Kotaro TSUBOYAMA
RESEARCH DIRECTIONS
Discpher key facts from large-scale biological dataLABORATORY
https://sites.google.com/view/tsubo-lab/PROFILE
March 2016 Medical School, The University of Tokyo (UTokyo)
March 2019 Department of computational biology and medical sciences, Graduate School of Frontier Sciences, UTokyo
April 2019 Institute for Quantitative Biosciences, UTokyo, JSPS PD/CPD fellow
March 2020 Rocklin lab, Northwestern University, JSPS CPD fellow
March 2021 Rocklin lab, Northwestern University, Long-Term Fellow of the Human Frontiers Science Program
April 2023, Lecturer, Institute of Industrial Science (IIS), UTokyo
FIELD OF INTEREST
Proteins are composed of 20 different amino acids, providing a vast range of functions and a high level of diversity. Because the possible space is too huge, it remains difficult to rationally design de novo proteins without a thorough understanding of the fundamental relationships between amino acid sequence, structure, and function. To overcome this challenge, we are combining large-scale measurements with machine learning, including deep learning. Then, based on this new knowledge, we design de novo proteins to verify and reanalyze the new findings. In this way, we repeat such analysis and design to achieve both an understanding of the fundamental laws of proteins and rational de novo protein design.
PUBLICATION
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Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation.
Kim TE, Tsuboyama K, Houliston S, Martell CM, Phoumyvong CM, Lemak A, Haddox HK, Arrowsmith CH, Rocklin GJ.Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2122676119. doi: 10.1073/pnas.2122676119. Epub 2022 Oct 3.
A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation.
Tsuboyama K, Osaki T, Matsuura-Suzuki E, Kozuka-Hata H, Okada Y, Oyama M, Ikeuchi Y, Iwasaki S, Tomari Y.PLoS Biol. 2020 Mar 12;18(3):e3000632. doi: 10.1371/journal.pbio.3000632. eCollection 2020 Mar.
PMID: 32163402 Conformational Activation of Argonaute by Distinct yet Coordinated Actions of the Hsp70 and Hsp90 Chaperone Systems. Tsuboyama K, Tadakuma H, Tomari Y.Mol Cell. 2018 May 17;70(4):722-729.e4. doi: 10.1016/j.molcel.2018.04.010. The ATG conjugation systems are important for degradation of the inner autophagosomal membrane Tsuboyama K, Koyama-Honda I, Sakamaki Y, Koike M, Morishita H, Mizushima N.Science. 2016 Nov 25;354(6315):1036-1041. doi: 10.1126/science.aaf6136. Epub 2016 Oct 20.
PMID: 27885029