Researchers devise new technique to plan HIV’s sweet shield in remarkable detail

Researchers devise new technique to plan HIV’s sweet shield in remarkable detail


  • Post By : Kumar Jeetendra

  • Source: Scripps Research Institute

  • Date: 26 Oct,2020

Scientists from Scripps Research and Los Alamos National Laboratory have devised a method for mapping in unprecedented detail the thickets of slippery sugar molecules which help protect HIV from the immune system.

Mapping these shields will give researchers a more comprehensive comprehension of why dinosaurs respond to some spots on the virus but not others, and may shape the design of new vaccines that target the most vulnerable and accessible websites on HIV and other viruses.

The sugar molecules, or”glycans,” are loose and stringy, and be the shields because they are hard for antibodies to grip and prevent access to the protein surface. The shields form on the outermost spike proteins of HIV and many other viruses, including SARS-CoV-2, the coronavirus that causes COVID-19, because these viruses have evolved sites on their spike proteins where glycan molecules–normally abundant in cells–will automatically attach.

“We finally have a way to capture the complete structures of these continuously fluctuating glycan shields, which to a great extent determine where antibodies can and can not bind to a virus like HIV,” says the study’s lead author Zachary Berndsen, PhD, a postdoctoral research associate in the structural sciences laboratory of Scripps Research Professor Andrew Ward, PhD.

The same wavy flexibility which makes these sugary molecules resistant to antibodies has made them impossible for investigators to capture with traditional atomic-scale imaging. In the new study, which appears in the Proceedings of the National Academy of Sciences, the scientists developed techniques , for the first time, allow these elusive molecules to be mapped in great detail on the surface of the HIV spike protein, called”Env.”

The Scripps Research team collaborated with the lab of Gnana Gnanakaran, PhD, staff scientist at Los Alamos National Laboratory, which is equipped with high performance computing resources that enabled fresh approaches for modeling the glycans.

Cryo-EM relies on averaging tens or hundreds of thousands of individual snapshots to create a clear picture, thus highly flexible molecules like glycans will appear only as a blur, if they show up at all.

But by integrating cryo-EM with the other technology, the researchers were able to recover this missing glycan signal and use it to map sites of vulnerability on the surface of Env.

“This is the first time that cryo-EM has been used together with computational modeling to describe the viral defense structure in atomic detail,” says Srirupa Chakraborty, PhD, co-lead writer and post-doctoral researcher at the Gnanakaran lab at Los Alamos National Laboratory.

There are chunks of glycans that seem to move and interact together. In between these glycan microdomains is where antibodies apparently have the opportunity to bind.”-Zachary Berndsen, Ph.D., study’s lead author

The new combined approach revealed the glycans’ structure and dynamic nature in extreme detail and aided the team better understand how these intricate dynamics affect the features observed in the cryo-EM maps. From this wealth of information, the team observed that individual glycans do not just wiggle around randomly on the spike protein surface, as once was thought, but rather clump together in tufts and thickets.

In principle, these vaccines’ effectiveness depends in part on the positioning and extent of the protecting glycans on these lab-made viral proteins. Therefore, Berndsen and colleagues applied their method to map the glycans on a modified HIV Env protein, BG505 SOSIP.664, which is used in an HIV vaccine currently being evaluated in clinical trials.

“We found spots on the surface of the protein that normally would be covered with glycans but were not –which may explain why antibody responses to that site have been noted in vaccination trials,” Berndsen states.

That finding, and others in the study, showed that Env’s glycan shield can change depending on what sort of cell is used to produce it. In HIV’s diseases of people, the virus uses human immune cells as factories to replicate its proteins. But viral proteins used to produce vaccines normally are generated in other types of mammalian cells.

In another surprise discovery, the team observed that if they used enzymes to gradually remove glycans from HIV Env, the entire protein started to fall apart. Berndsen and colleagues suspect that Env’s glycan shield, which has been considered merely a defense against antibodies, may also have a role in handling Env’s shape and stability, keeping it poised for disease.

The team expect their new glycan-mapping methods will be particularly beneficial in the design and development of vaccines–and not just for HIV. Lots of the techniques can be applied directly to other glycan-shielded viruses such as influenza viruses and coronaviruses, and can be extended to certain cancers in which glycans play a key role, the researchers say.

Journal reference:

Berndsen, Z.T., et al. (2020) Visualization of the HIV-1 Env glycan shield across scales.

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