Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

<p>Abstract</p> <p>Background</p> <p>Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s) between peptide-like (short segment) and protein-like (long segment) distributions. We generated ensembles embedded in globular proteins comprising segments 10–50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment <b>C</b>_α-<b>C</b>_αatomic distances.</p> <p>Results</p> <p>Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i) Short segments (10–22 residues) showed a distribution with a high frequency of secondary structure clusters. ii) Medium segments (23���26 residues) showed a distribution corresponding to an intermediate state of transitions. iii) Long segments (27–50 residues) showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure) well define most of the segment universes. Furthermore, we identified several conformational components that were unique to each structural class. Those characteristics suggest that protein segment conformation is described by compositions of the three common structural variables with large contributions and specific structural variables with small contributions.</p> <p>Conclusion</p> <p>The present results of the analyses of four protein structural classes show the universal role of three major components as segment conformational descriptors. The obtained perspectives of distribution changes related to the segment lengths using the three key components suggest both the adequacy and the possibility of further progress on the prediction strategies used in the recent <it>de novo </it>structure-prediction methods.</p

Spin-orbit coupling inactivity of Co2+^{2+} ion in geometrically frustrated magnet GeCo2_2O4_4

We report single-crystal neutron diffraction studies on a spinel antiferromagnet GeCo$_2$O$_4$, which exhibits magnetic order with a trigonal propagation vector and tetragonal lattice expansion ($c/a\simeq1.001$) below $T_{\rm N}=21$ K. For this inconsistency between spin and lattice in symmetry, magnetic Bragg reflections with a tetragonal propagation vector were discovered below $T_{\rm N}$. We discuss spin and orbital states of Co$^{2+}$ ion underlying the new magnetic component.Comment: 3 pages 2 figures, submitted to ICFCM proceeding (Journal of Physics: Conference Series, 2011

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins

<p>Abstract</p> <p>Background</p> <p>Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or superfamilies). We examined the internal structure and statistics in the fold space of 50 amino-acid residue segments taken from various protein folds. We used inter-residue contact patterns to measure the tertiary structural similarity among segments. Using this similarity measure, the segments were classified into a number (<it>K</it>_c) of clusters. We examined various <it>K</it>_cvalues for the clustering. The special resolution to differentiate the segment tertiary structures increases with increasing <it>K</it>_c. Furthermore, we constructed networks by linking structurally similar clusters.</p> <p>Results</p> <p>The network was partitioned persistently into four regions for <it>K</it>_c≥ 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For <it>K</it>_c≥ 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding.</p> <p>Conclusion</p> <p>Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks).</p

Report on the method for determining the location of the polar vortex boundary region

To determine the boundary region of the polar vortex objectively using the PV distribution on isentropic surfaces, the equivalent latitude(Eql) of the polar vortex boundary was calculated using a slightly modified form of the technique of E.R. Nash et al.(J. Geophys. Res., 101D, 9471, 1996). Using the NCEP/NCAR reanal- ysis data, the Eql of the polar vortex boundary region in the winter of 1999/2000 was calculated, and compared with the ozone mixing ratio in the lower stratosphere over Eureka observatory(80°N , 86°W ). The results indicate that this method determines the boundary region of the polar vortex well

Curcuma longaから分離したDiaporthe属エンドファイト糸状菌を用いたcurcuminから無色還元誘導体への微生物変換(発表論文抄録(2011))

We investigated the microbial conversion of curcumin (1) using endophytic fungi associated with the rhizome of Curcuma longa (Zingiberaceae). We found that Diaporthe sp., an endophytic filamentous fungus, converts curcumin (1) into four colorless derivatives, namely (3R,5R)-tetrahydrocurcumin (2), a novel (3R,5S)-hexahydrocurcumin (3) named neohexahydrocurcumin, (3S,5S)-octahydrocurcumin (4) and meso-octahydrocurcumin (5).We investigated the microbial conversion of curcumin (1) using endophytic fungi associated with the rhizome of Curcuma longa (Zingiberaceae). We found that Diaporthe sp., an endophytic filamentous fungus, converts curcumin (1) into four colorless derivatives, namely (3R,5R)-tetrahydrocurcumin (2), a novel (3R,5S)-hexahydrocurcumin (3) named neohexahydrocurcumin, (3S,5S)-octahydrocurcumin (4) and meso-octahydrocurcumin (5)

A Case of Hypereosinophilia-Associated Multiple Mass Lesions of Liver Showing Non-Granulomatous Eosinophilic Hepatic Necrosis

Hypereosinophilic syndrome (HES) is defi ned by elevation more than 1.5×109/L of presence of a peripheral blood count, evidence of organ involvement, and exclusion of secondary eosinophilia such as allergic, vasculitis, drugs, or parasite infection and also clonal eosinophilia. We present the HES case with hepatic involvement. The patient is 70-year-old male. He complained fever and back pain. Blood examination showed marked peripheral eosinophilia, elevation of transaminase and biliary enzymes. Multiple irregular mass lesions of the liver were pointed out by CT and MRI. The liver biopsy was done for differentiation from malignancy. In parenchyma, hepatic necrotic lesion was observed accompanying severe eosinophilic infi ltration with Charcot-Leyden’s crystals. There was granulomatous reaction. He was diagnosed as HES and got recovery due to steroid therapy. From the review of HES article, the hepatic histology is categorized into four types as below: 1) cholangitis type; 2) chronic active hepatitis type; 3) vasculopathic type, 4) hepatic necrosis type. Our case is classifi ed in hepatic necrosis type. This type seems to be important to distinguish malignant tumor and also visceral larva migrans by liver biopsy

On-The-Fly Observing System of the Nobeyama 45-m and ASTE 10-m Telescopes

We have developed spectral line On-The-Fly (OTF) observing mode for the Nobeyama Radio Observatory 45-m and the Atacama Submillimeter Telescope Experiment 10-m telescopes. Sets of digital autocorrelation spectrometers are available for OTF with heterodyne receivers mounted on the telescopes, including the focal-plane 5 x 5 array receiver, BEARS, on the 45-m. During OTF observations, the antenna is continuously driven to cover the mapped region rapidly, resulting in high observing efficiency and accuracy. Pointing of the antenna and readouts from the spectrometer are recorded as fast as 0.1 second. In this paper we report improvements made on software and instruments, requirements and optimization of observing parameters, data reduction process, and verification of the system. It is confirmed that, using optimal parameters, the OTF is about twice as efficient as conventional position-switch observing method.Comment: 11 pages, 13 figures, accepted for publication in PAS

Fe-K line probing of material around the AGN central engine with Suzaku

We systematically analyzed the high-quality Suzaku data of 88 Seyfert galaxies. We obtained a clear relation between the absorption column density and the equivalent width of the 6.4 keV line above 10$^{23}$ cm$^{-2}$, suggesting a wide-ranging column density of $10^{23-24.5}$ cm$^{-2}$ with a similar solid and a Fe abundance of 0.7--1.3 solar for Seyfert 2 galaxies. The EW of the 6.4 keV line for Seyfert 1 galaxies are typically 40--120 eV, suggesting the existence of Compton-thick matter like the torus with a column density of $>10^{23}$ cm$^{-2}$ and a solid angle of $(0.15-0.4)*4pi$, and no difference of neutral matter is visible between Seyfert 1 and 2 galaxies. An absorber with a lower column density of $10^{21-23}$ cm$^{-2}$ for Compton-thin Seyfert 2 galaxies is suggested to be not a torus but an interstellar medium. These constraints can be understood by the fact that the 6.4 keV line intensity ratio against the 10--50 keV flux is almost identical within a range of 2--3 in many Seyfert galaxies. Interestingly, objects exist with a low EW, 10--30 eV, of the 6.4 keV line, suggesting that those torus subtends only a small solid angle of $<0.2*4pi$. Ionized Fe-K$\alpha$ emission or absorption lines are detected from several percents of AGNs. Considering the ionization state and equivalent width, emitters and absorbers of ionized Fe-K lines can be explained by the same origin, and highly ionized matter is located at the broad line region. The rapid increase in EW of the ionized Fe-K emission lines at $N_{H}>10^{23}$ cm$^{-2}$ is found, like that of the cold material. It is found that these features seem to change for brighter objects with more than several $10^{44}$ erg/s such that the Fe-K line features become weak. We discuss this feature, together with the torus structure.Comment: 32 pages, 20 figures, ApJ accepte