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In San Francisco, a recent study has made significant progress in virology. Researchers at Gladstone Institutes and the Innovative Genomics Institute, led by Jennifer Doudna, PhD, used computational tools to predict the three-dimensional shapes of nearly 70,000 viral proteins, gaining new insights into their functions and roles in infection.

Describing the study, Jennifer Doudna stated, “As viruses with pandemic potential emerge, it’s important to establish how they’ll interact with human cells. Our new study provides a tool to predict what those newly emerging viruses can do.” The team used an open-access research platform called AlphaFold to predict the shapes of proteins from various species of viruses, providing the team with a unique opportunity to match the 3D shapes to the structures of proteins whose functions are already known, revealing previously unknown roles and functionalities of these viral proteins.

The study revealed that 38 percent of the newly predicted protein shapes matched previously known proteins, shedding light on the shared molecular mechanisms between viruses and cellular systems. The team also discovered a common strategy for evading host immune defenses shared across viruses that infect animals and bacteria-infecting viruses known as phages, suggesting a conserved mechanism throughout evolution.

Jason Nomburg, PhD, highlighted the essential role of computational tools in the study, stating: "This would not have been possible without recent advancements in computational tools that allow us to accurately and quickly predict and compare protein structures.”

The study also emphasized the rapid advancements in computational tools, allowing for the swift prediction of protein structures, which has previously been a challenge in virology. By sharing the 70,000 newly predicted viral protein structures and data from their analyses with the scientific community, the researchers have opened up opportunities for further discoveries and collaborations that could deepen knowledge of how viruses interact with their hosts.

This study reaches beyond virology and underlines the pivotal role of computational tools in broadening our understanding of complex biological systems. The study’s insights hold the potential to impact antiviral therapies against a variety of viruses, representing a significant stride in combating viral infections effectively. The breakthrough also underscores the transformative impact that recent advancements in computational tools have had on the field of virology, providing researchers with new ways to unravel the intricacies of viral infections and evolve innovative strategies for combating them.

The co-authors include Nathan Price, Yong K. Zhu, and Jennifer Doudna of Gladstone Institutes, UC Berkeley, and the Innovative Genomics Institute; and Erin E. Doherty and Daniel Bellieny-Rabelo of UC Berkeley and the Innovative Genomics Institute. The study was supported by various institutions and organizations, highlighting the collaborative effort behind this groundbreaking research.

This study not only unfolds new dimensions in virology but also underscores the indispensable role of computational tools in driving innovation and pushing the boundaries of scientific discovery.