Researcher Information

NAKAGAWA Natsumi

Assistant Professor

Interaction and regulatory mechanism of oligomer protein

Department of Chemistry, Organic and Biological Chemistry

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Theme

Study of posttranslational modification, stability, regulatory mechanism, and evolution on oligomer protein

FieldPeptide science, Biological chemistry, Evolution
KeywordPeptide, Protein, Oligomerization, Posttanslational modification, Tumor, Evolution

Introduction of Research

Protein oligomerization is a crucial strategy acquired by living organisms. During the evolution of living organisms, proteins have acquired more precise functional regulatory mechanisms through the modulation of oligomer formation. The tumor suppressor protein p53 requires homotetramer formation via the tetramerization domain for functional expression. Stabilized, formed tetramer, and activated in response to cellular stress such as genotoxic stress, p53 maintains genomic integrity by inducing cell cycle arrest and apoptosis. The function of p53 is regulated by various posttranslational modifications such as phosphorylation and methylation. So far, we have determined the mechanism of functional regulation by methylation of the tetramerization domain. p53, which is important for stress response, is expressed in the early vertebrate lamprey. Interestingly, the mammal tree shrew revealed that it has a more stable p53 tetramerization domain than humans, and found that methionine residues contribute significantly to structural stabilization. To date, we have been conducting research on the evolution of p53 structure / stability and functional regulatory mechanisms in vertebrates.

Representative Achievements

The tetramerization domain of the tree shrew p53 protein displays unique thermostability despite sharing high sequence identity with the human p53 protein.
Natsumi Nakagawa, Shuya Sakaguchi, Takao Nomura, Rui Kamada, James G. Omichinski, Kazuyasu Sakaguchi,
Biochem. Biophys. Res. Commun., 2020, 521, 681-686
Heterochiral Jun and Fos bZIP peptides form a coiled-coil heterodimer that is competent for DNA binding.
Rui Kamada, Natsumi Nakagawa, Taiji Oyama, Kazuyasu Sakaguchi,
J. Pept. Sci., 2017, 23, 644-649
Academic degreePh.D. (Hokkaido University), Ph.D.(Biochemistry) (University of Montreal)
Affiliated academic societyThe Japanese Peptide Society, Society of Evolutionary Studies, Japan, The Japanese Biochemical Society
Room addressScience Building 6, 6-5-02

Department of Chemistry, Organic and Biological Chemistry

NAKAGAWA Natsumi

Assistant Professor

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

My current research focuses on understanding how oligomeric proteins assemble, interact, and regulate their functions. Many essential proteins operate not as single molecules but as dynamic complexes, where even slight structural changes can significantly impact cellular activities. By integrating biochemical approaches with structural analysis, I aim to uncover the molecular logic that governs these interactions. Ultimately, I hope this knowledge will contribute to a deeper understanding of how complex biological systems maintain their functions and respond to environmental cues.

Functional regulation of peptides and proteins via oligomerization
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What made you decide to become a researcher?

One of the unexpected inspirations that led me to pursue a career in science came from music. A line from a song by my Japanese band, BUMP OF CHICKEN, says: “The footprints you count eventually become just numbers; what you really need to know lies between 1 and 0.” This lyric made me realize that the world is not binary. Biological phenomena are rarely simply “on” or “off” — they exist in gradients, shaped by subtle molecular dynamics. This perspective continues to guide how I approach science: with curiosity for what exist “in between,” and a desire to uncover the hidden layers of biological complexity.

My presentation at the research conference

During my Ph.D., I spent a year at the Université de Montréal through a double-degree program. This experience profoundly shaped my career, showing me how diverse research cultures and scientific approaches can be. Discussing ideas with researchers from different backgrounds pushed me to think more broadly and creatively. For young scientists, I strongly encourage studying or conducting research abroad. Being exposed to different perspectives not only advances your science but also expands your worldview in ways that stay with you throughout your career.

Montréal, visited for the first time in seven years after studying abroad
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Please tell us about yourself; things you are good at, your favorites, hobbies, and daily routines.

I love attending concerts and music festivals. Music helps me reset my mind and return to research with fresh energy. To fully enjoy live performances, I recently started incorporating light exercise into my daily routine — it has become a fun way to scientific life with something I truly enjoy.

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Department of Chemistry, Organic and Biological Chemistry

Chemistry, Biological Chemistry, Biological Chemistry

Graduate School of Chemical Sciences and Engineering, Biological Chemistry and Engineering Course, Biomolecular Chemistry Unit