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Hiroshi Hirota

Publications and source records attributed to Hiroshi Hirota.

At least 19 recordsLinked to original sources
PubMed2005

Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea.

Ascidians belonging to the suborder Phlebobranchia are known to accumulate high levels of a transition metal, vanadium, in their blood cells, called vanadocytes, although the mechanism for this biological phenomenon remains unclear. Recently, we identified vanadium(IV)-binding proteins, designated as Vanabins, from vanadium-accumulating ascidians. Here, we report the first 3D structure of Vanabin2 from an ascidian, Ascidia sydneiensis samea, in an aqueous solution. The structure revealed a novel bow-shaped conformation, with four alpha-helices connected by nine disulfide bonds. There are no structural homologues reported so far. The 15N heteronuclear single-quantum coherence (HSQC) perturbation experiments of Vanabin2 indicated that vanadyl cations, which are exclusively localized on the same face of the molecule, are coordinated by amine nitrogens derived from amino acid residues such as lysines, arginines, and histidines, as suggested by the electron paramagnetic resonance (EPR) results. The present NMR studies provide information that will contribute toward elucidating the mechanism of vanadium accumulation in ascidians.

Amino Acid Sequence↗
PubMed2005

Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.

The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. Here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermus thermophilus HB8, complexed with its ligand. This protein belongs to the YceI-like family in the Pfam database, and its sequence homologs are present in a broad range of bacteria and archaea. The structure consists of an extended, eight-stranded, antiparallel beta-barrel. In the hydrophobic pore of the barrel, the protein binds the polyisoprenoid chain by hydrophobic interactions. Its overall structure resembles the lipocalin fold, but there is no sequence homology between TT1927b and the lipocalin family of proteins.

Amino Acid Sequence↗
PubMed2005

Solution structure of the PWWP domain of the hepatoma-derived growth factor family.

Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded beta-barrel with a PWWP-specific long loop connecting beta2 and beta3 (PR-loop), followed by a helical region including two alpha-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the beta1/beta2 loop (beta-beta arch) and the beta3/beta4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity.

Amino Acid Motifs↗
PubMed2005

13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit.

13-Deoxytedanolide is a potent antitumor macrolide isolated from the marine sponge Mycale adhaerens. In spite of its remarkable activity, the mode of action of 13-deoxytedanolide has not been elucidated. [11-3H]-(11S)-13-Deoxydihydrotedanolide derived from the macrolide was used for identifying the target molecule from the yeast cell lysate. Fractionation of the binding protein revealed that the labeled 13-deoxytedanolide derivative strongly bound to the 80S ribosome as well as to the 60S large subunit, but not to the 40S small subunit. In agreement with this observation, 13-deoxytedanolide efficiently inhibited the polypeptide elongation. Interestingly, competition studies demonstrated that 13-deoxytedanolide shared the binding site on the 60S large subunit with pederin and its marine-derived analogues. These results indicate that 13-deoxytedanolide is a potent protein synthesis inhibitor and is the first macrolide to inhibit the eukaryotic ribosome.

Animals↗
PubMed2005

Structure-activity relationship study on 13-deoxytedanolide, a highly antitumor macrolide from the marine sponge Mycale adhaerens.

To obtain information of structure-activity relationships (SARs) of 13-deoxytedanolide, its chemical transformation has been carried out, targeting on such functional groups as an epoxide, hydroxyls, ketones, and olefins. A total of 10 derivatives have been prepared and their cytotoxicity against P388 murine leukemia cells and inhibitory activity of polypeptide elongation in yeast cell lysate provided some important SARs; the southern hemisphere comprises the pharmacophore, while the epoxide-bearing side chain is essential for the activity.

Animals↗
PubMed2005

Himeic acid A: a new ubiquitin-activating enzyme inhibitor isolated from a marine-derived fungus, Aspergillus sp.

A new ubiquitin-activating enzyme (E1) inhibitor, himeic acid A, was isolated from a culture of marine-derived fungus, Aspergillus sp. The structure was determined by spectroscopic analysis. The formation of an E1-ubiquitin (Ub) intermediate was 65% inhibited by himeic acid A at the concentration of 50 microM, while two new related compounds, himeic acids B and C, showed little inhibitory activity even at 100 microM.

Aspergillus↗
PubMed2005

A structure-based strategy for discovery of small ligands binding to functionally unknown proteins: combination of in silico screening and surface plasmon resonance measurements.

In the postgenomic era, many researchers and organizations have been engaged in structural and functional analyses of proteins. As a part of these efforts, searching for small organic compounds that bind specifically to target proteins is quite important. In this study, we have developed a rational strategy for ligand discovery based on the three-dimensional structures of target proteins, which were elucidated by X-ray crystallography and nuclear magnetic resonance spectroscopy. The strategy has three features: (i) rapid selection of candidate compounds by in silico screening, (ii) automated preparation of sample solutions with robotics, and (iii) reliable evaluation of the candidates with surface plasmon resonance. Applying the strategy to a protein, At2g24940 from Arabidopsis thaliana, we discovered four small ligands out of a commercially available library of about 150 000 compounds. Although these compounds had only weak affinities to the target protein, with dissociation constants ranging from 68 to 120 microM, they apparently possess common structural features. They would be leads for the development of specific inhibitors/drugs for At2g24940, and provide important clues toward elucidation of the protein function.

Arabidopsis Proteins↗
PubMed2004

Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).

Human CA125, encoded by the MUC16 gene, is an ovarian cancer antigen widely used for a serum assay. Its extracellular region consists of tandem repeats of SEA domains. In this study we determined the three-dimensional structure of the SEA domain from the murine MUC16 homologue using multidimensional NMR spectroscopy. The domain forms a unique alpha/beta sandwich fold composed of two alpha helices and four antiparallel beta strands and has a characteristic turn named the TY-turn between alpha1 and alpha2. The internal mobility of the main chain is low throughout the domain. The residues that form the hydrophobic core and the TY-turn are fully conserved in all SEA domain sequences, indicating that the fold is common in the family. Interestingly, no other residues are conserved throughout the family. Thus, the sequence alignment of the SEA domain family was refined on the basis of the three-dimensional structure, which allowed us to classify the SEA domains into several subfamilies. The residues on the surface differ between these subfamilies, suggesting that each subfamily has a different function. In the MUC16 SEA domains, the conserved surface residues, Asn-10, Thr-12, Arg-63, Asp-75, Asp-112, Ser-115, and Phe-117, are clustered on the beta sheet surface, which may be functionally important. The putative epitope (residues 58-77) for anti-MUC16 antibodies is located around the beta2 and beta3 strands. On the other hand the tissue tumor marker MUC1 has a SEA domain belonging to another subfamily, and its GSVVV motif for proteolytic cleavage is located in the short loop connecting beta2 and beta3.

Amino Acid Sequence↗
PubMed2004

Solution structure of a BolA-like protein from Mus musculus.

The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is still unknown. Here we determined the structure of a mouse BolA-like protein. The overall topology is alphabetabetaalphaalphabetaalpha, in which beta(1) and beta(2) are antiparallel, and beta(3) is parallel to beta(2). This fold is similar to the class II KH fold, except for the absence of the GXXG loop, which is well conserved in the KH fold. The conserved residues in the BolA-like proteins are assembled on the one side of the protein.

Amino Acid Sequence↗
PubMed2004

Solution structure of the RWD domain of the mouse GCN2 protein.

GCN2 is the alpha-subunit of the only translation initiation factor (eIF2alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. In this study, we determined the solution structure of the mouse GCN2 RWD domain using NMR spectroscopy. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices, with an alphabetabetabetabetaalphaalpha topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive beta-turns that overlap with each other by two residues (triple beta-turn). As putative binding sites with GCN1, a structure-based alignment allowed the identification of several surface residues in alpha-helix 3 that are characteristic of the GCN2 RWD domains. Despite the apparent absence of sequence similarity, the RWD structure significantly resembles that of ubiquitin-conjugating enzymes (E2s), with most of the structural differences in the region connecting beta-strand 4 and alpha-helix 3. The structural architecture, including the triple beta-turn, is fundamentally common among various RWD domains and E2s, but most of the surface residues on the structure vary. Thus, it appears that the RWD domain is a novel structural domain for protein-binding that plays specific roles in individual RWD-containing proteins.

Amino Acid Sequence↗
PubMed2004

Tetrapetalone A, a novel lipoxygenase inhibitor from Streptomyces sp.

A simple new assay was designed for lipoxygenase inhibitors. This assay was used to find the novel lipoxygenase inhibitor, tetrapetalone A (1). Tetrapetalone A (1), C26H33NO7, was isolated from Streptomyces sp. USF-4727 strain. Its planar structure was determined by spectroscopic evidence and by methylating with diazomethane to show the presence of a novel tetracyclic skeleton and a beta-D-rhodinosyl moiety. The stereochemistry of 1 was investigated by the coupling constant in the 1H-NMR spectrum, NOE correlations, modified Mosher's method and derivation. We have reported the structural elucidation of 1 in our previous paper. However, further investigation gave another structure for 1, which is described in this paper. Tetrapetalone A showed similar inhibitory activity against soybean lipoxygenase to the two well-known lipoxygenase inhibitors, kojic acid and NDGA, while methylated tetrapetalone A (2) showed little inhibitory activity, even at a concentration of 1 mM.

Drug Evaluation, Preclinical↗
PubMed2002

CYP3A4 inhibitory activity of new bisalkaloids, dipiperamides D and E, and cognates from white pepper.

Two new bisalkaloids, dipiperamides D and E, were isolated as inhibitors of a drug metabolizing enzyme cytochrome P450 (CYP) 3A4 from the white pepper, Piper nigrum. Their structures were elucidated by spectroscopic methods. Dipiperamides D and E showed potent CYP3A4 inhibition with IC(50) values of 0.79 and 0.12 microM, respectively, and other metabolites from the pepper were moderately active or inactive.

Alkaloids↗
PubMed2002

Conformation of ligands bound to the muscarinic acetylcholine receptor.

Many biogenic amines evoke a variety of physiological responses by acting on G protein-coupled receptors. We have determined the conformation of two acetylcholine analogs, (S)-methacholine and (2S,4R,5S)-muscarine, bound to the M(2) muscarinic acetylcholine receptor (M(2) mAChR) by NMR spectroscopy. The analysis of the transferred nuclear Overhauser effect indicated that the receptor selectively recognized the conformers of (S)-methacholine and (2S,4R,5S)-muscarine with the gauche O-C2-C1-N dihedral angle at +60 degrees. This is distinct from the predominant conformations of these ligands in solution with O-C2-C1-N dihedral angle (+80 to approximately 85 degrees ) in the absence of the M(2) mAChR, as assessed by analyses of the coupling constants and nuclear Overhauser effect spectroscopy. We have also built a molecular model of the M(2) mAChR-(S)-methacholine complex, based on the X-ray crystallographic structure of rhodopsin. This model indicated that the conformation with the gauche O-C2-C1-N dihedral angle at +55.5 degrees, which is similar to the one determined by NMR measurement, is energetically favored in the binding of (S)-methacholine to the receptor. We suggest that this conformation represents the binding of the agonist to the M(2) mAChR in the absence of G protein.

Animals↗