Halmos Researcher’s Efforts Focus on Visualizing Virus Variants
Associate Professor Louis R. Nemzer, Ph.D.
NSU Associate Professor Louis R. Nemzer, Ph.D., in the Department of Chemistry and Physics at the Halmos College of Arts and Sciences, developed a new method for visualizing amino acid substitutions in which changes in the physical and chemical properties are represented by vectors in a 3D space. While applicable to a wide range of biological applications, such as rational protein design, this work is particularly useful for understanding the behavior of COVID-19 variants and even predicting future threats.
Proteins are long chains of amino acids, and the most infamous today is certainly the spike protein of SARS-CoV-2, the virus responsible for COVID-19. Random mutations cause changes to its amino acid sequence, which leads to variants that may spread more easily or more effectively evade the human immune system.
As part of his research on amino acid properties, Nemzer created a new way to visualize changes in novel variants, utilizing recently available data on SARS-CoV-2 immune escape, which measures how well they can hide from the host’s antibodies. In addition, results were used from site-saturation mutagenesis experiments, in which all possible amino acid substitutions at a particular site in the spike protein were tested for their impact on binding affinity with ACE2 receptors.
“We live in the era of big data in biology, and the key now is finding new ways to visualize this vast amount of information to make the best use of it,” Nemzer said.
In some diagrams, the colors of the vectors show the impact of the substitution, while dashed lines indicate changes that require at least two nucleotide mutations to happen. He showed that sometimes clusters of chemically similar amino acids can have similar effects, but in other situations, only a specific change – such as swapping a charged amino acid in place of a neutral one – significantly reduces the virulence. The work is available now as a bioRxiv preprint.
REFERENCES: