Tsuyoshi Terakawa

Overview

I study molecular mechanisms of protein functions using methods such as coarse-grained molecular dynamics simulation, single-molecule fluorescence imaging, and nanopore sequencing. I am particularly interested in the proteins involved in transcription, replication, repair and higher-order strucral formation of DNA, and I would like to understand these molecular mechanisms based on physics laws. For that purpose, I believe that close combinations among experiments, theory, and simulations is essential. I am conducting research with the desire to "surprise the world a little with my research."

Career

• 2005-2009
  Faculty of Science and Engineering, Tokyo University of Science
  • Studied Biology, Physics, and Programming
  • Instructed by Prof. Takashi Kunisawa
  • Conducted research on the taxonomy of algae using bioinformatics
  • Received Bachelor degree in March 2009
• 2009-2014
  Graduate School of Science, Kyoto University
  • Instructed by Prof. Shoji Takada
  • Conducted reseearch on the molecular mechanism of the transcription factor p53 usin coarse-grained molecular dynamics simulations
  • Involved in the development of the coarse-grained molecular dynamics simulator CafeMol
  • Engaged in research as a JSPS Research Fellow (DC2)
  • Received Master degree in March 2011
  • Received Docter degree (Science) in March 2014
• 2014-2018
  Columbia University Medical Center
  • Instructed by Prof. Eric C. Greene
  • Engaged in research as a JSPS Postdoctoral Fellow for Oversears Research
  • Engaged in research as a Postdoctoral Research Fellow of the Uehara Memorial Foundation
  • Conducted research on the molecular mechanism of proteins involved in repair and structural formation of DNA using simulations and single-molecule fluorescence imaging
• 2014-2024
  Graduate School of Science, Kyoto University
  • Appointed as an assistant professor in 2018
  • Conducting research on the molecular mechanisms of proteins involved in DNA transcription, replication, repair, and structural formation by cimbining simulation and experimental methods.
  • Received the Young Scientist Award from the Biophysical Society of Japan in 2018
  • Engaged in research as a PRESTO researcher from 2019 to 2022

Projects Full Publications

MutS Corkscrewing

Using coarse-grained molecular dynamics simulations, we visualized the dynamics of MutS, a DNA base pair mismatch recognition protein, sliding along DNA while rotating around DNA. As a result, we found that the diffusion rate of MutS changed according to the DNA bending.

Lane Switch on Nucleosome

By verifying the coarse-grained molecular dynamics simulation results with biochemical experiments and nanopore sequencing, we revealed that DNA translocases push nucleosomes along DNA. We proposed the "Lane Switching" as the molecular mechanism.

Condensin is a Motor

Single-molecule fluorescence imaging using a DNA curtain device revealed that condensin, involved in the chromatin structural formation, is a molecular motor. The results were published in Science and featured on the cover. Now, we are studying its molecular mechanism.

p53 Dancing on DNA

Using coarse-grained molecular dynamics simulations, we visualized p53, a tumor-suppressive transcription factor, sliding on DNA. As a result, it was suggested that the DNA-binding region searches for the recognition site by "dancing" while diffusion on the DNA.