Artificial intelligence reveals never-before-described 3D structure in rotavirus spike protein

Of the three groups of rotaviruses that cause gastroenteritis in humans, designated groups A, B, and C, groups A and C primarily affect children and are the best characterized. On the other hand, in group B, which causes severe diarrhea mainly in adults, little is known about the spike of the virus spike protein, the so-called VP8* domain, which mediates infection of cells in the gut of the virus.

“Determining the structure of VP8* in group B rotavirus is important because it will help us understand how the virus infects gastrointestinal cells and develop strategies to prevent and treat this infection that causes severe diarrheal outbreaks ‘ said corresponding author, Dr. BV Venkataram Prasad, Professor. in Biochemistry and Molecular Biology from Baylor College of Medicine.

The team’s first step was to determine the 3D structure of VP8*B using X-ray crystallography, a time-consuming and laborious process. However, this traditional approach did not prevail in this case. The researchers then turned their attention to a recently developed artificial intelligence-based computer program called AlphaFold2.

“AlphaFold2 predicts the 3D structure of proteins based on their genetic sequence,” said Dr. Liya Hu, first author and corresponding co-author, assistant professor of biochemistry and molecular biology at Baylor. “We knew that the protein sequence of VP8* from rotavirus group B was about 10% similar to the sequence of VP8* from rotavirus A and C, so we also expected differences in the 3D structure. But we were surprised when AlphaFold2 predicted a 3D structure for VP8*B that was not only completely different from the VP8* domain in rotavirus A and C, but also that no other protein had previously been tagged with this structure.

With this information, the researchers returned to the lab bench and confirmed experimentally that the structure of VP8*B predicted by ALphaFold2 was indeed consistent with the actual structure of the protein using X-ray crystallography.

How rotavirus infects cells

Previous research has shown that rotaviruses A and C infect cells using the VP8* domain to bind to specific sugar moieties on histo-blood group antigens, including blood groups A, B, AB and O, which are present in many body cells. It has been suggested that the ability of different rotaviruses to bind different sugars to histogroup antigens might explain why some of these viruses specifically infect young children, while others infect other populations. In contrast to VP8* A and VP8* C, the sugar specificity of VP8* B has not been characterized so far.

“We screened VP8*B against a spectrum of sugars and found that it recognizes N-acetyllactosamine, a sugar common to many cells in the body that is not recognized by rotavirus A and C VP8*,” Hu said. “Such a 3D structure, which can also bind sugar, has not been described before. »

“I’m excited to identify a new 3D protein structure. I also await any discoveries that will follow as we study how the new structure interacts with cells to infect them and how this process compares to that of rotaviruses A and C,” said co-author Dr Prasad- Laboratory.

“Our laboratory has been working with the laboratory of Dr. Prasad to understand the importance of sugar-binding viruses in gastrointestinal infections,” said co-author Dr at Baylor. Estes is also a member of the Dan L. Duncan Comprehensive Cancer Center in Baylor. “We cannot yet grow the group B virus, but our lab will now try to grow these adult viruses in our human organoid systems, a miniature model of the human gut that can help us study the mechanism of entry and virus growth.” . may lead to new therapies that are still needed to treat diarrheal diseases. »

“This novel approach to determining the 3D structure of a protein represents a significant advance in the field of structural biology,” said Hu.

“I am excited about our discoveries of a novel 3D protein structure from an evolutionary perspective. This shows how viruses can evolve by incorporating structurally distinct modules with similar functionality, but how this structure arose in this group B rotavirus is quite intriguing,” said Prasad, Alvin Romansky Chair in Biochemistry and member of the Dan L Duncan Comprehensive Cancer Center.

The authors acknowledge support from NIH grants AI36040, AI080656, and P30 DK56338 and the Robert Welch Foundation (Q1279). Additional support was provided by the Gulf Coast Consortia’s Interdisciplinary Training of Scientists in Pharmacology (TIPS) program (Grant No. T32 GM120011), a user installation contract from the DOE Office of Science (DE-AC02-05CH11231), and the National Institutes of Health, National , Provided Institute for General Medical Sciences, Grant P30 GM124169-01.

Source of the story:

Materials provided by Baylor College of Medicine. Originally written by Ana María Rodríguez, Ph.D.. Note: Content can be edited for style and length.

Leave a Comment