Department of Biochemistry University of Oxford Department of Biochemistry
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Complete picture of flu virus envelope revealed

Researchers in the Biochemistry department have built a model of the intact influenza A virus outer envelope for the first time.

Influenza A virion on a mammaliam plasma membrane. GM3 glycolipids (green) on, and single transmembrane signalling proteins (orange) within, the host mammalian membrane. Forssman glycolipids (yellow), hemagglutinin proteins (red) and neuraminidase proteins (blue) of the virion

Influenza A virion on a mammaliam plasma membrane. Image courtesy of Heidi Koldsoe. The mammalian membrane has GM3 glycolipids (green) on it and single transmembrane signalling proteins (orange) within it. The virion has Forssman glycolipids (yellow), hemagglutinin proteins (red) and neuraminidase proteins (blue) (Click to enlarge)

The work, co-ordinated by postdoctoral fellow Dr Tyler Reddy and with fellow researchers from the department, has appeared in Structure (1).

By bringing together structural information from a variety of experimental sources, the researchers have uniquely included detailed analysis of the viral lipid envelope in their studies. Their model reveals characteristics that may help scientists understand how the virus survives in the wild and find new ways to combat it.

The influenza virus is surrounded by an envelope composed of a lipid bilayer and integral membrane proteins, including haemagglutinin (HA) and neuraminidase (NA) that are recognized by the immune system. Whilst there is considerable high-resolution structural information about influenza viral proteins, much less is known about the lipids in the envelope.

Understanding the structural dynamics of the membrane envelope is important because it could provide insights into aspects of viral function such as the wide-ranging survival times of the virus particles in different environments.

A feature related to this is influenza seasonality. 'The annual influenza epidemics that affect human populations in temperate climates tend to be seasonal,' comments Dr Reddy. 'You would typically get your flu jab in the winter because that is when infection is most likely. It turns out that we don't fully understand the basis for influenza seasonality.'

The ability of virus particles to survive in certain conditions may have serious consequences. The presence of influenza A in rivers is thought to allow waterfowl to be simultaneously exposed to source flu strains and residual anti-viral compounds excreted by local human populations, potentially giving rise to drug-resistant influenza strains.

For Dr Reddy, these intriguing features made the virus an attractive target for development of a computational model. By combining experimental data from X-ray crystallography, NMR spectroscopy, cryo-EM, and lipidomics, he and his colleagues have generated a model that reveals biophysical details of the protein-lipid interactions in the virus envelope.

The group used an approach known as a coarse-grained molecular dynamics simulation. Initial modeling was of a lipid-only ball (vesicle), and this was followed by analysis of interactions between lipids and three different viral proteins embedded into the envelope - HA, NA, and the M2 proton channel which is important for the viral life cycle. They explored the impact of different lipid compositions and different temperatures.

Zoom-in view of a representative region from the Forssman glycolipid-inclusive virion simulation at 323 K. Shown are viral proteins HA (red), NA (blue) and M2 (pink), and Forssman glycolipid (yellow), cholesterol (green) and other lipids (white) in the viral envelope

Zoom-in view of a representative region from the Forssman glycolipid-inclusive virion simulation at 323 K. Shown are viral proteins HA (red), NA (blue) and M2 (pink), and Forssman glycolipid (yellow), cholesterol (green) and other lipids (white) in the viral envelope. (Click to enlarge)

As Dr Reddy explains, the studies were complex and ambitious, demanding huge computational resources.

'Everything was challenging about this work. The influenza virus is a pleomorphic virus - it can adopt more than one overall shape and/or size - and this substantially complicates the structural biology of the virus. We decided to study the smallest observable spherical flu virion because this would be the most computationally tractable model.'

Even with the powerful supercomputers that Dr Reddy had access to, the simulations took an extremely large amount of 'wall clock time' (normal time) to achieve a short amount of 'simulation time.' He spent more than one year simply running and managing the 5 microsecond simulations described in the study.

One of the biological features that the group focused on was the effect of the Forssman glycolipid, the most abundant sphingolipid in the influenza A virion, on the dynamics of the membrane.

They observed that the glycolipid had a role in preventing protein aggregation and slowing down protein diffusion. Dr Reddy suggests that this may be due to the sugar head groups of the glycolipids impeding translational motion on the surface of the virion. These may also mask antibody accessibility of the M2 proton channels in the influenza envelope, the target of commonly prescribed anti-influenza drugs.

Dr Reddy and colleagues also found that the viral membrane proteins do not promiscuously clump together but spread out. This is key to the strength of the interactions between influenza A virions and host cells, which are determined by the number of viral membrane proteins that can engage with receptors. The glycoproteins spikes of the virion may be suitably spaced to be bound by bivalent immunoglobulin G - a feature that could be exploited in therapeutic design.

Although the group is a long way from being able to perform molecular dynamics simulations that span the year time scale, they now have a platform for looking at influenza A virion behaviour in silico. One approach may be to manipulate the structure using compounds that accelerate naturally occurring events, making them observable on tractable computational timescales.

Dr Reddy says that there are only a few research groups in the world doing similar 'full-scale' virus work. Usually the groups do not simulate the lipid envelope of the virion. The lack of high resolution structural data for the lipids in the envelope of influenza A is one of the major challenges that he and his colleagues had to deal with.

Their work presents the first complete view of the mobility of lipids and proteins in the envelope of influenza A.

Despite the huge challenges and risks in taking on the project, Dr Reddy knew that this was the right project for his personality. 'I almost never give up, which isn't always a good thing, but in research it can be a pretty useful trait.'

Judging by the interest that the work has stimulated around the world, his perseverance has paid off. 'I think there's a great chance that some of the governments around the world who have expressed an interest in this technology will adopt it in public health protection pipelines in the future.'


  1. Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza Virion. Reddy T, Shorthouse D, Parton DL, Jefferys E, Fowler PW, Chavent M, Baaden M and Sansom MSP. Structure (2015)












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