Shin-ichiro Narita

Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in Pseudomonas aeruginosa

The MexAB-OprM efflux pump of Pseudomonas aeruginosa is central to multidrug resistance of this organism, which infects immunocompromised hospital patients. The MexA, MexB, and OprM subunits were assumed to function as the membrane fusion protein, the body of the transporter, and the outer membrane channel protein, respectively. For better understanding of this important xenobiotic transporter, we show the x-ray crystallographic structure of MexA at a resolution of 2.40 Å. The global MexA structure showed unforeseen new features with a spiral assembly of six and seven protomers that were joined together at one end by a pseudo 2-fold image. The protomer showed a new protein structure with a tandem arrangement consisting of at least three domains and presumably one more. The rod domain had a long hairpin of twisted coiled-coil that extended to one end. The second domain adjacent to the rod α-helical domain was globular and constructed by a cluster of eight short β-sheets. The third domain located distal to the α-helical rod was globular and composed of seven short β-sheets and one short α-helix. The 13-mer was shaped like a woven rattan cylinder with a large internal tubular space and widely opened flared ends. The 6-mer and 7-mer had a funnel-like structure consisting of a tubular rod at one side and a widely opened flared funnel top at the other side. Based on these results, we constructed a model of the MexAB-OprM pump assembly. The three pairs of MexA dimers interacted with the periplasmic α-barrel domain of OprM via the α-helical hairpin, the second domain interacted with both MexB and OprM at their contact site, and the third and disordered domains probably interacted with the distal domain of MexB. In this fashion, the MexA subunit connected MexB and OprM, indicating that MexA is the membrane bridge protein.

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.

Electrical Properties of Black Phosphorus Single Crystals

Large single crystals of black phosphorus have been grown under high pressure, and by using the crystals, the Hall measurements have been done in a range from 4.2 K to 550 K. All the undoped samples have exhibited p -type conduction, while we have succeeded in obtaining n -type crystals by doping Te impurity. The effective acceptor concentrations N A -N D of the p -type samples and those of donor in n -type samples N D -N A have been in the range of 2∼5×10 15 cm -3 and 2∼3×10 16 cm -3 , respectively. From the intrinsic range of the conductivity, the energy gap has been estimated to be 0.335 eV, The acceptor and donor activation energies have been determined to be ∼18 meV and ∼39 meV, respectively. The Hall mobility of the hole reaches its maximum of 6.5×10 4 cm 2 /V·sec around 20 K. The anisotropies of the conductivity and the mobility along the three crystal axes have been investigated.

Growth of Large Single Crystals of Black Phosphorus under High Pressure

A large volume high pressure apparatus has made it possible to grow large single crystals of black phosphorus, P. After converting red P powder into black P under a high pressure of 10 kbar at high temperature, a melt of polycrystalline black P has been gradually solidified to bring about the growth of single crystals. Crystal sizes larger than 5×5×10 mm3 are, for the first time, adequate for various measurements of the physical properties expected for this narrow gap semiconductor with a special layered structure. An X-ray analysis has proved the good single crystalline structure.

Far-infrared cyclotron resonance absorptions in black phosphorus single crystals

Far-infrared cyclotron resonance absorptions in black phosphorus have been measured by using relatively large single crystals of n -type and p -type prepared by a large volume-high pressure technique at high temperature. The effective masses of the electron and the hole in the crystals have been determined along the three principal crystal axes and found to have appreciably large anisotropies. The experimental masses have been compared with the theoretical results so far published. The temperature and magnetic field dependences of the relaxation times of the carriers obtained from the half-widths of the cyclotron resonant peaks are discussed in the comparisons with the carrier mobilities in the results of the Hall measurements previously reported.

Electrical and optical properties of black phosphorus single crystals

Abstract Large single crystals of black phosphorus have been prepared by a large volume-high pressure technique at high temperature. Using the crystals, we have measured temperature dependences of the electrical conductivity and the Hall coefficient, the FIR cyclotron resonance absorption and the reflectance for synchrotron radiation. All samples obtained are p-type and the Hall mobility reaches 5×10 4 cm 2 v·sec around 20K. The anisotropies of the effective mass, the Hall mobility and the SOR reflectance along the three crystal directions, a, b, and c, have been observed.

D- state in silicon

Abstract D- state in phosphorus-doped silicon has been studied by means of longwavelength (submillimeter plus millimeter) photoconductivity measurements. The concentration dependence of the D- state spectra indicates the transition from an isolated D- state to a state of an electron bound to more than one neutral donors, Dn-. A [100] stress experiment reveals the effect of the donor core potential on the D- state.

Inelastic neutron scattering study of acoustic phonons of black phosphorus

Abstract Dispersion relations of acoustic phonons of the orthorhombic black phosphorus have been measured at room temperature and atmospheric pressure. Very anisotropic dispersion surfaces were observed along the three principal directions. Comparison is made between the present measurements and the recent calculations of dispersion curves by Kaneta et al.

D-States in Germainum

Isolated D - states in Sb-and As-doped germanium crystals have been studied by means of long-wavelength (submillimeter plus millimeter) photoconductivity measurements with a lamellar grating Fourier transform spectrometer at an extremely low temperature, 0.38 K. The electron binding energies of the isolated D - states are accurately determined and the shift of the D - state energy is clearly observed between the samples with different impurities. The many valley effect of the conduction band on the D - state energy is confirmed by comparing the spectra under high [111] stress with those of stress free. The energy shemes of the D - states in Sb-and As-doped germanium crystals are clarified.

Observation of cyclotron resonance absorptions due to excitonic ion and excitonic molecule ion in silicon

Abstract Cyclotron resonance experiment has been performed in uniaxially stressed Si under high excitation, and new resonance peaks are observed at low temperature. The origins of these peaks seem to be the cyclotron resonance absorptions of the excitonic ion and the excitonic molecule ion.