Journal articles: 'C2221 cell'

1

Choi, Hee-Lack, Naoya Enomoto, Nobuo Ishizawa, and Zenbe-e. Nakagawa. "X-ray diffraction data of Ti2O2(C2O4)(OH)2·H2O." Powder Diffraction 9, no. 3 (September 1994): 187–88. http://dx.doi.org/10.1017/s0885715600019199.

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X-ray powder diffraction data for Ti2O2(C2O4)(OH)2·H2O were obtained. The crystal system was determined to be orthorhombic with space group C2221. The unit cell parameters were refined to a = 1.0503(2) nm, b = 1.5509(3) nm, and c = 0.9700(1) nm.

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2

Saxena, Ajay, Anna Gries, Robert Schwarzenbacher, Gerhard M. Kostner, Peter Laggner, and Ruth Prassl. "Crystallization and preliminary X-ray crystallographic studies on apolipoprotein H (β2-glycoprotein-I) from human plasma." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1450–52. http://dx.doi.org/10.1107/s0907444998004557.

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Apolipoprotein-H (Apo-H, Mw ≃ 50 kDa) is a carbohydrate-rich human-plasma protein which exists in blood serum in the free form as well as distributed between several classes of lipoproteins. Single crystals of apo-H have been obtained and crystallographic data sets have been collected. The crystals belong to the orthorhombic space group C2221, with cell dimensions a = 158.47, b = 169.25, c = 113.28 Å (at 100 K). The data indicate that the crystallographic asymmetric unit contains one tetramer of the protein.

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Huyton, Trevor, and David I. Roper. "Crystallization and preliminary X-ray characterization of VanA from Enterococcus faecium BM4147: towards the molecular basis of bacterial resistance to the glycopeptide antibiotic vancomycin." Acta Crystallographica Section D Biological Crystallography 55, no. 8 (August 1, 1999): 1481–83. http://dx.doi.org/10.1107/s0907444999007155.

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A recombinant form of Enterococcus facieum BM4147 D-alanine-D-lactate ligase (VanA) has been prepared and crystallized. VanA was found to crystallize only in the presence of a phosphinate inhibitor analogue of D-alanine-D-alanine. The crystals grow in 40–45% ammonium sulfate, 0.1 M 3-(N-morpholino)-propanesulfonic acid pH 6.0 and reach dimensions of 0.4 × 0.2 × 0.1 mm. The crystals diffract to at least 2.5 Å and are in the centred orthorhombic space group C2221, with unit-cell dimensions a = 123.2, b = 225.4, c = 72.4 Å.

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Matsumura, Hiroyoshi, Takahiro Nagata, Mika Terada, Shunsuke Shirakata, Tsuyoshi Inoue, Takeo Yoshinaga, Yoshihisa Ueno, Hidetoshi Saze, Katsura Izui, and Yasushi Kai. "Crystallization and preliminary X-ray diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize." Acta Crystallographica Section D Biological Crystallography 55, no. 11 (November 1, 1999): 1937–38. http://dx.doi.org/10.1107/s0907444999010240.

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Phosphoenolpyruvate carboxylase is a key enzyme in the fixation of atmospheric CO2 in C4 and crassulacean acid metabolism (CAM) plants. The enzyme catalyzes the irreversible carboxylation of phosphoenolpyruvate to form oxaloacetate and inorganic phosphate, the first committed step in the fixation of external CO2 in these plants. The enzyme has been isolated from maize leaves and crystallized using the hanging-drop vapour-diffusion method with PEG 8000 as a precipitant at pH 7.5. The crystals belong to space group C2221, with unit-cell dimensions a = 160.2, b = 175.6, c = 255.5 Å, and diffract to 3.2 Å resolution.

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5

Fenske, Dieter, Kay Jansen, and Kurt Dehnicke. "Die Kristallstruktur von PPh4[MoOCl4(OCHNMe2)] / The Crystal Structure of PPh4[MoOCl4(OCHNMe2)]." Zeitschrift für Naturforschung B 41, no. 4 (April 1, 1986): 523–26. http://dx.doi.org/10.1515/znb-1986-0421.

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Green crystals of the title compound are formed in the reaction of (PPh4)2 [Mo2(O2C -Ph)4Cl2] ·2 CH2Cl2 with dimethyl formamide/carbon tetrachloride in the presence of water. According to the structural investigations by X-ray methods PPh4[MoCl4(O CHNMe2)] crystallizes orthorhombically in the space group C2221 with four formula units per unit cell (3132 observed, independent reflexions, R - 0.068). The cell dimensions are a = 792.1 pm, b = 1656.8 pm, c = 2211.3 pm. The structure consists of PPh4⊕ cations and anions [MoOCl4(OCHNMe2)]⊖, in which the coordination sphere of the molybdenum atom is of distorted octahedral geometry. The ligands are four equatorial chlorine atoms, one terminal O atom (Mo = O 165 pm) and the O atom of the dimethyl formamide molecule (MoO 232 pm). The IR spectrum is reported

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6

Gil, Fernando, Santiago Ramón-Maiques, Alberto Marina, Ignacio Fita, and Vicente Rubio. "N-Acetyl-L-glutamate kinase from Escherichia coli: cloning of the gene, purification and crystallization of the recombinant enzyme and preliminary X-ray analysis of the free and ligand-bound forms." Acta Crystallographica Section D Biological Crystallography 55, no. 7 (July 1, 1999): 1350–52. http://dx.doi.org/10.1107/s0907444999005351.

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The gene for Escherichia coli N-acetyl-L-glutamate kinase (NAGK) was cloned in a plasmid and expressed in E. coli, allowing enzyme purification in three steps. NAGK exhibits high specific activity (1.1 µmol s−1 mg−1), lacks Met1 and forms dimers (shown by cross-linking). Crystals of unliganded NAGK diffract to 2 Å and belong to space group P6122 or its enantiomorph P6522 (unit-cell parameters a = b = 78.6, c = 278.0 Å) with two monomers in the asymmetric unit. Crystals of NAGK with acetylglutamate and the ATP analogue AMPPNP diffract to 1.8 Å and belong to space group C2221 (unit-cell parameters a = 60.0, b = 71.9, c = 107.4 Å), with one monomer in the asymmetric unit. NAGK crystallization will allow the determination of proposed structural similarities to carbamate kinase.

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7

Faggiani, R., H. E. Howard-Lock, C. J. L. Lock, and M. A. Turner. "The reaction of chloro(triphenylphosphine)gold(I) with 1-methylthymine." Canadian Journal of Chemistry 65, no. 7 (July 1, 1987): 1568–75. http://dx.doi.org/10.1139/v87-264.

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1-Methylthyminato-N3-triphenylphosphinegold(I) was prepared by reacting chloro(triphenylphosphine)gold(I) with 1-methylthymine in aqueous methanol at pH 11. The product was examined by X-ray crystallography and was found to have the orthorhombic space group C2221 (no. 20) with cell dimensions a = 12.760(7) Å, b = 11.530(2) Å, c = 31.893(5) Å, and eight formula units in the unit cell. Data were collected with use of MoKα radiation and a Syntex P21, diffractometer. The crystal structure was determined by standard methods and refined to R = 0.112 and Rw = 0.076 on the basis of 4760 unique reflections. Bond lengths and bond angles are normal. Packing in the crystal lattice is dominated by the triphenylphosphine rings which arrange roughly as blades of a propellor and are the source of the crystal's chirality. The title and related compounds were also examined by 1H nmr, 13C nmr, and vibrational spectroscopy.

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8

Chandra, Vikas, Akanksha Nagpal, A. Srinivasan, and T. P. Singh. "Purification, crystallization and preliminary X-ray crystallographic analysis of a phospholipase A2 from Daboia russelli pulchella." Acta Crystallographica Section D Biological Crystallography 55, no. 4 (April 1, 1999): 925–26. http://dx.doi.org/10.1107/s090744499900058x.

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Phospholipases are esterolytic enzymes which hydrolyze glycerophospholipids. The pharmacological efficiency of phospholipase A2 (PLA2) enzymes is reflected by their specificity towards a tissue or organ. The Russell's viper has been classified into two classes. Class 1 contains Viper russelli russelli, Viper russelli siamensis and Viper russelli formosensis, whereas class 2 contains Daboia russelli pulchella. The sequence identity between the PLA2s from these two classes is 47%. The novel PLA2 from Daboia russelli pulchella has been crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitating agent. Crystals belong to the orthorhombic space group C2221 with unit-cell parameters a = 77.01, b = 92.29, c = 76.90 Å and two molecules in the asymmetric unit. These crystals diffract to about 2.49 Å resolution using a rotating-anode source.

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9

Bataille, Thierry, and Daniel Louër. "Powder and single-crystal X-ray diffraction study of the structure of [Y(H2O)]2(C2O4)(CO3)2." Acta Crystallographica Section B Structural Science 56, no. 6 (December 1, 2000): 998–1002. http://dx.doi.org/10.1107/s0108768100010004.

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From powder pattern indexing it has been demonstrated that [Y(H2O)]2(C2O4)(CO3)2, yttrium oxalate carbonate, crystallizes with orthorhombic symmetry, space group C2221, a = 7.8177 (7), b = 14.943 (1), c = 9.4845 (7) Å, V = 1108.0 (1) Å3, Z = 4. This unit cell displays a doubling of the c parameter, arising from weak diffraction lines observed in the powder diffraction pattern, with respect to results reported in the literature. The crystal structure has been solved ab initio using direct methods from powder data and has been confirmed by additional single-crystal data collected with a CCD area detector. The overall crystal structure is similar for both unit cells, except that an alternation of the carbonate groups in the direction parallel to the screw axis is displayed in the larger cell, while with the suggested half unit cell (space group C2mm) the carbonate groups would show only one orientation. The unit-cell determination strategy from single-crystal diffraction, collected with Nonius CAD-4 and Nonius Kappa CCD diffractometers, is discussed with respect to the results extracted from the powder diffraction pattern. The study demonstrates the power and usefulness of the full trace of a powder pattern for the detection of subtle structure details.

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10

Lee, Seungyeol, and Huifang Xu. "Using powder XRD and pair distribution function to determine anisotropic atomic displacement parameters of orthorhombic tridymite and tetragonal cristobalite." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 75, no. 2 (March 16, 2019): 160–67. http://dx.doi.org/10.1107/s2052520619000933.

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Determination of the crystal structures of low-temperature tridymite and cristobalite using single-crystal XRD has been challenging because they generally occur as metastable fine-grained crystals in the geological environment. Therefore, using powder diffraction and scattering techniques is critical to study the low-temperature crystals. Synchrotron powder X-ray diffraction (XRD), pair distribution function (PDF) and transmission electron microscopy were used to investigate the structure of orthorhombic tridymite with C2221 symmetry and tetragonal cristobalite with P41212 symmetry, including their anisotropic atomic displacement parameters (ADPs). Rietveld refinement was used to determine the unit-cell parameters, fractional coordinates and isotropic atomic displacement parameters (U iso) of the tridymite and cristobalite. The PDF method was used to determine ADPs for each atom. The results suggest that the crystal structure with high quality ADP values can be obtained using the combined methods of XRD and PDF analyses. The method can be used for characterizing crystals that are not suitable for single-crystal XRD.

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11

Fall, Alioune, Ndiouga Fall, Thierno Moussa Seck, Ibrahima Elhadj Thiam, Ousmane Diouf, and Mohamed Gaye. "Synthesis of Mono and Bis-Substituted Compounds 1-(2-hydroxybenzylidene) Carbonohydrazide and 1, 5-bis(2-Hydroxybenzaldehyde) Carbohydrazone: Study Spectroscopy and X-ray Diffraction." International Research Journal of Pure and Applied Chemistry 24, no. 5 (August 29, 2023): 34–45. http://dx.doi.org/10.9734/irjpac/2023/v24i5823.

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The unsymmetric monocarbonohydrazide Schiff base (H5L1) (1) and the symmetric dicarbonohydrazone (H4L2) (2) were prepared from a monocondensation reaction between carbonohydrazide and 2-hydroxybenzaldehyde, respectively, in 1/1 and 1/2 ratio. The compounds were characterized by elemental analysis, 1H and 13C NMR and FTIR spectroscopy. The NMR and FTIR data analysis revealed that compounds (1) and (2) are in the amide form in the solid state as well as in DMSO solution. The molecular structure of each Schiff base compound has been elucidated by single crystal X-ray diffraction analysis. Compound H5L1 (1) crystallizes in the monoclinic system in P21/c space group with cell parameters: a = 17.0790(2) Å, b = 11.07410(10) Å, c = 10.56110(10) Å, b = 106.5730(10) °, V = 1914.49(3) Å3 , Z = 4, R1 = 0.0432, wR2 = 0.1275 . The compound H4L2 (2) crystallizes in the orthorhombic system in C2221 space group with cell parameters; a = 4.5494 (1) Å, b = 12.2213 (2) Å, c = 27.4001 (6) Å, V = 1523.43 (5) Å3 , Z = 4, R1 = 0.039 , wR2 = 0.125 . Both compounds exhibit inter and intramolecular hydrogen bonds which consolidate the structures into three-dimensional networks.

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12

Montoya, Guillermo, Kai te Kaat, Ralf Moll, Günter Schäfer, and Irmgard Sinning. "Crystallization and preliminary X-ray diffraction studies on the conserved GTPase domain of the signal recognition particle from Acidianus ambivalens." Acta Crystallographica Section D Biological Crystallography 55, no. 11 (November 1, 1999): 1949–51. http://dx.doi.org/10.1107/s0907444999011348.

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The signal recognition particle (SRP) of bacteria consists of only one protein, known as Ffh or the SRP54 homologue, which forms a complex with 4.5S RNA. It also binds to signal peptides and contains a GTPase which displays interesting differences to Ras GTPases. The conserved NG-domain of Ffh from the archaebacterium Acidianus ambivalens was cloned and overexpressed with a C-terminal His tag in Escherichia coli. Crystallization experiments of the native protein as well as of the Thr112Ala mutant, which is deficient in GTP hydrolysis, resulted in crystals suitable for X-ray diffraction. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 64.5, b = 128.3, c = 72.0 Å. At cryogenic temperatures, the crystals diffracted to a resolution limit of 2.8 Å using a rotating-anode generator and contain one molecule per asymmetric unit. A native data set has been collected using synchrotron radiation to around 2.0 Å resolution. Selenomethionine protein was produced; its crystals diffract in-house to about 2.8 Å resolution.

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13

Cheng, Jen-Hao, Chien-Chih Huang, Yen-Hua Huang, and Cheng-Yang Huang. "Structural Basis for pH-Dependent Oligomerization of Dihydropyrimidinase from Pseudomonas aeruginosa PAO1." Bioinorganic Chemistry and Applications 2018 (January 30, 2018): 1–8. http://dx.doi.org/10.1155/2018/9564391.

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Dihydropyrimidinase, a dimetalloenzyme containing a carboxylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. Unlike all known dihydropyrimidinases, which are tetrameric, pseudomonal dihydropyrimidinase forms a dimer at neutral pH. In this paper, we report the crystal structure of P. aeruginosa dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). The crystals of P. aeruginosa dihydropyrimidinase belonged to space group C2221 with cell dimensions of a = 108.9, b = 155.7, and c = 235.6 Å. The structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 Å resolution. An asymmetric unit of the crystal contained four crystallographically independent P. aeruginosa dihydropyrimidinase monomers. Gel filtration chromatographic analysis of purified P. aeruginosa dihydropyrimidinase revealed a mixture of dimers and tetramers at pH 5.9. Thus, P. aeruginosa dihydropyrimidinase can form a stable tetramer both in the crystalline state and in the solution. Based on sequence analysis and structural comparison of the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and Thermus sp. dihydropyrimidinase, different oligomerization mechanisms are proposed.

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14

Hwang, Jisub, Hackwon Do, Youn-Soo Shim, and Jun Hyuck Lee. "Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Porphyromonas gingivalis." Crystals 13, no. 8 (August 18, 2023): 1274. http://dx.doi.org/10.3390/cryst13081274.

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Aspartate semialdehyde dehydrogenase (ASADH) catalyzes the biosynthesis of several essential amino acids, including lysine, methionine, and threonine, and bacterial cell components. Thus, ASADH is a crucial target for developing new antimicrobial agents that can potentially disrupt the biosynthesis of essential amino acids, thereby inhibiting the growth of pathogens. Herein, the crystal structures of ASADH obtained from Porphyromonas gingivalis (PgASADH, UniProtKB code A0A1R4DY25) were determined in apo- and adenosine-2′-5′-diphosphate (2′,5′-ADP)-bound complex forms at a resolution of 1.73 Å. The apo- and 2′,5′-ADP-complexed crystals of PgASADH belonged to the space groups of I212121 and C2221, respectively. Analytical size-exclusion chromatography showed a stable PgASADH dimer in a solution. Clustering analysis and structural comparison studies performed on PgASADH and previously known ASADHs revealed that ASADHs, including PgASADH, can be classified into three types depending on sequential and structural differences at the α-helical subdomain region. These findings provide valuable insights into developing structure-based species-specific new antibacterial drugs against the oral pathogen P. gingivalis.

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Basak, A. K., A. Howells, J. T. Eaton, D. S. Moss, C. E. Naylor, J. Miller, and R. W. Titball. "Crystallization and preliminary X-ray diffraction studies of α-toxin from two different strains (NCTC8237 and CER89L43) of Clostridium perfringens." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1425–28. http://dx.doi.org/10.1107/s0907444998005186.

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The α-toxin of Clostridium perfringens is the major virulence determinant for gas gangrene in man. The gene encoding the α-toxin has been cloned into E. coli from two strains of the bacterium (NCTC8237 and CER89L43) and subsequently purified to homogeneity. The two strains of α-toxin differ by five amino acids, resulting in the toxin from NCTC8237 being sensitive to chymotrypsin digestion while that from CER89L43 is resistant. The α-toxin from each of these strains has been crystallized in two different forms by the hanging-drop vapour-diffusion method at 293 K. CER89L43 form I crystals belong to space group R32 and have two molecules in the crystallographic asymmetric unit and a unit cell with a = b = 151.4, c = 195.5 Å, α = β = 90, γ = 120°. The crystals diffracted to d min = 1.90 Å. The characteristics of the NCTC8237 form I crystals have already been reported. The form II crystals from both strains belong to space group C2221 with one molecule in the crystallographic asymmetric unit and, for strain CER89L43, have cell dimensions a = 61.05, b = 177.50, c = 79.05 Å, α = β = γ = 90°, while for strain NCTC8237 the cell dimensions are a = 60.50, b = 175.70, c = 80.20 Å, α = β = γ = 90°. The crystals diffracted to maximum resolutions of 1.85 and 2.1 Å for the CER89L43 and the NCTC8237 strains, respectively.

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16

Yeates, Todd O., and Alexander McPherson. "The structure of bovine β-lactoglobulin in crystals grown at pH 3.8 exhibiting novel threefold twinning." Acta Crystallographica Section F Structural Biology Communications 75, no. 10 (September 20, 2019): 640–45. http://dx.doi.org/10.1107/s2053230x1901224x.

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Bovine β-lactoglobulin was crystallized from 3 M NaCl buffered at pH 3.8 with sodium citrate as thick hexagonal prisms of greater than 1 mm in edge length. Analyses of the X-ray diffraction intensities using three different current algorithms were unanimous in specifying the space group to be P6322, with unit-cell dimensions a = b = 75.47, c = 140.79 Å. No progress could be made, however, towards an acceptable solution by molecular replacement using this symmetry. In the end, it was found that the true space group was C2221, a subgroup of P6322, with a = 65.89, b = 114.12, c = 140.51 Å, with the apparent 622 symmetry arising from an unusual threefold or tritohedral twinning. An assembly based on a model of the protein in another crystal form (PDB entry 1beb) containing three molecules in the asymmetric unit was refined to 2.3 Å resolution with a final R factor of 0.23 and R free of 0.26. NCS restraints were maintained throughout. For the most part, the molecules found in this crystal form are virtually the same as in PDB entry 1beb, although there are numerous local variations, particularly in loop elements, rotamer conformation differences and some alterations, including additions, at the termini.

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17

Yeo, Lily, and Kenneth DM Harris. "Temperature-dependent structural properties of a solid urea inclusion compound containing chiral guest molecules: 2-bromotetradecane/urea." Canadian Journal of Chemistry 77, no. 12 (December 5, 1999): 2105–18. http://dx.doi.org/10.1139/v99-215.

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Periodic structural properties of the 2-bromotetradecane/urea inclusion compound have been investigated as a function of temperature. Differential scanning calorimetry between 298 and 98 K identified three well-defined regimes, denoted the high-, intermediate-, and low-temperature phases. The structural properties of each phase (at 293, 207, and 142 K, respectively) have been investigated by single crystal X-ray diffraction. In the high-temperature phase, the inclusion compound has the hexagonal urea tunnel structure (P6122) characteristic of the conventional urea inclusion compounds, with substantial orientational disorder of the guest molecules. In the intermediate-temperature phase, the symmetry is lowered to orthorhombic (C2221), although the host structure remains close to the hexagonal tunnel structure of the high-temperature phase and there is no clear evidence for increased orientational ordering of the guest molecules. In the low-temperature phase, the urea tunnel structure is monoclinic (P21), and is based on a 2 × 2 × 1 supercell of the hexagonal cell of the high-temperature structure. There are four independent types of tunnel, three of which are strongly distorted from hexagonal geometry. Within these distorted tunnels, there is a comparatively narrow distribution of guest molecule orientations, which correlate well with the observed distortions of the tunnels. The 2-bromotetradecane/urea inclusion compound highlights several issues of wider relevance concerning the structural properties of solid inclusion compounds.Key words: urea inclusion compounds, X-ray diffraction, phase transitions, chiral recognition, incommensurate solid, 2-bromotetradecane/urea.

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18

Donovan, Katherine A., Sarah C. Atkinson, Sarah A. Kessans, Fen Peng, Tim F. Cooper, Michael D. W. Griffin, Geoffrey B. Jameson, and Renwick C. J. Dobson. "Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: a case study involving pyruvate kinase." Acta Crystallographica Section D Structural Biology 72, no. 4 (March 24, 2016): 512–19. http://dx.doi.org/10.1107/s205979831600142x.

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Pyruvate kinase is a key regulatory enzyme involved in the glycolytic pathway. The crystal structure ofEscherichia colitype I pyruvate kinase was first solved in 1995 at 2.5 Å resolution. However, the space group was ambiguous, being either primitive orthorhombic (P212121) orC-centred orthorhombic (C2221). Here, the structure determination and refinement ofE. colitype I pyruvate kinase to 2.28 Å resolution are presented. Using the same crystallization conditions as reported previously, the enzyme was found to crystallize in space groupP21. Determination of the space group was complicated owing to anisotropic data, pseudo-translational noncrystallographic symmetry and the pseudo-merohedrally twinned nature of the crystal, which was found to have very close to 50% twinning, leading to apparent orthorhombic symmetry and absences that were not inconsistent withP212121. The unit cell contained two tetramers in the asymmetric unit (3720 residues) and, when compared with the orthorhombic structure, virtually all of the residues could be easily modelled into the density. Averaging of reflections into the lower symmetry space group with twinning provided tidier electron density that allowed ∼30 missing residues of the lid domain to be modelled for the first time. Moreover, residues in a flexible loop could be modelled and sulfate molecules are found in the allosteric binding domain, identifying the pocket that binds the allosteric activator fructose 1,6-bisphosphate in this isozyme for the first time. Lastly, we note the pedagogical benefits of difficult structures to emerging crystallographers.

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Dandare, Shamsudeen Umar, Maria Håkansson, L. Anders Svensson, David J. Timson, and Christopher C. R. Allen. "Expression, purification and crystallization of a novel metagenome-derived salicylaldehyde dehydrogenase from Alpine soil." Acta Crystallographica Section F Structural Biology Communications 78, no. 4 (March 28, 2022): 161–69. http://dx.doi.org/10.1107/s2053230x22002345.

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Salicylaldehyde dehydrogenase (SALD) catalyses the last reaction in the upper pathway of naphthalene degradation: the oxidation of salicylaldehyde to salicylate. This enzyme has been isolated and studied from a few organisms that belong to the betaproteobacteria and gammaproteobacteria, predominantly Pseudomonas putida. Furthermore, there is only one crystal structure of this enzyme, which was obtained from P. putida G7. Here, crystallographic studies and analysis of the crystal structure of an Alpine soil metagenome-derived SALD (SALDAP) from an alphaproteobacterium are presented. The SALDAP gene was discovered using gene-targeted sequence assembly and it was cloned into a pLATE51 vector. The recombinant protein was overexpressed in Escherichia coli BL21 (DE3) cells and the soluble protein was purified to homogeneity. The protein crystallized at 20°C and diffraction data from the crystals were collected at a resolution of 1.9 Å. The crystal belonged to the orthorhombic space group C2221, with unit-cell parameters a = 116.8, b = 121.7, c = 318.0 Å. Analysis of the crystal structure revealed its conformation to be similar to the organization of the aldehyde dehydrogenase superfamily with three domains: the catalytic, NAD+-binding and bridging domains. The crystal structure of NahF from P. putida G7 was found to be the best structural homologue of SALDAP, even though the enzymes share only 48% amino-acid identity. Interestingly, a carboxylic acid (protocatechuic acid) was found to be a putative ligand of the enzyme and differential scanning fluorimetry was employed to confirm ligand binding. These findings open up the possibility of studying the mechanism(s) of product inhibition and biocatalysis of carboxylic acids using this enzyme and other related aldehyde dehydrogenases.

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Chen, Qiujia, Suk-Hee Lee, and Millie Georgiadis. "Preliminary crystallographic analysis of SETMAR bound to DNA." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C206. http://dx.doi.org/10.1107/s2053273314097939.

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SETMAR, a recently identified double strand break (DSB) repair enzyme in the human genome, contains an N-terminal SET domain and a C-terminal MAR domain. This chimeric protein arose through the fusion of a mariner-family DNA transposase gene, Hsmar1, downstream of a SET histone methyltransferase gene approximately 50 million years ago [1]. Although the SETMAR transposase domain retains the ability to bind terminal inverted repeat (TIR) DNA sequence, which is the hallmark of DNA transposons, it is no longer a functional transposase [2]. Nonetheless, the transposase domain with only 19 amino acid substitutions as compared to the ancestral Hsmar1 transposase has been under a strong selective evolutionary pressure suggesting that the transposase domain is functionally important. Determining how SETMAR interacts with DNA is central to understanding the molecular basis of its evolved DNA repair activity. Toward this goal, we have focused initially on the interaction of the DNA-binding domain (DBD) of the SETMAR transposase domain with TIR DNA. The DBD of SETMAR has been overexpressed and purified. A complex formed between SETMAR DBD and its transposon TIR DNA has been crystallized by using the hanging-drop vapor diffusion method. The crystals diffract to 3.15 Å resolution and exhibit orthorhombic symmetry (C2221), with unit-cell dimensions of a=72.233 Å, b=164.385 Å, and c=67.957 Å. As there is no suitable search model available, we are currently pursuing experimental phasing approaches in order to solve this structure. We anticipate the structural analysis of DBD of SETMAR bound to transposon DNA will provide insight into the mechanism by which SETMAR recognizes both TIR and non-TIR DNA.

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21

Audette, Gerald F., Douglas J. Olson, Andrew R. Ross, J. Wilson Quail, and Louis T. Delbaere. "Examination of the structural basis for O(H) blood group specificity by Ulex europaeus Lectin I." Canadian Journal of Chemistry 80, no. 8 (August 1, 2002): 1010–21. http://dx.doi.org/10.1139/v02-134.

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The structural basis for carbohydrate specificity of the first lectin from Ulex europaeus (UE-I) is reported. UE-I is a dimeric metalloglycoprotein that binds the H-type 2 human blood group determinant (α-L-Fucα(1[Formula: see text]2)-β;-D-Galβ(1[Formula: see text]4)-β-D-GlcNAcα-), the blood group determinant present on the surface of O-type erythrocytes. The structural characteristics of UE-I involved in carbohydrate recognition have been examined using mass spectrometry (MS) and X-ray diffraction analysis. MS analysis allowed for discrimination between the different primary structures reported for UE-I. To examine the binding of the H-type 2 blood group determinant by UE-I, the methyl glycosides of the fucose monosaccharide (α-L-Fuc-OMe), known to exhibit primary binding specificity, and the H-type 2 trisaccharide (H-type 2-OMe) were, in two separate experiments, co-crystallized into the binding site of UE-I. The UE-I:α-L-Fuc-OMe complex crystallizes in the monoclinic space group P21, with unit cell dimensions a = 71.81, b = 69.00, and c = 119.02 Å, and β = 106.76°. Two UE-I dimers are observed to be present within the asymmetric unit, and the model has been refined to a R-value and RFree of 0.202 and 0.289, respectively, to 2.3 Å resolution. The preliminary model of the UE-I:H-type 2-OMe complex has been refined at 3.0 Å resolution. The UE-I:H-type 2-OMe complex crystallizes in the orthorhombic space group C2221, with unit cell dimensions a = 88.80, b = 164.75, and c = 77.42 Å, and a single UE-I dimer is present within the asymmetric unit. The carbohydrate recognition domain of UE-I has been identified to be comprised of residues Glu44, Thr86, Asp87, Arg102, Ala103, Gly104, Gly105, Tyr106, Ile129, Val133, Asn134, Trp136, Tyr219, and Arg222. Several critical protein-carbohydrate interactions have been identified, including the role of the hydrophobic interaction between the Thr86 side chain and C-5-CH3 of the α-L-Fuc-OMe. The role of these interactions in carbohydrate recognition-binding by UE-I, as well as differences between the observed and previously modeled complexes, are discussed. Key words: Ulex europaeus lectin I, H-type 2 human blood group determinant, protein-carbohydrate interactions, X-ray crystallography, chemical mapping.

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Schelcher, Celine, Sarah Valencia, Henri-Jacques Delecluse, Matthew Hicks, and Alison J. Sinclair. "Mutation of a Single Amino Acid Residue in the Basic Region of the Epstein-Barr Virus (EBV) Lytic Cycle Switch Protein Zta (BZLF1) Prevents Reactivation of EBV from Latency." Journal of Virology 79, no. 21 (November 1, 2005): 13822–28. http://dx.doi.org/10.1128/jvi.79.21.13822-13828.2005.

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ABSTRACT Zta, the product of the BZLF1 gene carried by Epstein-Barr virus (EBV), is crucial for reactivation of EBV from latency. Zta is a member of the bZIP family of transcription factors, and in common with many of these, Zta possesses a conserved cysteine residue in its basic region (C189) and a further cysteine residue in its ZIP region (C222). We demonstrate that C189 is required to reactivate EBV from latency but C222 is not and that this single amino acid affects two independent functions of Zta, (i) binding to a Zta-responsive site and (ii) manipulating the cell cycle.

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Otsuta, Shoma, Tatsumi Kitahara, Hironori Nakazima, Takahiro Karimata, and Kohei Ito. "Structure optimization of polymer electrolyte fuel cell." Proceedings of the National Symposium on Power and Energy Systems 2021.25 (2021): C221. http://dx.doi.org/10.1299/jsmepes.2021.25.c221.

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Cho, Daisuke, Takao Nakagaki, and Yuta Itoh. "C221 Experimental Study on Temperature Distribution Measurement in Polymer Electrolyte Fuel Cell." Proceedings of the Thermal Engineering Conference 2009 (2009): 239–40. http://dx.doi.org/10.1299/jsmeted.2009.239.

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MATSUMOTO, Hiroshi, Fumiya TERAI, Masahiro HIROTA, and Toshio SHUDO. "Hydrogen production in an electrolyzer cell with sintered metal fiber flow field." Proceedings of the National Symposium on Power and Energy Systems 2016.21 (2016): C221. http://dx.doi.org/10.1299/jsmepes.2016.21.c221.

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Cott, G. R., K. Sugahara, and R. J. Mason. "Stimulation of net active ion transport across alveolar type II cell monolayers." American Journal of Physiology-Cell Physiology 250, no. 2 (February 1, 1986): C222—C227. http://dx.doi.org/10.1152/ajpcell.1986.250.2.c222.

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The active transcellular transport of electrolytes across the alveolar epithelium probably plays an important role in alveolar fluid homeostasis by helping to maintain the alveolus relatively free of fluid. To better understand the factors regulating active ion transport across alveolar epithelial cells, we examined the effect of a number of pharmacologically active agents on the bioelectric properties of alveolar type II cells in primary culture. Alveolar type II cells were isolated from adult male rats and cultured on collagen-coated Millipore filters for 6-14 days. The bioelectric properties of these monolayers were determined in Ussing-type chambers. The addition of 10(-3) M 8-bromoadenosine 3',5'-cyclic monophosphate (8-BrcAMP) increased the short-circuit current (Isc) from 2.9 +/- 0.75 to 6.9 +/- 0.73 microA/cm2 (means +/- SE; n = 8) and decreased the transepithelial resistance. Cholera toxin, 3-isobutyl-1-methylxanthine, and terbutaline sulfate produced similar increases in Isc and decreases in resistance. The Isc stimulated by 8-BrcAMP was Na but not Cl dependent and could be blocked by amiloride but not by furosemide. Thus 8-BrcAMP and agents that increase intracellular cAMP can stimulate a Na-dependent net active ion transport across alveolar type II cell monolayers. Similar regulatory mechanisms may be involved in controlling solute and fluid movement across the alveolar epithelium in vivo.

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Stavenuiter, Fabian, Alexander B. Meijer, Erica Sellink, and Koen Mertens. "Factor VII Activating Protease (FSAP): Functional Implications of the “Marburg-1” Polymorphism." Blood 114, no. 22 (November 20, 2009): 2126. http://dx.doi.org/10.1182/blood.v114.22.2126.2126.

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Abstract Abstract 2126 Poster Board II-104 Introduction FSAP is a plasma serine protease first reported as an activator of single-chain urokinase-type plasminogen activator (scuPA) and Factor VII (FVII), suggesting a key role in hemostasis and thrombosis. Numerous additional functions have been proposed, including inhibition of smooth muscle cell proliferation and migration. Rigorous studies have been limited by the difficulty of obtaining intact FSAP from blood or recombinant sources due to autocatalytic activity which is stimulated through interaction with negatively charged surfaces. About 5-10% of healthy individuals carry a polymorphism (Marburg-1) at position c221 (G534Q) located in one of the 8 surface binding loops of the serine protease domain. This polymorphism has been proposed to be associated with impaired activation of scuPA in vitro, suggesting a putative defect in fibrinolysis. Epidemiological studies have remained inconclusive with regard to prothrombotic implications of this polymorphism. Residue c221 has been described as highly important in serine proteases. For prothrombin the D221Q mutation has been associated with a severe defect in fibrinogen clotting. Similarly, patients who are hemizygous for a c221 substitution in FIX (A221V) suffer from haemophilia B. In general, in Na+ -dependent serine proteases like FVII, FIX, and thrombin, residue c221 contributes to activity and substrate specificity. Objectives: Our aim was to investigate, using intact recombinant (r) FSAP, the effect of the M1-polymorphism on FSAP biological activity. Results Various stable cell lines (HEK293-, BHK-, LOVO-, and CHO cells) expressing normal rFSAP (wt) and its Marburg-1 (M1) variant were produced. Irrespective to the cell type used, rFSAP was found to be cleaved after expression due to autocatalytic cleavage. However, wtFSAP was found to be more sensitive to proteolytic processing than its M1-variant. Moreover, wtFSAP was found to be completely inactivated whereas the M1-variant could be purified in its two-chain form. To overcome the problem of autocatalytic degradation, for wtFSAP we constructed a FSAP-variant in which the natural activation site (R313-I314) was replaced by a cleavage site for the bacterial protease thermolysin. Thermolysin-activated rFSAP displayed the same affinity for chromogenic peptide substrates (S2288) as pdFSAP (Km 0.38 mM) and retained its capability to activate scuPA (Km 62 nM). Vmax for scuPA activation was increased through interaction with negative charged surfaces like polyphosphate and heparin (2- and 3-fold, respectively), whereas no effect on the hydrolysis of S2288 was found. In contrast, the M1-variant displayed severely reduced affinity for S2288 (6.5-fold) and hardly any scuPA activation. Interestingly, addition of heparin or polyphosphate showed positive effects on the hydrolysis of both substrates by the M1-variant. Compared to wtFSAP, however, both the Km and Vmax were still heavily affected. Surprisingly, wtFSAP proved incapable of cleaving purified FVII, even in the presence of calcium-ions and lipid vesicles of varying composition, including up to 40 mol% negative phospholipids such as phosphatidylserine and cardiolipin (CL). On membranes of 100% CL FVII cleavage did occur, but this resulted in transient activation and rapid degradation. The M1-variant, however, displayed no FVII cleavage under any of the conditions tested. Finally, we found that Na+, in absence of CaCl2, affects the maximal rate of S2288 hydrolysis by rFSAP, with a maximal effect at physiological relevant concentrations. The Na+ concentrations needed to reach maximal catalytic activity of the M1-variant were found 8 - 10 fold above physiologically relevant levels. Conclusions While rFSAP indeed activates scuPA, FVII appears surprisingly resistant to activation by rFSAP. The M1-variant does not activate FVII either, but does display reduced scuPA activation. The M1-polymorphism, being a Gly to Glu substitution at position c221, makes the protease less responsive to Na+. This is compatible with its location in the putative Na+-binding loops. Whether or not the reduced scuPA activation has any physiological impact remains unclear. Disclosures: No relevant conflicts of interest to declare.

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Shuttleworth, T. J., and C. M. Wood. "Changes in pHi associated with activation of ion secretion in avian nasal salt gland cells." American Journal of Physiology-Cell Physiology 262, no. 1 (January 1, 1992): C221—C228. http://dx.doi.org/10.1152/ajpcell.1992.262.1.c221.

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The fluorescent pH-sensitive dye 2',7'-bis(2-carboxyethyl)-5(6)- carboxyfluorescein (BCECF) was used to determine changes in intracellular pH (pHi) associated with activation of secretion in isolated cells from the salt-secreting avian nasal gland. A correction procedure overcoming artifacts due to BCECF leakage is described. Resting pHi averaged 7.15 +/- 0.03 and was unaffected by the nominal removal of medium HCO3- or by the addition of the anion-exchange inhibitor 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS) but was significantly reduced by amiloride (7.07 +/- 0.02). Muscarinic activation of secretion resulted in a rapid intracellular acidification that was compensated by mechanisms which raised pHi to restore approximately resting levels within 5 min. The principal mechanism involved was amiloride-sensitive and independent of any sustained intracellular Ca2+ concentration change. Recovery of pHi was also aided by HCO3(-)-dependent and DIDS-sensitive mechanisms not seen in the resting cell. The direction of the latter was pHi-dependent, with DIDS further decreasing pHi in acidified cells and increasing pHi in alkalinized cells. This suggests that the DIDS-sensitive pathways are activated under conditions where pHi has been shifted away from resting levels in either direction and act primarily to restore resting pHi.

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Silverman, H. S., F. Di Lisa, R. C. Hui, H. Miyata, S. J. Sollott, R. G. Hanford, E. G. Lakatta, and M. D. Stern. "Regulation of intracellular free Mg2+ and contraction in single adult mammalian cardiac myocytes." American Journal of Physiology-Cell Physiology 266, no. 1 (January 1, 1994): C222—C233. http://dx.doi.org/10.1152/ajpcell.1994.266.1.c222.

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Studies in isolated cardiac myocytes have increased our understanding of intracellular Ca2+ regulation. Because less is known about Mg2+ regulation, adult rat ventricular myocytes were loaded with the Mg(2+)-sensitive fluorescent probe mag-indo 1, and changes in intracellular Mg2+ concentration ([Mg2+]i) and cell length were examined under a variety of conditions. The fluorescent signal was calibrated intracellularly and found to differ slightly from that for the probe in solution. Roughly 40% of the signal was intramitochondrial; the remainder was localized in the cytosol. Basal [Mg2+]i averaged 1.02 +/- 0.03 mM (n = 53 cells). No change in [Mg2+]i was observed during a single electrically stimulated contraction, and only a minor increase was seen during rapid electrical stimulation, which was expected to raise intracellular Ca2+ concentration ([Ca2+]i) to approximately 1 microM. An acid shift in intracellular pH of approximately 1 pH unit was accompanied by a small change in [Mg2+]i (0.34 +/- 0.03 mM, n = 6, P < 0.05). No change in [Mg2+]i was observed when cells were superfused with 15 mM Mg2+, despite marked changes in contraction. [Mg2+]i more than doubled when cells were depleted of ATP by exposure to hypoxia or metabolic inhibitors. The increase in [Mg2+]i was abrupt and occurred at the time of the failure of contraction, plateauing as rigor contracture developed. Reoxygenation was accompanied by a gradual fall in [Mg2+]i in cells that recovered mechanical function, and in a subset of cells that underwent hypercontracture. Studies in cell suspensions confirmed that rapid cellular energy depletion was accompanied by increases in [Mg2+]i and parallel decreases in ATP. Thus [Mg2+]i was largely insensitive to changes in [Ca2+]i or pHi and extracellular [Mg2+] but was rapidly altered by changes in energy state in a manner that was related to specific changes in cell morphology and contractile function.

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Kimball, Scot R., Rick L. Horetsky, and Leonard S. Jefferson. "Signal transduction pathways involved in the regulation of protein synthesis by insulin in L6 myoblasts." American Journal of Physiology-Cell Physiology 274, no. 1 (January 1, 1998): C221—C228. http://dx.doi.org/10.1152/ajpcell.1998.274.1.c221.

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The phosphorylation states of three proteins implicated in the action of insulin on translation were investigated, i.e., 70-kDa ribosomal protein S6 kinase (p70 S6k ), eukaryotic initiation factor (eIF) 4E, and the eIF-4E binding protein 4E-BP1. Addition of insulin caused a stimulation of protein synthesis in L6 myoblasts in culture, an effect that was blocked by inhibitors of phosphatidylinositide-3-OH kinase (wortmannin), p70 S6k (rapamycin), and mitogen-activated protein kinase (MAP kinase) kinase (PD-98059). The stimulation of protein synthesis was accompanied by increased phosphorylation of p70 S6k , an effect that was blocked by rapamycin and wortmannin but not PD-98059. Insulin caused dephosphorylation of eIF-4E, an effect that appeared to be mediated by the p70 S6k pathway. Insulin also stimulated phosphorylation of 4E-BP1 as well as dissociation of the 4E-BP1 ⋅ eIF-4E complex. Both rapamycin and wortmannin completely blocked the insulin-induced changes in 4E-BP1 phosphorylation and association of 4E-BP1 and eIF-4E; PD-98059 had no effect on either parameter. Finally, insulin stimulated formation of the active eIF-4G ⋅ eIF-4E complex, an effect that was not prevented by any of the inhibitors. Overall, the results suggest that insulin stimulates protein synthesis in L6 myoblasts in part through utilization of both the p70 S6k and MAP kinase signal transduction pathways.

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FUJII, Katsuhiro, Yutaka IIZUKA, Suguru UEMURA, and Yutaka TABE. "Visualization of Condensed Water at the MPL/Catalyst Layer Interface in a Polymer Electrolyte Fuel Cell." Proceedings of the National Symposium on Power and Energy Systems 2021.25 (2021): C222. http://dx.doi.org/10.1299/jsmepes.2021.25.c222.

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Sabatino, Piera, Simona Fermani, Alberto Ripamonti, Alberto Cassetta, Sandra Scagliarini, and Paolo Trost. "Crystallization and preliminary X-ray study of chloroplast glyceraldehyde-3-phosphate dehydrogenase." Acta Crystallographica Section D Biological Crystallography 55, no. 2 (February 1, 1999): 566–67. http://dx.doi.org/10.1107/s090744499801302x.

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Glyceraldehyde-3-phosphate dehydrogenase from spinach chloroplasts has been crystallized by vapour diffusion in the pH range 7–8.5 in (NH4)2SO4 and Tris–HCl buffer or potassium phosphate buffer at room temperature. Crystals of the A4 isoform, grown at pH 8.5 in Tris–HCl buffer, diffract to 3.0 Å (at 100 K) using synchrotron radiation. The crystals belong to the orthorhombic C222 space group, with unit-cell dimensions a = 145.9, b = 185.9 and c = 106.3 Å, and probably contain one tetramer per asymmetric unit. Structure determination by molecular replacement is in progress.

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Maloney, Judith A., Oxana M. Tsygankova, Lijun Yang, Qiuyang Li, Agnieszka Szot, Kemal Baysal, and John R. Williamson. "Activation of ERK by Ca2+store depletion in rat liver epithelial cells." American Journal of Physiology-Cell Physiology 276, no. 1 (January 1, 1999): C221—C230. http://dx.doi.org/10.1152/ajpcell.1999.276.1.c221.

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In rat liver epithelial (WB) cells, Ca2+ pool depletion induced by two independent methods resulted in activation of extracellular signal-regulated protein kinase (ERK). In the first method, Ca2+ pool depletion by thapsigargin increased the activity of ERK, even when rise in cytosolic Ca2+ was blocked with the Ca2+ chelator BAPTA-AM. For the second method, addition of extracellular EGTA at a concentration shown to deplete intracellular Ca2+pools also increased ERK activity. In each instance, ERK activation, as measured by an immunocomplex kinase assay, was greatly reduced by the tyrosine kinase inhibitor genistein, suggesting that Ca2+ store depletion increased ERK activity through a tyrosine kinase pathway. The intracellular Ca2+-releasing agent thapsigargin increased Fyn activity, which was unaffected by BAPTA-AM pretreatment, suggesting that Fyn activity was unaffected by increased cytosolic free Ca2+. Furthermore, depletion of intracellular Ca2+ with EGTA caused inactivation of protein phosphatase 2A and protein tyrosine phosphatases. ANG II-induced activations of Fyn, Raf-1, and ERK were augmented in cells pretreated with BAPTA-AM, but ANG II-induced expression of the dual-specificity phosphatase mitogen-activated protein kinase phosphatase-1 was blocked by BAPTA-AM pretreatment. Together these results indicate that ERK activity is regulated by the balance of phosphorylation vs. dephosphorylation reactions in intact cells and that the amount of Ca2+stored in intracellular pools plays an important role in this regulation.

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Uchida, Teruhisa, Takaaki Furubayashi, Toshihiko Nakata, and Mitsuru Matsumoto. "C221 Feasibility study of fuel cell vehicle considering endogenous technological development and exogenous cost change." Proceedings of the National Symposium on Power and Energy Systems 2014.19 (2014): 283–86. http://dx.doi.org/10.1299/jsmepes.2014.19.283.

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TANAKA, Junya, and Toshio SHUDO. "Performance improvement and CO₂ removal behavior in a direct methanol fuel cell with porous flow filed made of sintered metal powder." Proceedings of the National Symposium on Power and Energy Systems 2016.21 (2016): C222. http://dx.doi.org/10.1299/jsmepes.2016.21.c222.

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Trivedi, Mahendra Kumar, Alice Branton, Dahryn Trivedi, and Snehasis Jana. "Elasticity Profile of Skin, Neuronal, Cardiac, and Skeletal Muscle Cells after Treatment with the Biofield Energy Healing-Based Proprietary Test Formulation." Journal of Biotechnology and Biomedical Science 2, no. 4 (July 13, 2021): 19–29. http://dx.doi.org/10.14302/issn.2576-6694.jbbs-21-3819.

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The present study aimed to evaluate the effect of the Trivedi Effect®- Biofield Energy Treated/Blessed Test formulation/item (TI) composed of minerals (magnesium, zinc, copper, calcium, selenium, and iron), vitamins (ascorbic acid, pyridoxine HCl, alpha tocopherol, cyanocobalamin, and cholecalciferol), Panax ginseng extract, CBD isolates, and β-carotene on elasticity of skin, heart, muscle, and neuronal cells in the H9C2 (rat cardiomyocytes), C2C12 (mouse myoblast cells), HaCaT (human keratinocytes), and SH-SY5Y (human neuroblastoma cells) cell line in DMEM medium. The test formulation constituents were divided into two parts; one section was defined as untreated test formulation (UT), while the other portion of test formulation received Biofield Energy Healing/Blessing Treatment (BT) by a renowned Biofield Energy Healer, Mr. Mahendra Kumar Trivedi. The test items were treated with Biofield Energy Healing/Blessing Treatment and divided as Biofield Energy Treated/Blessed (BT) and untreated (UT) test items. MTT data showed that the test formulation in various concentrations was found as safe and nontoxic in the tested concentrations with viability range from 73% to 307%. Young’s modulus (YM) is a measure of cell stiffness, a decrease in YM value indicates increase elasticity of the cells and vice-versa. YM in H9C2 cells were decreased by 9.6% and 66.1% in the BT-DMEM + UT-TI group at 0.1 and 1 µg/mL respectively, as compared with untreated test group. However, C2C21 cells showed increased YM by 443.9% at 1 µg/mL in the UT-DMEM + BT-TI group, while 869.6% increased YM in the BT-DMEM + UT-TI group at 1 µg/mL as compared with untreated test group. However, 314% increased YM was reported in the BT-DMEM + BT-TI group at 1 µg/mL as compared with the untreated test group. However, the value of YM was significantly decreased in the HaCaT cell line by 247.7% (at 1 µg/mL), 225.8% (at 0.1 µg/mL), and 97.9% (at 1 µg/mL) in the UT-DMEM + BT-TI, BT-DMEM + UT-TI, and BT-DMEM + BT-TI group respectively, as compared with the untreated group. In addition, YM was significantly decreased in the SH-SY5Y cell line by 92.6%, 18.1%, and 26.6% at 1 µg/mL in the UT-DMEM + BT-TI, BT-DMEM + UT-TI, and BT-DMEM + BT-TI group respectively, as compared with the untreated group. Overall, the results showed the significant decreased YM among the SH-SY5Y, HaCaT, and H9C2 cells, while it was increased in the C2C21 cell line. Thus, the mechanical properties of cells such as cellular function, including shape, motility, differentiation, division, and adhesion to its surrounding extracellular matrix were improved. Overall, it can be useful in many disease progressions with improved cellular elasticity and its associated complications/symptoms.

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Choi, Woong, Jonghyeon Son, Aekyung Park, Hongshi Jin, Seung Chul Shin, Jun Hyuck Lee, T. Doohun Kim, and Han-Woo Kim. "Identification, Characterization, and Preliminary X-ray Diffraction Analysis of a Single Stranded DNA Binding Protein (LjSSB) from Psychrophilic Lacinutrix jangbogonensis PAMC 27137." Crystals 12, no. 4 (April 11, 2022): 538. http://dx.doi.org/10.3390/cryst12040538.

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Single-stranded DNA-binding proteins (SSBs) are essential for DNA metabolism, including repair and replication, in all organisms. SSBs have potential applications in molecular biology and in analytical methods. In this study, for the first time, we purified, structurally characterized, and analyzed psychrophilic SSB (LjSSB) from Lacinutrix jangbogonensis PAMC 27137 isolated from the Antarctic region. LjSSB has a relatively short amino acid sequence, consisting of 111 residues, with a molecular mass of 12.6 kDa. LjSSB protein was overexpressed in Escherichia coli BL21 (DE3) and analyzed for binding affinity using 20- and 35-mer deoxythymidine oligonucleotides (dT). In addition, the crystal structure of LjSSB at a resolution 2.6 Å was obtained. The LjSSB protein crystal belongs to the space group C222 with the unit cell parameters of a = 106.58 Å, b = 234.14 Å, c = 66.14 Å. The crystal structure was solved using molecular replacement, and subsequent iterative structure refinements and model building are currently under progress. Further, the complete structural information of LjSSB will provide a novel strategy for protein engineering and for the application on molecular biological techniques.

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Hu, Ming, Meili Xie, Xiaobo Cui, Junyan Huang, Xiaohui Cheng, Lijiang Liu, Shunping Yan, Shengyi Liu, and Chaobo Tong. "Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus." Genes 14, no. 7 (July 10, 2023): 1421. http://dx.doi.org/10.3390/genes14071421.

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SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.

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Bannister, P., and A. Memon. "Trends in Incidence of Primary Liver Cancer in the Elderly (Aged 65+ Years) in England, 1971-2010." Journal of Global Oncology 4, Supplement 2 (October 1, 2018): 12s. http://dx.doi.org/10.1200/jgo.18.69000.

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Background: About 45% of the cases of liver cancer in England are diagnosed in the elderly. Since the 1990s, there has been a substantial increase in the incidence of liver cancer, and it has been projected that the incidence of rates will continue to increase to 15/100,000 by 2035. Aim: To determine the trends of incidence of liver cancer in the elderly in England during the period 1971-2010. Methods: Population-based national cancer registration data (obtained from the Office for National Statistics) were analyzed to determine the incidence of liver cancer (ICD-9 code: 155, ICD-10 code: C22) by age, gender, morphologic subtype and level of deprivation. Microsoft Excel and SPSS software were used for the analysis. Results: During the 40-year period, a total of 42,800 cases of liver cancer in the elderly were registered in England (58% male, 42% female). The number of cases increased by 462% - from 2,019 in 1971-75 (404 cases/year) to 11,345 in 2006-10 (2269 cases/year). The incidence rate (per 100,000) increased from 9.0 in 1971-75 to 37.4 in 2006-10 in males (316% increase); and from 4.6 to 19.6 in females (326% increase). In males, the incidence rates of liver cell carcinoma (ICD-10 code: C22.0) increased by 140% and the intrahepatic bile duct carcinoma (ICD-10 code: C22.1) by 2467%; whereas in females the incidence rates increased by 22% and 2260%, respectively. As for level of deprivation, the largest increase in incidence was observed in the least deprived population (721% in males, 690% in females). Conclusion: During the past four decades, there has been a remarkable increase in the incidence of liver cancer in the elderly in England. The relatively large increase in liver cell carcinoma in males, those in the least deprived category, and substantial increase in intrahepatic bile duct carcinoma in both genders warrant further investigation. These findings are also relevant for the planning of oncology services, resource allocation, screening for early diagnosis and public health education for primary prevention of liver cancer.

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Feng, Han-Zhong, and J. P. Jin. "Coexistence of cardiac troponin T variants reduces heart efficiency." American Journal of Physiology-Heart and Circulatory Physiology 299, no. 1 (July 2010): H97—H105. http://dx.doi.org/10.1152/ajpheart.01105.2009.

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Corresponding to the synchronized contraction of the myocardium and rhythmic pumping function of the heart, a single form of cardiac troponin T (cTnT) is present in the adult cardiac muscle of humans and most other vertebrate species. Alternative splicing variants of cTnT are found in failing human hearts and animal dilated cardiomyopathies. Biochemical analyses have shown that these cTnT variants are functional and produce shifted myofilament Ca2+ sensitivity. We proposed a hypothesis that the coexistence of two or more functionally distinct TnT variants in the adult ventricular muscle that is normally activated as a syncytium may decrease heart function and cause cardiomyopathy (Huang et al., Am J Physiol Cell Physiol 294: C213–C222, 2008). In the present study, we studied transgenic mouse hearts expressing one or two cTnT variants in addition to normal adult cTnT to investigate whether desynchronized myofilament activation decreases ventricular efficiency. The function of ex vivo working hearts was examined in the absence of systemic neurohumoral influence. The results showed that the transgenic mouse hearts produced lower maximum left ventricular pressure, slower contractile and relaxation velocities, and decreased stroke volume compared with wild-type controls. Ventricular pumping efficiency, calculated by the ejection integral versus total systolic integral and cardiac work versus oxygen consumption, was significantly lower in transgenic mouse hearts and corresponded to the number of cTnT variants present. The results indicated a pathogenic mechanism in which the coexistence of functionally different cTnT variants in cardiac muscle reduces myocardial efficiency due to desynchronized thin filament activation.

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Adorante, Joseph S., and Jeffrey L. Edelman. "Letters to the Editor." American Journal of Physiology-Cell Physiology 273, no. 4 (October 1, 1997): C1435—C1436. http://dx.doi.org/10.1152/ajpcell.1997.273.4.c1435.

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The following is the abstract of the article discussed in the subsequent letter: Mitchell, Claire H., Jin Jun Zhang, Liwei Wang, and Tim J. C. Jacob. Volume-sensitive chloride current in pigmented ciliary epithelial cells: role of phospholipases. Am. J. Physiol. 272 ( Cell Physiol. 41): C212–C222, 1997.—The whole cell recording technique was used to examine an outwardly rectifying chloride current activated by hypotonic shock in bovine pigmented ciliary epithelial (PCE) cells. Removal of internal and external Ca2+ did not affect the activation of these currents, but they were abolished by the phospholipase C inhibitor neomycin. The current was blocked by 5-nitro-2-(3-phenylpropylamino)benzoic acid, 4-acetamido-4′-isothiocyanostilbene-2,2′-disulfonic acid, and 4,4′-diisothiocyanostilbene-2,2′-disulfonic acid (DIDS) in a voltage-dependent manner, but tamoxifen, dideoxyforskolin, and quinidine did not affect it. This blocking profile differs from that of the volume-sensitive chloride channel in neighboring nonpigmented ciliary epithelial cells (Wu, J., J. J. Zhang, H. Koppel, and T. J. C. Jacob. J. Physiol. Lond. 491: 743–755, 1996), and this difference implies that the volume responses of the two cell types are mediated by different chloride channels (Jacob, T. J. C., and J. J. Zhang. J. Physiol. Lond. In press). Intracellular administration of guanosine 5′- O-(3-thiotriphosphate) (GTPγS) to PCE cells induced a transient, time-independent, outwardly rectifying chloride current that closely resembled the current activated by hypotonic shock. DIDS produced a voltage-dependent block of the GTPγS-activated current similar to the block of the hypotonically activated current. Intracellular neomycin completely prevented activation of this current as did incubation of the cells in calphostin C, an inhibitor of protein kinase C (PKC). Removal of Ca2+ did not affect activation of the current by GTPγS but extended the duration of the response. Inhibition of phospholipase A2 (PLA2) with p-bromophenacyl bromide prevented the activation of the hypotonically induced current and also inhibited the current once activated by hypotonic solution. The findings imply that the hypotonic response in PCE cells is mediated by both phospholipase C (PLC) and PLA2. Both phospholipases generate arachidonic acid, and, in addition, the PLC pathway regulates the PLA2 pathway via a PKC-dependent phosphorylation of PLA2.

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Das, Debanu, Fumiaki Yumoto, Kristopher Kuchenbecker, Ashley Deacon, Robert Fletterick, and Ian Wilson. "Understanding disease mutations from the crystal structure of SOX9 with DNA." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1398. http://dx.doi.org/10.1107/s205327331408601x.

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SRY(Sex determining Region Y)-box or SOX transcription factors are important in early development and maintenance of different cell pools after birth. Of the ~20 SOX proteins (SRY, SOX1-SOX15, SOX17, SOX18, SOX21 and SOX30), SOX2, SOX9 and SOX10 mutations are primarily disease-associated: SOX2 with Combined Pituitary Hormone Deficiency, Microphthalmia, Septo-optic dysplasia and anophthalmic syndrome; SOX9 with Campomelic Dysplasia (affects development of the reproductive and skeletal system); and SOX10 (~94% sequence identity to SOX9) with Waardenburg Syndrome (affects audition and pigmentation in hair, eyes and skin; and specifically with WS types 2 and 4). As part of our Protein Structure Initiative (PSI)-Biology partnership, we performed structural and mutational analyses including x-ray crystallography and surface plasmon resonance assays, on the DNA-binding HMG domain of SOX9 with duplex DNA. Crystals were obtained in C222 space group and the structure was determined by molecular replacement to 2.77 Å resolution with final Rcryst/Rfree of 24.8/27.8%. The overall structure of the SOX9-DNA complex is similar to other SOX/SRY protein complexes. The SOX9-DNA protein-DNA interactions suggested a panel of mutations to assay for biochemical activity, which allowed us to understand the molecular basis of five mutations identified in Campomelic Dysplasia. These mutated residues have direct contact with DNA as well as indirect contacts, i.e., these mutations lead to allosteric secondary structure changes in the protein, which affect residues in direct contact with DNA. Due to the very high sequence identity between SOX9 and SOX10, our crystal structure also helps to rationalize the effect of SOX10 mutations in Waardenburg Syndrome. This work is supported by NIH grants U54 GM094586 and U01 GM094614. SSRL operations are funded by DOE BES, and the SSRL SMB program by DOE BER, NIH NCRR BTP and NIH NIGMS.

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Jeong, Yoon Chae, and Ki Seog Lee. "Overexpression, purification, crystallization and preliminary X-ray crystallographic characterization of the receiver domain of the response regulator PhoP from Enterococcus faecalis ATCC 29212." Applied Biological Chemistry 62, no. 1 (November 7, 2019). http://dx.doi.org/10.1186/s13765-019-0473-x.

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Abstract Phosphate (Pho) regulon plays a critical role in bacterial phosphate homeostasis. It is regulated by two-component system (TCS) that comprises a sensor histidine kinase and transcriptional response regulator (RR). PhoP from Enterococcus faecalis (EfPhoP) belongs to the OmpR subfamily of RRs. It has not yet been structurally characterized because it is difficult to crystallize it to full-length form. In this study, a truncated form of EfPhoP containing the receiver domain (EfPhoP-RD) was constructed, purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. The crystal of EfPhoP-RD diffracted to 3.5 Å resolution and belonged to the orthorhombic space group C2221, with unit-cell parameters a = 118.74, b = 189.83, c = 189.88 Å. The asymmetric unit contains approximately 12 molecules, corresponding to a Matthews coefficient (Vm) of 2.50 Å3 Da−1 with a solvent content of 50.9%.

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Li, Ting, Guang Fan, Xiangkun Ge, Tao Wang, Apeng Yu, and Liumin Deng. "Crystal Structure of Tengchongite with a Revised Chemical Formula Ca(UO2)6(MoO4OH)2O2(OH)4·9H2O." Canadian Mineralogist, April 18, 2022. http://dx.doi.org/10.3749/canmin.2000127.

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ABSTRACT Tengchongite, a uranyl molybdate mineral from Tengchong County, Yunnan Province, China, was originally described as orthorhombic, with space group A2122, unit-cell parameters a = 15.616(4) Å, b = 13.043(6) Å, c = 17.716(14) Å, V = 3608 Å3, and an ideal chemistry CaO·6UO2·2MO3·12H2O. Its ideal chemical formula is given as Ca(UO2)6(MoO4)2O5·12H2O in the current IMA-CNMNC List of Mineral Names. Tengchongite is the only mineral with a U:Mo ratio of 3:1, the second-highest ratio of all natural and synthetic uranyl molybdate materials, but its crystal structure remained undetermined until now. This study reports the structure determination of tengchongite from the type sample and a revision of its chemical formula to Ca(UO2)6(MoO4OH)2O2(OH)4·9H2O. Tengchongite is orthorhombic, with space group C2221, Z = 4, a = 13.0866(8) Å, b = 17.6794(12) Å, c = 15.6800(9) Å, and V = 3627.8(4) Å3. Its crystal structure was refined from single-crystal X-ray diffraction data to R1 = 0.0323 for 6055 unique observed reflections. The fundamental building blocks of the tengchongite structure are sheets consisting of six-membered clusters of edge-sharing UO7 pentagonal bipyramids, which are connected by sharing vertices among them, as well as edges and vertices with MoO5 trigonal bipyramids. These sheets, parallel to [010], are linked together by Ca2+ and H2O groups. Tengchongite represents a new type of structural connectivity between U- and Mo-polyhedra for uranyl molybdate minerals.

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Vincent, John, Kyle Edwards, Courtney Petersen, Nathaniel Gilbert, and Matthew Thompson. "X-ray Crystal Structure of Dichromium-transferrin with Synergistic Anion Malonate (P24-061-19)." Current Developments in Nutrition 3, Supplement_1 (June 1, 2019). http://dx.doi.org/10.1093/cdn/nzz044.p24-061-19.

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Abstract Objectives Transferrin, Tf, the protein that transports iron, as Fe(III) from the blood to the tissues via endocytosis, is believed to also transport chromium(III), Cr(III). Under physiological conditions, transferrin binds Fe(III) and Cr(III), but can bind other metal ions such as titanium(IV), Ti(IV), such as in the blood of patients with Ti-containing implants. Questions have arisen whether similar protein and non-protein ligands are bound to the alternative metal ions in transferrin. Methods Human serum Cr(III)2-Tf was prepared in a buffered solution at pH 7.4 containing 25 mM bicarbonate at 37°C. The hanging drop vapor diffusion method was used for crystallization. The crystallization conditions contained 100 mM Hepes (pH 7.0, 20 mM disodium malonate, 14% PEG3350, 20% glycerol, and 55 mg/mL transferrin. Results Cr(III)2-Tf crystallized in the space group C2221 with unit cell dimensions a = 137.05 Å, b = 158.01 Å, and c = 107.14 Å and α = β = γ = 90°. The C-terminal lobe is in the closed confirmation, while the N-terminal lobe is in the open confirmation. The C-terminal metal-binding site has four protein-provided ligands (two tyrosines, one histidine, and one aspartate) to the Cr(III) center, while six coordination is completed by two oxygens from a malonate anion. Thus, under the crystallization conditions, malonate displaces `the synergistic bicarbonate anion normally at the metal-binding site. The N-terminal metal binding site possesses only one protein-provided ligand (tyrosine) while the other binding sites about the Cr(III) center are filled by a (bi)carbonate anion and water molecules. Conclusions Under the conditions of crystallization, the C-terminal lobe of transferrin binds Cr(III) in a similar fashion to Fe(III) and Ti(IV), although the ligation at the N-terminal binding site varies. These similarities and differences in coordination have implications for the relative ability of transferrin to bind and release Fe, Cr, and Ti. Funding Sources The University of Alabama College of Arts and Sciences Research Award.

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Zhou, Yanting, Xiandeng Li, Peifang Luo, Huiting Chen, Yan Zhou, Xueting Zheng, Yuan Yin, et al. "Identification of abemaciclib derivatives targeting cyclin-dependent kinase 4 and 6 using molecular dynamics, binding free energy calculation, synthesis, and pharmacological evaluation." Frontiers in Pharmacology 14 (May 10, 2023). http://dx.doi.org/10.3389/fphar.2023.1154654.

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CDK4/6 plays a crucial role in various cancers and is an effective anticancer drug target. However, the gap between clinical requirements and approved CDK4/6 drugs is unresolved. Thus, there is an urgent need to develop selective and oral CDK4/6 inhibitors, particularly for monotherapy. Here, we studied the interaction between abemaciclib and human CDK6 using molecular dynamics simulations, binding free energy calculations, and energy decomposition. V101 and H100 formed stable hydrogen bonds with the amine-pyrimidine group, and K43 interacted with the imidazole ring via an unstable hydrogen bond. Meanwhile, I19, V27, A41, and L152 interacted with abemaciclib through π-alkyl interactions. Based on the binding model, abemaciclib was divided into four regions. With one region modification, 43 compounds were designed and evaluated using molecular docking. From each region, three favorable groups were selected and combined with each other to obtain 81 compounds. Among them, C2231-A, which was obtained by removing the methylene group from C2231, showed better inhibition than C2231. Kinase profiling revealed that C2231-A showed inhibitory activity similar to that of abemaciclib; additionally, C2231-A inhibited the growth of MDA-MB-231 cells to a greater extent than did abemaciclib. Based on molecular dynamics simulation, C2231-A was identified as a promising candidate compound with considerable inhibitory effects on human breast cancer cell lines.

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Guaitarilla, David Alejandro, Juan Pablo Ortiz-Pérez, Jhon Jairo Calderón-Leytón, Miguel A. Gómez-Martínez, Carlos Mauricio Trujillo-Torres, and Ronald A. Fernández. "Vocalizaciones asociadas al comportamiento colonial de Cacicus chrysonotus leucoramphus (Icteridae) en Colombia." Biota Colombiana 22, no. 1 (January 1, 2021). http://dx.doi.org/10.21068/c2021.v22n01a09.

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Con el objetivo de evaluar la asociación entre las vocalizaciones y los comportamientos del cacique montano norteño (Cacicus chrysonotus leucoramphus), se tomaron registros acústicos y conductuales de la especie en cuatro localidades de los Andes de Nariño, en el sur de Colombia. Se registraron seis tipos de vocalizaciones asociadas a por lo menos una de las tres categorías conductuales identificadas (vigilancia, alerta y defensa territorial), y una vocalización registrada en un único evento de cortejo. Vocalizaciones con valores más altos de ancho de banda y modulación de frecuencia resultaron asociadas a defensa territorial, mientras que vocalizaciones con valores bajos de ancho de banda y poca modulación cumplieron funciones de vigilancia y alerta. Los resultados indican similitudes en el comportamiento vocal y social con respecto a estudios en otras especies como Cacicus cela y Cacicus haemorrhous. C. c. leucoramphus utiliza vocalizaciones específicas en un determinado contexto conductual, pudiendo algunas de ellas ser reutilizadas en varios comportamientos. Este estudio describe por primera vez el contexto social en el que se asocian las vocalizaciones y conductas en esta especie.

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Zuk, Anna Karolina, Anna Karolina Zuk, Beata Burczynska, Dong Li, Lucy Ghali, Stephen Dilworth, and Xuesong Wen. "Modelling and Validating Three-Dimensional Human Breast and Cancerous Human Breast Tissues In Vitro." Clinical Oncology and Research, April 21, 2020, 1–9. http://dx.doi.org/10.31487/j.cor.2020.04.05.

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In this study three dimensional (3-D) in vitro models of normal breast and breast cancer tissues were developed to mimic closely the in vivo tissue microenvironment and therefore providing reliable models for in vitro studies as well as testing of novel cancer therapies. Normal and cancerous human breast cell lines were used to construct 3-D artificial tissues, where de-epidermalised dermis (DED) was used as a scaffold for both models. Morphological analyses were conducted using haematoxylin and eosin staining. Biomarkers including keratin 5 and 19 as well as α smooth muscle actin and mucin 1 were used to confirm and validate the reliability of the proposed models using immunohistochemical techniques. Findings suggest that the 3-D in vitro models described in this work can serve as functional models of both human normal and cancerous breast tissues. Multiple structures similar to ducts and lobules of human breast in vivo were observed in 3-D in vitro models by the use of H&E, some breast cancer colonies seen in the cancerous 3-D model were similar to the ducto-lobular structures observed in normal 3-D model of the breast but the former cells were more loosely connected, irregular and largely disorganized. The established 3-D in vitro model of normal breast showed the development of ducto-lobular structures composed of an inner cell layer which was stained positive with α mucin 1 antibody, a biomarker that is characteristic for luminal cells; and also an outer basal layer of cells that was stained positive for α smooth muscle actin, a biomarker of myoepithelial cells.. Keratin staining in 3-D in vitro models also resembled the pattern observed in vivo where keratin 5 was detected in both luminal and myoepithelial cells of normal breast model (NTERT cells), whereas keratin 19 was present in breast cancer model (C2321 cells). These 3-D models successfully recapitulate both normal and pathological tissue architecture of breast tissue and has the potential for various applications in the evaluation of breast cancer progression and treatment.

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Journal articles on the topic 'C2221 cell'

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