, such as dehydration. Theoretical studies have long suggested that capsids may undergo a low-energy “buckling transition,” or an abrupt change in shape, to accommodate such stresses, but direct experimental evidence has been lacking.
Research by Abhishek Mohr and colleagues from research institutes in Germany, Sweden, the UK, Australia, Singapore and the US is filling that gap. They created an aerosol by spraying the virus-containing liquid very finely into a sample chamber with very low humidity.
While the droplet travels for just over a second, some of the surrounding liquid evaporates, mimicking the natural dehydration process. At some point, they meet an X-ray laser beam, essentially taking a snapshot of the capsid. “We used single-particle imaging to investigate morphological changes in viral capsids during aerosolization,” says Abhishek Mohr. He and his colleagues collected diffraction patterns from hundreds of thousands of individual MS2 particles.
As co-author and MPSD group leader Kartik Ayyer explains, the team initially aimed to capture only the final dry state. However, many particles were produced at different points in the drying process, making this experiment more powerful.
This was actually a good thing. By classifying the snapshots from fully hydrated to fully dry, or somewhere in between, we were able to reconstruct the trajectory of structural changes. ”
Kartik Ayyer, Max Planck Institute for Structural Mechanics of Matter
amazing asymmetry
One of the key findings of this study was the observation of buckling of MS2 capsids as they transition from a hydrated state to a dehydrated state. Buckling can be compared to a thin plastic bottle that expands in certain areas when negative pressure is applied, rather than contracting uniformly. The researchers observed that in the hydrated state, the capsid exhibits almost perfect icosahedral symmetry, as measured by cryo-electron microscopy. “However, as dehydration progresses, the capsid adopts a more compact structure, deviating significantly from icosahedral symmetry,” Mohr explains.
Importantly, the changes were not uniform throughout the capsid. Instead, the transition occurred locally, with some regions appearing to change before others. “This discovery is particularly important as it provides direct experimental evidence for a mechanism that was previously predicted only theoretically,” added Richard Bean, lead scientist for the European XFEL’s SPB/SFX instrument.
The observation also challenged common assumptions about the virus. “Many people had the impression that this capsule was a solid container, and this is completely different from what we saw,” Iyer explains. Instead, capsids appear to be able to mechanically adapt to changing conditions.
Buckling molecule “trigger”
This study also investigated the molecular mechanisms underlying these morphological changes. “Molecular dynamics simulations revealed that a flexible segment of the protein called the FG loop plays a key role in the observed structural changes,” said Mohr. “These movements caused the FG loops around the triple and pentapores of the capsid to contract, resulting in a more compact structure.”
The researchers speculate that this contraction is caused by the loss of stabilizing water molecules, which are important for maintaining the expanded conformation of the FG loop. This local destabilization likely acts as a protective mechanism and may reduce the degree to which the viral genome is exposed during desiccation.
New applications of machine learning
Critical to this study was a methodological innovation. By integrating single particle imaging (SPI) with advanced machine learning techniques such as β-variational autoencoder (β-VAE), researchers were able to analyze structural heterogeneity across large data sets of diffraction patterns. “Using β-VAE allowed us to sort particles into a continuous latent space, capturing changes in size and shape with remarkable accuracy,” Mohr explains.
This approach not only identified the endpoints of the structural transition from hydrated to dehydrated states, but also mapped the intermediate structures that bridge these states. “This kind of detailed analysis was not possible using traditional ensemble averaging methods,” Bean added.
He continued, “The ability to capture and analyze the structural landscape of viral capsids in real time is a major advance in structural biology using single-particle imaging. The methods employed in this study can be extended to other biomolecular systems and provide a powerful tool for investigating dynamic processes that are difficult to study using other methods.”
How viruses survive in the air
The structural adaptability observed in the capsid provides fundamental insight into how viruses tolerate environmental stress. This knowledge is especially true regarding viruses transmitted by aerosols, including many pathogens that affect the human body.
“By elucidating the mechanisms that enable viral resilience, the work of Abhishek Mohr and his colleagues can lay the foundation for potential applications in virology and public health, for example in the development of antiviral strategies,” said Sakura Pascarelli, Scientific Director of European XFEL. This discovery sheds light on an important aspect of virus survival. “These results not only advance our understanding of virus dynamics, but also open new avenues for research and innovation in virology and structural biology,” Pascarelli emphasized.
Further studies are planned to investigate the observed behavior under more realistic conditions. “In this experiment, we used a very clean liquid that completely evaporated,” warns Iyer. “Real saliva contains not only proteins but also salts and other substances that do not evaporate. The next step is to use saliva surrogates, which will allow us to determine what role changes in the shape of the virus’s shell play in real life.”
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Max Planck Institute for Structure and Dynamics of Matter
Reference magazines:
Mohr, A. others. (2026) High-throughput in situ single-particle X-ray imaging of dehydrated virus capsids. Light: Science and Applications. DOI:10.1038/s41377-026-02262-0. https://www.nature.com/articles/s41377-026-02262-0.
