Research Interview 3
By Shizu YAMAGUCHI
July 24, 2015
What do you think about genome sequences? Some people might imagine analyses of huge amount of data with A, T, G, C. Genome means whole bioinformation of human, but it doesn’t control all of our health. Protein also plays an important role in our cells.
Assistant Prof Hafumi Nishi’s research focuses on protein and genome. It’s possible that studying both genome and protein in Kinoshita Lab.
“Distribution of single nucleotide variants on protein-protein interaction sites” She won the 15th Young Scientist Award by PSSJ. She researched where and how single nucleotide variants exist from the structural point of view. There are ordinary and unusual patterns of variants.
Cells contain many proteins inside. Protein is a folded peptide chain consisted of amino acid. Chains of proteins contact each other in a cell, and the surface is called interaction site. Center of the site promotes chemical reaction while its edge doesn’t do so much.
Genome variants mean differences between individual genome and reference genome. Reference genome has standard arrangement for comparing with other genome data. Common variants, many people are having, are usually on the edge of interaction site. If common variants were on center of the site, many people would be suffered from disorder cause of variants.
She confirmed this tendency by analyzing genome data on her hypothesis that common variants are on edge and rare variants exist randomly on the interaction site.
Then, how about unusual cases?
She watched one unique variant that arginine changed into glutamine. It’s one example of 20 rare variants. Both molecules are amino acid, but they have quite different construction. Thus, the alternation may have remarkable influence than usual. Additionally, many people have this variant and it lies on center of the site.
She noticed that other scientist’s research showed the answer. Proteins get stronger in the plural than in the single. A cell contains many proteins, and weakness of binding due to the variant doesn’t have bad influence on humans’ body.
She showed that cells overcome risky genome variant. Because she researched both genome and protein, she could reach the conclusion.
She says, “genome is basic information of our body, and proteins are dwarf working in our cells”.
Hafumi NISHI
Doctor of Science
Researcher at Nagoya University (2009-2010)
Postdoctoral fellow at NIH, America (2010-2012)
Contract Assistant Professor at Yokohama City University (2013)
JSPS Research Fellow at Yokohama City University (2013-2014)
Assistant Professor at Tohoku University (2014-)
