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Tsuboyama Lab
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A lab that uncovers the principles of proteins and designs new proteins.
AboutAbout the lab
Uncovering the rules for designing biomolecules.
The Tsuboyama Lab aims to design proteins artificially and rationally, and works to uncover the principles governing protein properties and functions.
Proteins are molecules made of chains of amino acids, and because the number of possible sequence combinations is astronomically large, they exhibit a wide variety of functions.
For this reason, it is difficult to rationally design new proteins without a thorough understanding of the features that underlie their properties and functions.
To address this, the lab combines large-scale analysis methods with machine learning, including deep learning.
Key terms
- Artificial protein
- A protein made by humans designing, from scratch, an amino acid sequence that does not exist in nature
- Machine learning
- A method that lets computers learn rules from large amounts of data so they can make predictions and decisions
- Cytoplasm
- The part inside the cell membrane that fills the space around the nucleus, where many chemical reactions take place
NewsLab news
View More ↗ResearchResearch themes
The lab aims to design biomolecules, especially proteins, artificially and rationally, and works to elucidate the principles behind protein properties, features, and functions. It combines large-scale analysis methods with machine learning, including deep learning.
*Illustrative imageProtein-Protein Interactions
Interactions between proteins are involved in every biological function, including signal transduction and metabolism, and are also important for designing functional artificial proteins. The lab aims to clarify which features are important for these interactions.
*Illustrative imageProtein Lifespan and Stability
Proteins are broken down by processes such as autophagy as soon as they are synthesized, which maintains protein quality. The lab investigates the mechanisms that determine protein lifespan, including which proteins are stable and which become unstable inside cells.
*Illustrative imageProteins That Reach the Inside of Cells
Many of the interactions between important proteins involved in diseases such as cancer take place in the cytoplasm. With medical applications of artificial proteins in mind, the lab is investigating the features required for proteins to enter the cytoplasm.
MembersFaculty
The members of the Tsuboyama Lab include faculty, Research Fellows of the Japan Society for the Promotion of Science, project researchers, collaborative researchers, academic specialists, and doctoral and master's students.As of 2026
- LecturerKotaro TsuboyamaPublications ↗
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “PDB 2jua EBI” Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute / Public domain (cropped)
- Protein-Protein Interactions: “Resistosome Model” Rkott / CC BY-SA 4.0 (cropped)
- Protein Lifespan and Stability: “26S proteasome structure” FridoFoe / CC BY-SA 3.0 (cropped)
- Proteins That Reach the Inside of Cells: “LSM fluorescence image of HeLa immortalized cells showing fluorescent staining of cellular compartments. Nuclei are labeled in blue, the cytoplasm in orange, and vesicular transport–associated proteins in red” WillredDallto / CC BY-SA 4.0 (cropped)
- Related lab (Nishimasu Lab): “Acidaminococcus sp. Cas12a PDB 5B43” Deposition authors: Yamano, T., Nishimasu, H., Hirano, H., Nakane, T., Ishitani, R., Nureki, O.; Visualization author: Synpath / CC0 (cropped)
- Related lab (Tsumoto Lab): “Antibody IgG2” TimVickers at English Wikipedia / Public domain (cropped)
- Related lab (Okamoto Lab): “DNA methylation H o” Qubeat / CC BY-SA 4.0 (cropped)
- Related lab (Ikeuchi Lab): “Human Cerebral Organoids ( )” NIAID / CC BY 2.0 (cropped)
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