structure of a data block db
Báo cáo khoa học: Unravelling the functional interaction structure of a cellular network from temporal slope information of experimental data docx
... structure of the HOG pathway in S cerevisiae MAP kinase cascades typically composed of three tiers of protein kinases, a MAP kinase (MAPK), a MAPK kinase (MAPKK) and a MAPKK kinase (MAPKKK), are common ... not always achievable due to many practical limitations, we need to consider a new method that can be applicable to time-series experimental data without parameter perturbations and that can make ... can be obtained by properly chosen n parameter perturbations All these approaches are based on parameter perturbation experiments which are, however, not always achievable in many practical cases...
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Báo cáo sinh học: " A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data" pdf
... is regulated often by a small number of other genes [3,4] so a reasonable representation of a network is a sparse graph A sparse graph is a graph parametrized by a sparse matrix W, a matrix with ... the class of linear models, the abundance value of a gene is treated as a weighted sum of the abundance values of other genes A high-dimensional transcript profile is a vector of abundance values ... networks Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node...
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the meaning and structure of a narrative a systemic functional analysis
... the syntactic structure of language, it prefers placing the function of language as central (what language does and how language does it) rather than placing the elements of language and their ... explore the meaning and structure of Torquay? But I said Turkey! as a text The analysis is based on the framework of Hallidays (1994)An Introduction to Functional Grammar, Halliday and 21 Hasans (1997) ... Re-examine some of the most important issues related to the experiential aspect of functional grammar Analyze the meaning and structure of a narrative based on the systemic functional analysis...
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Tài liệu Báo cáo " The meaning and structure of a science fiction story: a sysyemic functional analysis " doc
... declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative declarative ... declarative declarative declarative declarative declarative declarative declarative declarative imperative declarative declarative Modality ability/neg ability/pos ability/neg ability/neg ability/neg ... relational was III Senser mental see Existent relational were Actor material descended Actor material landed Actor material put on Goal Actor material opened Goal Actor material climbed 10 Actor material...
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Tài liệu Báo cáo khoa học: ˚ The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species docx
... atoms of Asp11 and Asn23 (Fig 3) in an arrangement similar to what is observed in VPRK Both PRK and VPRK have calcium bound at Ca3 SPRK also has an aspartic acid residue at position at 200, and ... hexa62 Table Data collection and refinement statistics for SPRK ˚ Resolution (A) Space group Cell parameters ˚ a- axis (A) ˚ b-axis (A) ˚ c-axis (A) b angle (°) Number of observations (24 – maximum ... initial comparative studies showed that the catalytic turnover was at least twice that of PRK, but substrate affinity was reduced SPRK was compared with PRK and was found to be remarkable stable against...
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Tài liệu Báo cáo khoa học: Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation docx
... Number of ion pairsa Number of hydrogen bonds Main chain–main chain Main chain–side chain Side chain–side chain Total ˚ Exposed surface areab (A2 ) ˚ Apolarc (A2 ) ˚ Buried surface areab (A2 ) ˚ Apolarc ... Structural aspects of cold adaptation surface with their hydrophilic nature may enhance favourable electrostatic interaction with water at low temperature and, at the same time, result in an anionic ... whereas the overall exposed surface areas of the psychro- and the mesophilic enzymes are larger than for the thermophile enzyme, mainly as a result of larger area of apolar atoms, the meso- and...
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Báo cáo khoa học: Hexameric ring structure of a thermophilic archaeon NADH oxidase that produces predominantly H2O pot
... protein was then obtained by negative staining with 2% uranyl acetate (B) Multivariate statistical analysis of NOXtp (a) The average (AV) of 939 translationally, but not rotationally, aligned particles ... Significantly, this structural feature of NOXtp is highly similar to that of valosine-containing protein-like ATPase from Th acidophilum, an archaeal member of the AAA family (ATPases associated ... The standard proteins are ferritin (440 kDa), catalase (232 kDa), albumin (67 kDa) and ovalbumin (43 kDa) obtained from the translationally, but not rotationally, aligned images revealed a six-fold...
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Báo cáo khoa học: Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea pot
... et al crystal structure of a cellulase was reported; it was a catalytic domain of Hypocrea jecorina Cel 6A (HjeCel 6A, formerly designated cellobiohydrolase II), a GH6 cellobiohydrolase from an ascomycete ... HinCel 6A and CcCel6C (Fig 2) indicated that Asp150 and Asp334 of CcCel6C are the potential catalytic residues and could act as a proton donor and a base, respectively Another aspartic acid residue ... CLUSTALW2 server, and manual adjustment was carried out based on the comparison of the crystal structures The numbering of amino acid residues and secondary structures (a1 a8 and b0–bVII) are given Residues...
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hydrothermal synthesis and crystal structure of a novel one - dimensional tritungstate
... 380 B Yan, et al.r Inorganic Chemistry Communications (2000) 379–382 Fig Packing view of ŽC H 10 N2 wW3 O10 x along the b-axis 2.4 X-ray Crystallographic Studies X-ray crystallographic data of were ... crystallographic data 7.9% in the temperature range 300–4808C indicating the release of en molecules Ž calc, 8.0% The infrared spectra of present the following information: strong absorption bands at 935 and ... organicrinorganic hybrid phases are obtained and structurally identified using the single crystal X-ray diffraction method Brief crystal data of one of the phases, a mono- Results and Discussion The...
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Báo cáo khoa học: Structure of a trypanosomatid mitochondrial cytochrome c with heme attached via only one thioether bond and implications for the substrate recognition requirements of heme lyase potx
... observation that heme lyase is unable to mature a bacterial class I c-type cytochrome, Paracoccus denitrificans cytochrome c550 [33] Moreover, many taxa that have heme lyase apparently have separate ... and T brucei apocytochrome c (J W A Allen, unpub2826 A Normalised absorbance of the alanine of the AXXCH motif (Ala25) (in green) and the unsaturated vinyl group of the heme ˚ (cyan) are separated ... free-living phagotrophic flagellates (e.g Bodo saltans), photosynthetic algae (e.g Euglena gracilis), and parasitic trypanosomatids [e.g the causal agents of the tropical diseases African sleeping...
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Báo cáo khoa học: The crystal structure of a xyloglucan-specific endo-b-1,4glucanase from Geotrichum sp. M128 xyloglucanase reveals a key amino acid residue for substrate specificity potx
... precipitant Prior to data collection, a crystal was transferred into Analysis of substrate specificity Substrate specificity was analyzed using xyloglucan tetradecasaccharide, XXXGXXXG, prepared as ... structural refinement of Table Statistics for data collection using the Beamline BL44B2 at SPring-8 and structure refinement of XEG Parameter Data collection ˚ Wavelength (A) ˚ Resolutiona (A) Rmergea,b ... at various concentrations of the substrate, tamarind seed xyloglucan (Dainippon Sumitomo Pharma, Osaka, Japan), in 50 mm sodium acetate buffer (pH 5.5) at 45 °C for 15 The bicinchoninate assay...
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Báo cáo khoa học: Crystal structure of a cold-adapted class C b-lactamase potx
... Glu272–Arg148 21 19 14 092 8248 5844 –1 6.5 No of hydrogen bonds (side chain–side chain) Aromatic stacking ˚ ASA total (A2 ) ˚ ASA apolar (A2 ) ˚ ASA polar (A2 ) Formal global charge Theoretical pIb ... molecular replacement method, based on the structure of the class C b-lactamase from E cloacae P99 (Protein Data Bank code 2BLT) as a search model The model was ˚ solved to a resolution of 2.2 A A ... Grenoble, France) on a MarResearch CCD Data processing, molecular replacement and refinement of Pse fluorescens TAE4 b-lactamase Data were processed with the hkl suite package [45] A molecular replacement...
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Báo cáo khoa học: The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima pdf
... 5’-AAAAGGTCGACATCTGGATGGCGACGAAAGACACGATC-3’ 5’-GATCGTGTCTTTCGTCGCCATCCAGATGTCGACCTTTT-3’ D36N-1 5’-CATCCTTCCCTATCTCAACATCCAGCTGGTTTACT-3’ D341N-1 5’-AAGGGGAGAACTCAACGGAACACCGGAGG-3’ 5’-CACTCTCGAAGAGTTCATAAACGAAGTGAAGAAGAATCTC-3’ ... performed as described previously [17] Table Primer sequences TmIDH mutant Primer sequence R186M 5’-CCTGGAGAAATCGATCATGAGCTTCGCTCAGTCGTG-3’ 5’-CACGACTGAGCGAAGCTCATGATCGATTTCTCCAGG-3’ 5’-AAAAGGTCGACATCTGGATGGCGACGAAAGACACGATC-3’ ... lacked interdomain Structure and thermal stability of T maritima ˚ ionic networks at a cut-off of 4.0 A and the size of the networks were not as dramatically increased at 4.2 and ˚ 6.0 A cut-offs...
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Báo cáo khoa học: Inhibitory properties and solution structure of a potent Bowman–Birk protease inhibitor from lentil (Lens culinaris, L) seeds ppt
... Statistics for the total amount of experimental data are reported in Table A simulated annealing (SA) procedure was used starting from a randomly generated linear polypeptide chain The actual ... inammation-mediating proteases [16] More recently, a number of patents on the use of BBIs against various apparently unrelated diseases have appeared [1719] The molecular basis of these BBI activities ... Ramachandran Plot for the 20 deposited structures Table S1 Experimental vicinal coupling constants and calculated values for the most representative structure This material is available as part...
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Báo cáo khoa học: Three-dimensional structure of a thermostable native cellobiohydrolase, CBH IB, and molecular characterization of the cel7 gene from the filamentous fungus, Talaromyces emersonii ppt
... (GenBank: AAA19802), T reesei (GenBank CAA49596), A niger (GenBank AAF04491), H grisea (GenBank AAD11942) and A aculeatus (GenBank BAA25183) gave sequence identity values of 65%, 64%, 73%, 51% and ... classification of cellulases Eur J Biochem 258, 200–206 68 Takashima, S., Iikura, H., Nakamura, A. , Hidaka, M., Masaki, H & Uozumi, T (1998) Isolation of the gene and characterization of the enzymatic ... distortion was 1.8°, the standard deviation of the hydrogen bond energies was 0.7 and overall G-factor, a measure of the normality of the structure, was 0.0 Fig SDS/PAGE and activity analysis of recombinant...
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Báo cáo khoa học: Crystal structure of a staphylokinase variant A model for reduced antigenicity pptx
... X-ray diffraction data were collected using an in-house Rigaku rotating anode X-ray generator with a MAR Research MAR345 image plate detector The radiation Ê wavelength was 1.5418 A The crystal ... surface area and the interactions in the dimer interface The total buried surface areas of the a a or head± Ê tail geometries were more than 1000 A2 , much larger than the average buried surface area ... the SAK dimer models Accessible surface areas are calculated with a probe radius 1.4 A added to the van der Waals radius Dimer model Buried surface Ê area (A2 ) Hydrogen bonds Salt bridges A 77Arg...
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Báo cáo khoa học: Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand pot
... efficient analytical calculation of the accessible surface area and their gradient for macromolecules J Comput Chem 19, 319–333 12 Kajander T, Cortajarena AL & Regan L (2006) Consensus design as a tool ... pairwise backbone alignment of CTPR3 (Protein Data Bank ID: 1Na0) and FEBS Journal 277 (2010) 1058–1066 ª 2010 The Authors Journal compilation ª 2010 FEBS A L Cortajarena et al A C Structure of designed ... individual units in the ASU (Fig 1B,D) Each CTPR390 unit is composed of three TPR repeats (AB-helix pair) and an additional C-terminal capping helix (Acap) The only way for molecules AB–AB–AB–Acap...
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Báo cáo khoa học: Inhibitor-mediated stabilization of the conformational structure of a histone deacetylase-like amidohydrolase pptx
... Inhibitor-mediated stabilization of HDAH 31 Ray S, Bhattacharyya M & Chakrabarti A (2005) Conformational study of spectrin in presence of submolar concentrations of denaturants J Fluoresc 15, 61–70 32 Chakrabarti ... Eqns 5, and 9) KC, ratio of off-pathway intermediate C and denatured state D; kf, the folding rate in the absence of denaturant; KI, ratio of on-pathway intermediate I and denatured state D; mf ... Ray et al [31] and Chakrabarti et al [32], although the observed changes in the biophysical parameters were much smaller as compared with the denaturation of HDAH Saturating concentrations of...
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Báo cáo khoa học: A possible physiological function and the tertiary structure of a 4-kDa peptide in legumes potx
... the 4-kDa peptide N-terminal primer: 5¢-AACCATGGCTAAAGCAGATTGTAATGG TGCATGT-3¢; the 4-kDa peptide C-terminal primer: 5¢-AAGAATTCTTATTATCCAGTTGGATGTATGCA GAA-3¢ The amplified sequence was cloned ... were amplified by PCR strategy using the azuki bean and mung bean genomic DNAs as templates and the synthetic primers legF1 (5¢-AGC AGCAGATTGTAATGGTG-3¢) and legR1 (5¢-CAGC ACTTCAGAATCAGAGTC-3¢) ... with crystal structure Biochemistry 29, 10545–10555 21 Nagata, K., Hatanaka, H., Kohda, D., Kataoka, H., Nagasawa, H., Isogai, A. , Ishizaki, H., Suzuki, A & Inagaki, F (1995) Threedimensional solution...
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Báo cáo Y học: Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein doc
... HN Ha Hb Asp1 Val2 Ala3 Ser4 Asp5 Ala6 Lys7 Ala8 Ala9 Ala10 Glu11 Leu12 Val13 Ala14 Ala15 Asn16 Ala17 Lys18 Ala19 Ala20 Ala21 Glu22 Leu23 Val24 Ala25 Ala26 Asn27 Ala28 Lys29 Ala30 Ala31 Ala32 ... Liepinsh et al (Eur J Biochem 269) Table Sequence alignment of TTTT and VVVV2KE TTTT VVVV2KE D D TASDAAAAAAL VASDAKAAAEL 13 TAANAKAAAEL VAANAKAAAEL hydrogen bonds involving the hydroxyl groups of the ... determine the relative magnitude of the JHa,Hb couplings of CbH2 methylene groups The ROESY 24 TAANAAAAAAA VAANAKAAAEA 35 TAR VARCONH2 spectrum at 15 °C (mixing time 50 ms) was used to identify...
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