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Biomedical subjects

Ryuichi Kato

Publications and source records attributed to Ryuichi Kato.

At least 19 recordsLinked to original sources
PubMed2006

Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope.

The HNK-1 carbohydrate epitope is found in various neural cell adhesion molecules. Two glucuronyltransferases (GlcAT-P and GlcAT-S) are involved in the biosynthesis of HNK-1 carbohydrate. Our previous study on the crystal structure of GlcAT-P revealed the reaction and substrate recognition mechanisms of this enzyme. Comparative analyses of the enzymatic activities of GlcAT-S and GlcAT-P showed that there are notable differences in the acceptor substrate specificities of these enzymes. To elucidate differences between their specificities, we now solved the crystal structure of GlcAT-S. Residues interacting with UDP molecule, which is a part of the donor substrate, are highly conserved between GlcAT-P and GlcAT-S. On the other hand, there are some differences between these proteins in the manner they recognize their respective acceptor substrates. Phe245, one of the most important GlcAT-P residues for the recognition of acceptors, is a tryptophan in GlcAT-S. In addition, Val320, which is located on the C-terminal long loop of the neighboring molecule in the dimer and critical in the recognition of the acceptor sugar molecule by the GlcAT-P dimer, is an alanine in GlcAT-S. These differences play key roles in establishing the distinct specificity for the acceptor substrate by GlcAT-S, which is further supported by site-directed mutagenesis of GlcAT-S and a computer-aided model building of GlcAT-S/substrate complexes.

Amino Acid Sequence↗
PubMed2006

Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain.

ESCRT-II, a complex that sorts ubiquitinated membrane proteins to lysosomes, localizes to endosomes through interaction between the Vps36 subunit's GLUE domain and phosphatidylinositides (PIs). In yeast, a ubiquitin (Ub)-interacting NZF domain is inserted in Vps36 GLUE, whereas its mammalian counterpart, Eap45 GLUE, lacks the NZF domain. In the Eap45 GLUE-Ub complex structure, Ub binds far from the proposed PI-binding site of Eap45 GLUE, suggesting their independent binding.

Amino Acid Motifs↗
PubMed2006

Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1.

Family of Rab11-interacting protein (FIP)3/Arfophlin-1 and FIP4/Arfophilin-2 are dual effectors for Rab11 and ADP ribosylation factor (ARF)5/ARF6, which are involved in membrane delivery from recycling endosomes to the plasma membrane during cytokinesis. Here, we define the distinct C-terminal binding regions of FIP3 and FIP4 for Rab11 and ARF5/ARF6. Furthermore, we determined the crystal structure of Rab11 in complex with the Rab11-binding domain (RBD) of FIP3. The long amphiphilic alpha-helix of FIP3-RBD forms a parallel coiled-coil homodimer, with two symmetric interfaces with two Rab11 molecules. The hydrophobic side of the RBD helix is involved in homodimerization and mediates the interaction with the Rab11 switch 1 region, whereas the opposite hydrophilic side interacts with the Rab11 switch 2 and is the major factor contributing to the binding specificity. The bivalent interaction of FIP3 with Rab11 at the C terminus allows FIP3 to coordinately function with other binding partners, including ARFs.

ADP-Ribosylation Factors↗
PubMed2006

Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition.

The galectins are a family of beta-galactoside-binding animal lectins with a conserved carbohydrate recognition domain (CRD). They have a high affinity for small beta-galactosides, but binding specificity for complex glycoconjugates varies considerably within the family. The ligand recognition is essential for their proper function, and the structures of several galectins have suggested their mechanism of carbohydrate binding. Galectin-9 has two tandem CRDs with a short linker, and we report the crystal structures of mouse galectin-9 N-terminal CRD (NCRD) in the absence and the presence of four ligand complexes. All structures form the same dimer, which is quite different from the canonical 2-fold symmetric dimer seen for galectin-1 and -2. The beta-galactoside recognition mechanism in the galectin-9 NCRD is highly conserved among other galectins. In the apo form structure, water molecules mimic the ligand hydrogen-bond network. The galectin-9 NCRD can bind both N-acetyllactosamine (Galbeta1-4GlcNAc) and T-antigen (Galbeta1-3GalNAc) with the proper location of Arg-64. Moreover, the structure of the N-acetyllactosamine dimer (Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc) complex shows a unique binding mode of galectin-9. Finally, surface plasmon resonance assay showed that the galectin-9 NCRD forms a homophilic dimer not only in the crystal but also in solution.

Amino Acid Sequence↗
PubMed2006

Effect of testosterone on intracavernous pressure elicited with electrical stimulation of the medial preoptic area and cavernous nerve in male rats.

We studied the effects of castration and testosterone (T) replacement on intracavernous pressure (ICP) elicited with electrical stimulation of the medial preoptic area (MPOA) and cavernous nerve (CN) in male rats. We measured the ICP during electrical stimulation of the MPOA and CN in castrated male rats with and without testosterone replacement. The experimental group consisted of 20-week-old male rats at 2 weeks (n=8), 4 weeks (n=8) and 8 weeks (n=8) after castration, and at 8 weeks after castration with T replacement (n=4). Intact 20-week-old rats (n=8) served as controls. The erectile response was expressed as the ICP/blood pressure (BP) ratio. The ICP/BP ratios during CN stimulation of the animals at 2, 4, and 8 weeks after castration were significantly lower than those of the intact animals. However, the erectile responses were not eliminated. In contrast to these peripherally evoked responses, erectile responses elicited by electrical stimulation of the MPOA were eliminated following castration. After testosterone replacement, both erectile responses were restored. Testosterone plays important roles in both the central and peripheral neural pathways for the maintenance and restoration of erectile capacity. The central control of erection shows more extensive changes following testosterone replacement than the peripheral control.

Animals↗
PubMed2006

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

Automation↗
PubMed2006

Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting.

Hrs has an essential role in sorting of monoubiquitinated receptors to multivesicular bodies for lysosomal degradation, through recognition of ubiquitinated receptors by its ubiquitin-interacting motif (UIM). Here, we present the structure of a complex of Hrs-UIM and ubiquitin at 1.7-A resolution. Hrs-UIM forms a single alpha-helix, which binds two ubiquitin molecules, one on either side. These two ubiquitin molecules are related by pseudo two-fold screw symmetry along the helical axis of the UIM, corresponding to a shift by two residues on the UIM helix. Both ubiquitin molecules interact with the UIM in the same manner, using the Ile44 surface, with equal binding affinities. Mutational experiments show that both binding sites of Hrs-UIM are required for efficient degradative protein sorting. Hrs-UIM belongs to a new subclass of double-sided UIMs, in contrast to its yeast homolog Vps27p, which has two tandem single-sided UIMs.

Amino Acid Motifs↗
PubMed2006

Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.

Emp46p and Emp47p are type I membrane proteins, which cycle between the endoplasmic reticulum (ER) and the Golgi apparatus by vesicles coated with coat protein complexes I and II (COPI and COPII). They are considered to function as cargo receptors for exporting N-linked glycoproteins from the ER. We have determined crystal structures of the carbohydrate recognition domains (CRDs) of Emp46p and Emp47p of Saccharomyces cerevisiae, in the absence and presence of metal ions. Both proteins fold as a beta-sandwich, and resemble that of the mammalian ortholog, p58/ERGIC-53. However, the nature of metal binding is distinct from that of Ca(2+)-dependent p58/ERGIC-53. Interestingly, the CRD of Emp46p does not bind Ca(2+) ion but instead binds K(+) ion at the edge of a concave beta-sheet whose position is distinct from the corresponding site of the Ca(2+) ion in p58/ERGIC-53. Binding of K(+) ion to Emp46p appears essential for transport of a subset of glycoproteins because the Y131F mutant of Emp46p, which cannot bind K(+) ion fails to rescue the transport in disruptants of EMP46 and EMP47 genes. In contrast the CRD of Emp47p binds no metal ions at all. Furthermore, the CRD of Emp46p binds to glycoproteins carrying high mannosetype glycans and the is promoted by binding not the addition of Ca(2+) or K(+) ion in These results suggest that Emp46p can be regarded as a Ca(2+)-independent intracellular lectin at the ER exit sites.

Amino Acid Sequence↗
PubMed2006

A possible association between coronary plaque instability and complex plaques in abdominal aorta.

OBJECTIVE: Coronary plaque instability causes myocardial infarction (MI). Angiographic lesions with such instability are complex lesions. Complex carotid plaques were reported to be prevalent in unstable angina. We investigated associations between coronary plaque instability, such as MI and angiographic complex coronary lesions, and aortic plaques. METHODS AND RESULTS: Aortic MRI was performed in 146 patients undergoing coronary angiography, of whom 108 had coronary artery disease (CAD) and 44 also had MI. Prevalence of plaques in thoracic and abdominal aortas was higher in patients with than without CAD (73% and 94% versus 32% and 79%), but it was similar in CAD patients with and without MI. Notably, complex plaques in abdominal aorta were more prevalent in CAD patients with than without MI (36% versus 14%; P<0.025). In multivariate analysis, abdominal complex plaques were associated with MI (odds ratio [OR], 4.5; 95% CI, 1.5 to 13.8). Among patients without MI, thoracic and abdominal complex plaques were more prevalent in patients with than without complex coronary lesions (22% and 33% versus 2% and 7%; P<0.05). Abdominal complex plaques were also associated with complex coronary lesions (OR, 9.8; 95% CI, 1.1 to 85.9). CONCLUSIONS: Complex plaques in abdominal aorta were associated with MI and complex coronary lesions, suggesting a link between coronary and aortic plaque instability.

Adult↗
PubMed2006

Vagal nerve-mediated vasospasm-induced lethal ventricular fibrillation.

We report a case of variant angina complicated by lethal ventricular fibrillation. Serial ambulatory electrocardiogram monitoring revealed high-frequency spectra reflecting augmented vagal nerve activity preceding the vasospastic episodes. Our case suggests that heart rate variability analysis can help identify potential unexpected sudden cardiac death in patients with variant angina.

Angina Pectoris↗
PubMed2006

Outcome analysis for conservative management of Peyronie's disease.

BACKGROUND: We retrospectively analysed the outcomes of conservative management of Peyronie's disease and determined the factors predicting successful outcome. METHODS: The study involved 31 patients with Peyronie's disease who were treated at our institute between 1985 and 2003. We assessed the efficacy of vitamin E for the improvement of the symptoms, and the factors which contributed to successful outcome with conservative management using multivariate analysis. RESULTS: There was no statistically significant difference in the relief rate between the vitamin E and no-medication groups. The overall estimated relief rate was 67.5% at 2 years from presentation. The multivariate analysis revealed plaque size to be the only significant factor predicting the relief from all symptoms in patients with conservative management. The rate was 100% in patients having a plaque size of 20 mm or smaller and 20.0% in those having a size of larger than 20 mm (P=0.005). CONCLUSIONS: We could not confirm the benefit of vitamin E for Peyronie's disease. Plaque size was the only significant factor predicting the relief from all symptoms. Patients with larger plaque might fail to respond to the conservative management.

Follow-Up Studies↗
PubMed2005

Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.

Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The complex crystal structure demonstrates that the first site is a hydrophobic patch on helices alpha1 and alpha2. NMR and biochemical data revealed that the N-terminal half of helix alpha3 of Tom1-GAT constitutes the second, stronger binding site. The double-sided ubiquitin binding enhances the efficiency of recognition of ubiquitinated proteins by Tom1.

Amino Acid Sequence↗
PubMed2005

Age-related alteration of neurturin receptor GFRa2 and nNOS in pelvic ganglia.

Neurturin is a neurotrophic factor that is widely expressed in cavernous tissue and retrogradely transported to penis-projecting neurons via its receptor, glial cell line derived neurotrophic factor family receptor alpha-2 (GFRa2). To investigate the influence of aging on neural function on the penis, we examined the expression of GFRa2 mRNA in the major pelvic ganglion and its relationship to neuronal nitric oxide synthase (nNOS)- and tyrosine hydroxylase (TH)-positive neurons. GFRa2 and nNOS mRNA expression levels in RT-PCR showed age-related decreases in 1-, 3-, 6-, 12-, 18- and 24-month-old rats. In situ hybridization also revealed that the number of GFRa2-positive neurons in pelvic ganglia decreased with aging. A double-labeling study revealed the co-expression of GFRa2 and nNOS, which simultaneously decreased in old adult (24 months) and young castrated rats compared with young adult rats (3 months). These results suggest that aging and castration influence the numbers of nNOS- and GFRa2-positive neurons. Higher age might affect not only cavernous tissue but also the neural plasticity of the cavernous nerve related to erectile function.

Aging↗
PubMed2005

Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic.

Crystallization of protein-protein complexes is an important step in the studies of biological functions of proteins. However, weak and transient, even though specific, interactions often present difficulties in crystallization of protein complexes due to the heterogeneity of the sample mixture. For example, the gamma1-ear domain of the AP-1 complex and the GAE domain of GGA1, responsible for the interaction with accessory proteins involved in vesicular transport, are known to interact with target proteins with affinities of the order of 1-100 microM. Such low affinities have hampered crystallization trials of the complexes. To overcome this problem, the gamma1-ear and GAE domains were first co-crystallized with excess amounts of the peptides. Co-crystals of both domains were obtained and the complex structures were determined at 2.5-2.9 A resolution. Based on the crystal packing of gamma1-ear and the cognate peptide, gamma1-ear fused with a peptide tag at the N-terminus was prepared. The peptide-tagged gamma1-ear readily crystallized and the crystal diffracted far better, 1.9-2.2 A resolution, compared with the co-crystallized complex, giving significantly more details without affecting the overall complex structure.

ADP-Ribosylation Factors↗