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Current Research Summaries

  • [Mini review] Specific Binding and Catalytic Activation of the MAPK-MKP Complex

    Mitogen-activated protein kinases (MAPKs) are one of the most important enzymes in various cellular activities, and the MAPK signaling pathway is implicated in many disorders. MAPK phosphatases (MKPs) are regulators that contain a MAPK-binding domain (MBD) for MAPK recognition, and a catalytic domain (CD), for dephosphorylation and inactivation of MAPKs. Due to their crucial role in regulating the MAPK pathway, MKPs are regarded as a potential drug target in various diseases. Attempts have also been made to regulate the MAPK pathway by reducing the MKP activity. For drug development, it is important to understand the key features of MAPK-MKP complex formation. This review summarizes the studies on MAPK-MKP complexes, mainly focusing on their selective recognition and catalytic activation.

  • [Article] Crystal structure of unphosphorylated Spo0F from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier

    Spo0F is a response regulator that modulates sporulation, undergoes phosphorylation for phosphorelay signal transduction, and interacts with various regulatory proteins; however, the mechanisms through which phosphorylation induces structural changes and regulates interactions with binding partners remain unclear. Here, we determined the unphosphorylated crystal structure of Spo0F from the psychrophilic bacterium Paenisporosarcina sp. TG-14 (PaSpo0F) and established a phosphorylation-state structural model. We found that PaSpo0F underwent structural changes (Lys54 and Lys102) by phosphorylation and generated new interactions (Lys102/Gln10 and Lys54/Glu84) to stabilize the β4/α4 and β1/α1 loop structures, which are important target-protein binding sites. Analysis of Bacillus subtilis Spo0 variants revealed movement by BsSpo0F Thr82 and Tyr84 residues following interaction with BsSpo0B, providing insight into the movement of corresponding residues in PaSpo0F (Thr80 and Tyr82), with further analysis of BsSpo0F/BsRapH interaction revealing alterations in the β4/α4 loop region. These results suggest that phosphorylation-induced structural rearrangement might be essential for PaSpo0F activation and expand the understanding of Spo0F-specific activation mechanisms during sporulation.

  • [Crystallization] Crystallization and preliminary X-ray analysis of API5-FGF2 complex

    API5 is a unique oncogenic, non-BIR type IAP nuclear protein and is up-regulated in several cancers. It exerts several functions, such as apoptosis inhibition, cell cycle progression, cancer immune escape, and anticancer drug resistance. Although structural studies of API have revealed that API5 mediates protein-protein interactions, its detailed molecular functions remain unknown. Since FGF2 is one of API5’s major interacting proteins, structural studies of the API5–FGF2 complex will provide insight into both proteins’ molecular function. We overexpressed and purified API5 and FGF2 in Escherichia coli and crystallized the API–FGF2 complex using polyethylene glycol (PEG) 6000 as a precipitant. Diffraction data were collected to a 2.7 Å resolution using synchrotron X-rays. Preliminary diffraction analysis revealed that the API5–FGF2 complex crystal belongs to the space group P212121 with the following unit cell parameters: a = 46.862, b = 76.523, c = 208.161 Å. One asymmetric unit with 49.9% solvent contains one API5-FGF2 complex. Molecular replacement calculation, using API5 and FGF2 coordinates, provided a clear electron density map for an API5–FGF2 complex.

  • [Crystallization] Purification and preliminary analysis of the ATP-dependent unfoldase HslU from the gram-positive bacterium Staphylococcus aureus

    The gram-positive bacterium Staphylococcus aureus is a common cause of abscesses, sinusitis and food poisoning. The emergence of antibiotic-resistant strains has caused significant clinical issues worldwide. The HslU-HslV complex was first identified as a prokaryotic homolog of eukaryotic proteasomes. HslU is an unfoldase that mediates the unfolding of the substrate proteins, and it works with the protease HslV in the complex. To date, the protein complex has been mostly studied in gram-negative bacteria. In this study, we report the purification and crystallization of the full-length HslU from S. aureus. The crystal diffracted X-rays to a 3.5 Å resolution, revealing that the crystals belong to space group P21, with unit cell parameters of a = 166.5, b = 189.6, c = 226.6 Å, and β = 108.1°. We solved the phage problem by molecular replacement using the structure of HslU from Haemophilus influenzae as a search model. The cell content analysis with this molecular replacement solution revealed that 24 molecules are contained in the asymmetric unit. This structure provides insight into the structural and mechanistic difference of the HslUV complex of gram-positive bacteria.

  • [Crystallization] Purification, crystallization, and preliminary X-ray diffraction data analysis for PB1 dimer of P62/SQSTM1

    Autophagy is a degradation pathway that targets many cellular components and plays a particularly important role in protein degradation and recycling. This process is very complex and several proteins participate in this process. One of them, P62/SQSTM1, is related to the N-end rule and induces protein degradation through autophagy. The P62/SQSTM1 makes a huge oligomer, and this oligomerization is known to play an important role in its mechanism. This oligomerization takes two steps. First, the PB1 domain of P62/SQSTM1 makes the base oligomer, and then, when the ligand binds to the ZZ domain of P62/SQSTM1, it induces a higher oligomer by the disulfide bond of the two cysteines. To understand the oligomerization mechanism of P62/SQSTM1, we need to know the dimerization of the PB1 domain. In this study, crystals of PB1 dimer were made and the crystals were diffracted by X-ray to collect usable data up to 3.2A. We are analyzing the structure using the molecular replacement (MR) method.