A Common Vaccine? New Pc Mannequin of Flu Virus Reveals Promise

The dynamic motion of H1N1 proteins exposes beforehand unknown vulnerabilities.

The World Well being Group reviews that there are roughly 1 billion circumstances of influenza yearly, with 3-5 million extreme circumstances and as many as 650,000 influenza-related respiratory fatalities worldwide. To be efficient, seasonal flu vaccines should be up to date annually to align with the predominant strains of the virus. When the vaccine is a match for the prevalent pressure, it gives substantial safety. Nonetheless, if the vaccine and virus strains will not be a match, the vaccine could present restricted protection.

The hemagglutinin (HA) and neuraminidase (NA) glycoproteins are the first targets of the flu vaccine. The HA protein facilitates the virus’s attachment to host cells, whereas the NA protein acts as a scissor to detach the HA from the cell membrane, enabling the virus to multiply. Regardless of earlier research on the properties of those glycoproteins, a whole understanding of their motion doesn’t exist.

For the primary time, researchers on the College of California San Diego have created an atomic-level laptop mannequin of the H1N1 virus that reveals new vulnerabilities by means of glycoprotein “respiration” and “tilting” actions. This work, printed in ACS Central Science, suggests attainable methods for the design of future vaccines and antivirals in opposition to influenza.

“After we first noticed how dynamic these glycoproteins had been, the massive diploma of respiration and tilting, we really puzzled if there was one thing incorrect with our simulations,” said Distinguished Professor of Chemistry and Biochemistry Rommie Amaro, who’s the principal investigator on the undertaking. “As soon as we knew our fashions had been appropriate, we realized the big potential this discovery held. This analysis may very well be used to develop strategies of conserving the protein locked open in order that it might be always accessible to antibodies.”

Historically, flu vaccines have focused the pinnacle of the HA protein based mostly on nonetheless photographs that confirmed the protein in a good formation with little motion. Amaro’s mannequin confirmed the dynamic nature of the HA protein and revealed a respiration motion that uncovered a beforehand unknown web site of immune response, often called an epitope.

Pc mannequin of H1N1 influenza virus – 160 million atoms of element. Credit score: College of California – San Diego

This discovery complemented earlier work from one of many paper’s co-authors, Ian A. Wilson, Hansen Professor of Structural Biology at The Scripps Analysis Institute, who had found an antibody that was broadly neutralizing — in different phrases, not strain-specific — and certain to part of the protein that appeared unexposed. This instructed that the glycoproteins had been extra dynamic than beforehand thought, permitting the antibody a chance to connect. Simulating the respiration motion of the HA protein established a connection.

NA proteins additionally confirmed motion on the atomic stage with a head-tilting motion. This supplied a key perception to co-authors Julia Lederhofer and Masaru Kanekiyo on the Nationwide Institute of Allergy and Infectious Illnesses. Once they checked out convalescent plasma — that is, plasma from patients recovering from the flu — they found antibodies specifically targeting what is called the “dark side” of NA underneath the head. Without seeing the movement of NA proteins, it wasn’t clear how the antibodies were accessing the epitope. The simulations Amaro’s lab created showed an incredible range of motion that gave insight into how the epitope was exposed for antibody binding.

The H1N1 simulation Amaro’s team created contains an enormous amount of detail — 160 million atoms worth. A simulation of this size and complexity can only run on a few select machines in the world. For this work, the Amaro lab used Titan at Oak Ridge National Lab, formerly one of the largest and fastest computers in the world.

Amaro is making the data available to other researchers who can uncover even more about how the influenza virus moves, grows, and evolves. “We’re mainly interested in HA and NA, but there are other proteins, the M2 ion channel, membrane interactions, glycans, and so many other possibilities,” Amaro stated. “This also paves the way for other groups to apply similar methods to other viruses. We’ve modeled SARS-CoV-2 in the past and now H1N1, but there are other flu variants, MERS, RSV, HIV — this is just the beginning.”

Reference: “Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities” by Lorenzo Casalino, Christian Seitz, Julia Lederhofer, Yaroslav Tsybovsky, Ian A. Wilson, Masaru Kanekiyo and Rommie E. Amaro, 8 December 2022, ACS Central Science.
DOI: 10.1021/acscentsci.2c00981

The study was funded by the National Institutes of Health, the National Science Foundation, the US Department of Energy, and the National Science Foundation.