Researcher Information

ABE Kazuhiro

Professor

Understanding molecular mechanism of biological macromolecules at the chemical level, manupilate it, and creat it

Department of Chemistry, Organic and Biological Chemistry

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Theme

Elucidating molecular mechanisms of membrane transport proteins including active tansporters

FieldBiochemistry, Structural biology, Molecular biology
KeywordX-ray crystallography, Cryo-EM, Primary transporters, Membrane proteins, P-type ATPases, Gastric proton pump, Phospholipid Flippase, Sodium pump, Lipid transport proteins

Introduction of Research

If thermal equilibrium means death, the asymmetric distribution of various substrates across the memebrane of the living cells is one of the impotant basis of the living system. This is created and maintaind by a number of active transporters including P-type ATPases, which mediate uphill transport a variety of substgrates, ranging from small cations to large phospholipids against their electrochemical gradient by utilizing ATP as an energy source. Employing biochemistry and structural biology, we try to elucidate how these protein molecules, which play a fundamental role in life, work at the "chemical" level.

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Gastric proton pump acidifies our stomach to pH 1
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Lipid flippase, which mediate phospholipid flipping, is involved in cellular apoptosis
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Drug development with AI x Organic chemistry x Structural analysis

Representative Achievements

Structure and function of H+/K+ pump mutants reveal Na+/K+ pump mechanism.Young, V.C., Nakanishi, H., Meyer, D.J., Nishizawa, T., Artigas, P & Abe, K. Nat. Commun., 13, 5270 (2022)
Gastric proton pump with two occluded K+ engineered with sodium pump-mimetic mutations. Abe, K., Yamamoto, K., Irie, K., Nishizawa, T. & Oshima, A. Nat. Commun., 12, 5709 (2021)
Transport cycle of plasma membrane flippase ATP11C by cryo-EM. Nakanishi, H., Nishizawa, T., Irie, K., Segawa, K., Nureki, O., Fujiyoshi, Y., Nagata, S. & *Abe, K. Cell Rep., 32, 108208 (2020)
A single K+-binding in the crystal structure of the gastric proton pump. Yamamoto, K., Dubey, V., Irie, K., Nakanishi, H., Khandelia, H., Fujiyoshi, Y. & Abe, K. eLife, 8, e47701 (2019)
Crystal structures of the gastric proton pump.Abe, K., Irie, K., Nakanishi, H., Suzuki, H. & Fujiyoshi, Y. Nature, 556, 214-218 (2018)

Related industries

Chemistry, Drug development, Medicine
Academic degreePh D
Self Introduction

From Sapporo. I am working on X-ray crystallography and cryo-EM single particle analysis to elucidate molecular mechanism of membrane transport proteins including gastric proton pump and other P-type ATPases. Big fun for beer in a microbrewery.

Academic background1999 B Sc, Faculty of Science, Hokkaido University
2001 M Sc, Graduate school of Science, Hokkaido University
2004 Ph D, Graduate School of Science, Hokkaido University
2003-2007 JSPS Research Fellow
2004- Posdoc, Graduate Shool of Science, Kyoto University
2012- Assistant Professor, Cellular and Structgural Physiology Institute, Nagoya University
2016- Associate Professor, Cellular and Structgural Physiology Institute, Nagoya University
2024- Professor, Faculty of Science, Hokkaido University
Affiliated academic societyThe Japanese Biochemical Society, The Biophysical Society of Japan, The Pharmaceutical Society of Japan
ProjectJST CREST, Cell Dynamics "Lipid scrambring system regulated by higher-order structure interaction"
Room addressScience Bulding 7 7-208

Department of Chemistry, Organic and Biological Chemistry

ABE Kazuhiro

Professor

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What is the research theme that you are currently focusing on?

We focus on membrane proteins expressed on the surface of cells, especially active transporters. By looking at the shape (structure) of these proteins using an electron microscope, we can understand how it works. Once the structure has been determined, we can design a compound that fits inside it- it has a potential to be a drug. Employing artificial intelligence for the compound design, we are trying to develop new drugs.

Molecular Biochemistry of primary active transporters. Visit our HP for details
https://wwwchem.sci.hokudai.ac.jp/~molbio/home-en/
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What made you decide to become a researcher?

I started working on the gastric proton pump, which is still an important target of our research, when I was a student here in Hokkaido University. When we have food intake, our stomach becomes veeery acidic (pH 1). The gastric proton pump is responsible for gastric acid secretion. Among the many pumps or transporters expressed in our body, no other tissue, except the stomach, has a pH of 1. In other words, this gastric proton pump is the “strongest” pump in our body. To understand why this guy is the strongest pump, I decided to become a scientist.

The strongest cation transporting protein, gastric proton pump.
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Please tell us what you think is good about your lab (staff, students, laboratory equipment, the number of papers published, etc.)

Our lab started in April 2024, so it is a new and small lab with only me as a staff, one post-doc, one PhD student, and four B4 students. So far, our official language is English, as the majority of the members are non-Japanese. I believe that our small lab allows us to work intimately with each other and conduct meticulous research. Also, we recently installed a coffee maker, and anyone can enjoy a cup of freshly brewed coffee for 100 yen. If you are interested in our research, please come to our lab with a 100-yen coin in your hand😊

Our coffee machine and lab members
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Please tell us about yourself; things you are good at, your favorites, hobbies, and daily routines.

It might be a boring answer, but research is my hobby. But when it comes to research on gastric proton pump, I am proud to say that I am one of the best in this planet😉 Now I have many friends and colleagues all over the world related to our scientific interest. Sometimes I visit them at conferences or for collaborations. After work, I always look for a microbrewery in the visiting area, and have a beer with them, which is also kind of my hobby.

Microbrewery with my colleagues
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