Kyoto University · Biochemistry, Genetics and Molecular Biology
Professor Masahiro Shirakawa's research lab specializes in molecular and structural biology, focusing on post-translational modifications such as ubiquitination and SUMOylation, and their roles in regulating cellular signaling and protein homeostasis. The lab employs advanced biophysical techniques—including NMR spectroscopy, electron spin resonance, and molecular dynamics simulations—to investigate the molecular mechanisms of protein-protein interactions, particularly those involving ubiquitin-binding domains and SUMO-interacting motifs. A key focus is also on developing novel nanoscale biosensors, such as fluorescent nanodiamonds functionalized for real-time, high-resolution detection of intracellular pH and metabolites like ATP. The lab integrates structural biology with functional biochemistry to uncover the physicochemical principles underlying protein regulation and signaling in health and disease.
Figures are computed from collected data and may differ slightly.
Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves as a signalling function that controls a wide variety of cellular processes. To date, two major forms of polyubiquitin chain have been functionally characterized, in which the isopeptide bond linkages involve Lys48 or Lys63. Lys48-linked polyubiquitin tagging is mostly used to target proteins for degradation by the proteasome, whereas Lys63-linked polyubiquitination has been linked to
Nanoscale measurements provide insight into the nano world. For instance, nanometric spatiotemporal distribution of intracellular pH is regulated by and regulates a variety of biological processes. However, there is no general method to fabricate nanoscale pH sensors. Here, we, to endow pH-sensing functions, tailor the surface properties of a fluorescent nanodiamond (FND) containing nitrogen-vacancy centers (NV centers) by coating the FND with an ionic chemical layer. The longitudinal relaxation
Adenosine triphosphate (ATP) is an immensely well-studied metabolite serving multiple key biochemical roles as the major chemical energy currency in living systems, a building block of ribonucleic acids, and a phosphoryl group donor in kinase-mediated signaling. Intriguingly, ATP has been recently proposed to act as a <i>hydrotrope</i> that inhibits aggregation of amyloidogenic proteins; however, the underlying mechanism and the general physicochemical effect that coexistence with ATP exerts on
Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves signaling functions that control several cellular processes. The ubiquitination signal is recognized by downstream effectors, many of which carry a ubiquitin-interacting motif (UIM). Such interactions can be modulated by regulators carrying a ubiquitin-like (UbL) domain, which binds UIM by mimicking ubiquitination. Of them, HR23B regulates the proteasomal targeting of ubiquitinated su
Post-translational modification by small ubiquitin-like modifier (SUMO) proteins has been implicated in the regulation of a variety of cellular events. The functions of sumoylation are often mediated by downstream effector proteins harboring SUMO-interacting motifs (SIMs) that are composed of a hydrophobic core and a stretch of acidic residues. MBD1-containing chromatin-associated factor 1 (MCAF1), a transcription repressor, interacts with SUMO-2/3 and SUMO-1, with a preference for SUMO-2/3. We
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