Masato Yoshimura

Structure of human monoamine oxidase A at 2.2-A resolution: the control of opening the entry for substrates/inhibitors.

The mitochondrial outer membrane-anchored monoamine oxidase (MAO) is a biochemically important flavoenzyme that catalyzes the deamination of biogenic and xenobiotic amines. Its two subtypes, MAOA and MAOB, are linked to several psychiatric disorders and therefore are interesting targets for drug design. To understand the relationship between structure and function of this enzyme, we extended our previous low-resolution rat MAOA structure to the high-resolution wild-type and G110A mutant human MAOA structures at 2.2 and 2.17 Å, respectively. The high-resolution MAOA structures are similar to those of rat MAOA and human MAOB, but different from the known structure of human MAOA [De Colibus L, et al. (2005) Proc Natl Acad Sci USA 102:12684–12689], specifically regarding residues 108–118 and 210–216, which surround the substrate/inhibitor cavity. The results confirm that the inhibitor selectivity of MAOA and MAOB is caused by the structural differences arising from Ile-335 in MAOA vs. Tyr-326 in MAOB. The structures exhibit a C-terminal transmembrane helix with clear electron density, as is also seen in rat MAOA. Mutations on one residue of loop 108–118, G110, which is far from the active center but close to the membrane surface, cause the solubilized enzyme to undergo a dramatic drop in activity, but have less effect when the enzyme is anchored in the membrane. These results suggest that the flexibility of loop 108–118, facilitated by anchoring the enzyme into the membrane, is essential for controlling substrate access to the active site. We report on the observation of the structure–function relationship between a transmembrane helical anchor and an extra-membrane domain.

Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end

The OprM lipoprotein of Pseudomonas aeruginosa is a member of the MexAB-OprM xenobiotic-antibiotic transporter subunits that is assumed to serve as the drug discharge duct across the outer membrane. The channel structure must differ from that of the porin-type open pore because the protein facilitates the exit of antibiotics but not the entry. For better understanding of the structure-function linkage of this important pump subunit, we studied the x-ray crystallographic structure of OprM at the 2.56-Å resolution. The overall structure exhibited trimeric assembly of the OprM monomer that consisted mainly of two domains: the membrane-anchoring β-barrel and the cavity-forming α-barrel. OprM anchors the outer membrane by two modes of membrane insertions. One is via the covalently attached NH2-terminal fatty acids and the other is the β-barrel structure consensus on the outer membrane-spanning proteins. The β-barrel had a pore opening with a diameter of about 6–8 Å, which is not large enough to accommodate the exit of any antibiotics. The periplasmic α-barrel was about 100 Å long formed mainly by a bundle of α-helices that formed a solvent-filled cavity of about 25,000 Å3. The proximal end of the cavity was tightly sealed, thereby not permitting the entry of any molecule. The result of this structure was that the resting state of OprM had a small outer membrane pore and a tightly closed periplasmic end, which sounds plausible because the protein should not allow free access of antibiotics. However, these observations raised another unsolved problem about the mechanism of opening of the OprM cavity ends. The crystal structure offers possible mechanisms of pore opening and pump assembly.

Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure

Hepatitis E virus (HEV) is a causative agent of acute hepatitis. The crystal structure of HEV-like particles (HEV-LP) consisting of capsid protein was determined at 3.5-Å resolution. The capsid protein exhibited a quite different folding at the protruding and middle domains from the members of the families of Caliciviridae and Tombusviridae, while the shell domain shared the common folding. Tyr-288 at the 5-fold axis plays key roles in the assembly of HEV-LP, and aromatic amino acid residues are well conserved among the structurally related viruses. Mutational analyses indicated that the protruding domain is involved in the binding to the cells susceptive to HEV infection and has some neutralization epitopes. These structural and biological findings are important for understanding the molecular mechanisms of assembly and entry of HEV and also provide clues in the development of preventive and prophylactic measures for hepatitis E.

The Structure of Rat Liver Vault at 3.5 Angstrom Resolution

Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.

Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection

Betanodaviruses cause massive mortality in marine fish species with viral nervous necrosis. The structure of a T = 3 Grouper nervous necrosis virus-like particle (GNNV-LP) is determined by the ab initio method with non-crystallographic symmetry averaging at 3.6 Å resolution. Each capsid protein (CP) shows three major domains: (i) the N-terminal arm, an inter-subunit extension at the inner surface; (ii) the shell domain (S-domain), a jelly-roll structure; and (iii) the protrusion domain (P-domain) formed by three-fold trimeric protrusions. In addition, we have determined structures of the T = 1 subviral particles (SVPs) of (i) the delta-P-domain mutant (residues 35−217) at 3.1 Å resolution; and (ii) the N-ARM deletion mutant (residues 35−338) at 7 Å resolution; and (iii) the structure of the individual P-domain (residues 214−338) at 1.2 Å resolution. The P-domain reveals a novel DxD motif asymmetrically coordinating two Ca2+ ions, and seems to play a prominent role in the calcium-mediated trimerization of the GNNV CPs during the initial capsid assembly process. The flexible N-ARM (N-terminal arginine-rich motif) appears to serve as a molecular switch for T = 1 or T = 3 assembly. Finally, we find that polyethylene glycol, which is incorporated into the P-domain during the crystallization process, enhances GNNV infection. The present structural studies together with the biological assays enhance our understanding of the role of the P-domain of GNNV in the capsid assembly and viral infection by this betanodavirus.

A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry

A vault from rat liver was crystallized in space group C2. Rotational symmetry searches indicated that the particle has 39-fold dihedral symmetry.

Growth of K2Al2B2O7 crystal for UV light generation

Abstract A new nonlinear optical alumino-borate crystal, K 2 Al 2 B 2 O 7 (KAB) with dimensions of 21×18×13 mm 3 , has been grown using a modified middle-seeded solution growth method. The significant abilities of KAB crystals for the generation of power ultraviolet (UV) light have been demonstrated. Crystalline KAB has been successfully used to generate the third harmonics of 1064.2 nm light. The dependence of the average power of the 355 nm third harmonic radiation on the Nd:YAG laser power has been studied. 200 mW average power UV pulses at 193 nm were generated in KAB by mixing the Nd:YAG laser and sum-frequency generation of a RbTiOAsO 4 (RTA) optical parametric oscillation at 10 kHz. No degradation in the output power was observed after 50 h operation.

Cesium accumulation at CsB3O5 optical surface

Abstract Structure and element composition of polished CsB 3 O 5 surface have been studied. It has been shown that crystal surface is covered by thick layer (>50 A) of amorphous phase. This surface compound contains Cs, B and O and contaminated by hydrocarbons adsorbed on the surface. Element depth profiling produced by ion sputtering reveals quick and monotonic drop of C signal accompanied by increases of B and O signals with stabilization at depths higher than ∼20 A. The distribution of Cs over depth is irregular, top surface cesium content is ∼30% higher then that achieved for higher sputtering times. Being removed by sputtering, this top surface layer enriched by Cs is restored by few hours keeping at 24 °C in vacuum or air.

Crystallization and preliminary crystallographic analysis of rat monoamine oxidase A complexed with clorgyline.

Monoamine oxidase (MAO) is an FAD-containing mitochondrial outer-membrane protein which catalyzes the degradation of several neurotransmitters in the central nervous system. The two subtypes of MAO, MAOA and MAOB, have similar primary sequences but different substrate and inhibitor specificities. The structure of human MAOB has recently been determined, but the structure of MAOA remains unknown. To clarify the mechanisms underlying their unique substrate and inhibitor recognition and thereby facilitate the development of new specific inhibitors to treat MAO-related neurological disorders, rat MAOA was crystallized in a complex with the specific inhibitor clorgyline. Diffraction data were collected to 3.2 A resolution. The crystal belongs to the space group P4(3)2(1)2, with unit-cell parameters a = b = 158.2, c = 258.4 A.

Ab initio crystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell

Ab initio phasing by non-crystallographic symmetry averaging coupled with solvent flattening has previously been used to determine the structure of canine parvovirus. As CPV particles were located at general positions, initial phases were generated with a spherical shell deviating from the centre of symmetry. In many virus crystals, the viral particles are located at positions with a centre of symmetry in the unit cell. Thus, the initial phases calculated with a spherical shell model have a centre of symmetry. The inherent difficulty in structural determination was breaking the centre of symmetry in the initial phase. The centric nature of the initial phases of the rice dwarf virus crystal, however, was successfully broken at low resolution by iteration of the density-modification method described by Tsao et al. (1992). In this study, ab initio phasing was tested for seven viruses ranging from 82 to 344 A in radius. Although the crystal structures of the initial spherical shell models for each virus had a centre of symmetry, the centric natures of the initial phases were successfully broken by non-crystallographic symmetry averaging coupled with solvent flattening at a low resolution; these phases were then successfully extended to high-resolution measurements. A novel procedure of ab initio phasing for spherical virus crystals is proposed.