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W J Cook

Publications and source records attributed to W J Cook.

At least 73 records · Page 4Linked to original sources
PubMed1990

Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution.

The three-dimensional structure of thymidine phosphorylase from Escherichia coli has been determined at 2.8 A resolution using multiple-isomorphous-replacement techniques. The amino acid sequence deduced from the deoA DNA sequence is also reported. Thymidine phosphorylase exists in the crystal as an S-shaped dimer in which the subunits are related by a crystallographic 2-fold axis. Each subunit is composed of a small alpha-helical domain of six helices and a large alpha/beta domain. The alpha/beta domain includes a six-stranded mixed beta-sheet and a four-stranded antiparallel beta-sheet. The active site has been identified by difference Fourier analyses of the binding of thymine and thymidine and lies in a cavity between the small and large domains. The central beta-sheet is splayed open to accommodate a putative phosphate-binding site which is probably occupied by a sulfate ion in the crystal.

Amino Acid Sequence↗
PubMed1990

Crystallization and preliminary X-ray investigation of recombinant Lactobacillus leichmannii nucleoside deoxyribosyltransferase.

Crystals of recombinant bacterial nucleoside deoxyribosyltransferase have been grown from solutions of ammonium sulfate. The crystals are cubic, space group I23 or I2(1)3; the axial length is 151.1(2) A. The crystals are stable to x-rays for at least 5 days and diffract beyond 2.8-A resolution. It appears that the molecule, which is a hexamer, utilizes the symmetry of the space group, resulting in two or three subunits per asymmetric unit.

Chromatography, Gel↗
PubMed1990

Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution.

The three-dimensional structure of human erythrocytic purine nucleoside phosphorylase has been determined at 3.2 A resolution using x-ray diffraction data. Intensity data were measured using radiation from the Synchrotron Radiation Source, Daresbury, England, and oscillation film techniques. Phases were determined by using multiple isomorphous replacement methods with four heavy-atom derivatives and were improved using solvent flattening techniques. Purine nucleoside phosphorylase exists in the crystal as a trimer in which subunits are related by a crystallographic 3-fold axis. Each subunit contains an eight-stranded mixed beta-sheet and a five-stranded mixed beta-sheet which join to form a distorted beta-barrel structure. This core beta-structure is flanked by seven alpha-helices in a manner that generates a novel folding pattern. The active site, which was characterized from binding of the substrate analogs 8-iodoguanine and 5'-iodoformycin B, is located near the subunit-subunit boundary within the trimer and involves seven different segments from one subunit and an additional short segment from an adjacent subunit. In the crystal, the phosphate-binding site is probably occupied by a sulfate ion. The specificity of purine nucleoside phosphorylase for guanine, hypoxanthine, and their analogs can be explained on the basis of the arrangement of hydrogen bond donors and acceptors in the active site.

Amino Acid Sequence↗
PubMed1990

Crystallization and preliminary x-ray investigation of recombinant human granulocyte-macrophage colony-stimulating factor.

Crystals of recombinant human granulocyte-macrophage colony-stimulating factor have been grown from solutions of polyethylene glycol 8000. The crystals are orthorhombic, space group P2(1)2(1)2(1); the axes are a = 45.5(1), b = 58.7(1) and c = 127.3(1) A. The crystals are stable to x-rays for at least 3 days and diffract beyond 2.8-A resolution. Although the molecule exists as a monomer in solution, it crystallizes with two or three molecules in the asymmetric unit.

Chemical Phenomena↗
PubMed1988

Structure of calmodulin refined at 2.2 A resolution.

The crystal structure of mammalian calmodulin has been refined at 2.2 A (1 A = 0.1 nm) resolution using a restrained least-squares method. The final crystallographic R-factor, based on 6685 reflections in the range 2.2 A less than or equal to d less than or equal to 5.0 A with intensities exceeding 2.5 sigma, is 0.175. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.7 degrees, respectively. The refined model includes residues 5 to 147, four Ca2+ and 69 water molecules per molecule of calmodulin. The electron density for residues 1 to 4 and 148 is poorly defined, and they are not included in the model. The molecule is shaped somewhat like a dumbbell, with an overall length of 65 A; the two lobes are connected by a seven-turn alpha-helix. Prominent secondary structural features include seven alpha-helices, four Ca2+-binding loops, and two short, double-stranded antiparallel beta-sheets between pairs of adjacent Ca2+-binding loops. The four Ca2+-binding domains in calmodulin have a typical EF hand conformation (helix-loop-helix) and are similar to those described in other Ca2+-binding proteins. The X-ray structure determination of calmodulin shows a large hydrophobic cleft in each half of the molecule. These hydrophobic regions probably represent the sites of interaction with many of the pharmacological agents known to bind to calmodulin.

Amino Acid Sequence↗
PubMed1988

Crystallization and preliminary X-ray analyses of two neuraminidases from influenza B virus strains B/Hong Kong/8/73 and B/Lee/40.

Crystals of neuraminidase heads from two different influenza B virus strains have been grown. Neuraminidase crystals of influenza B/Hong Kong/8/73 were grown from solutions of potassium phosphate. The crystals are tetragonal prisms, space group I422; the axes are a = 123 A and c = 165 A. Influenza B/Lee/40 neuraminidase crystals were grown from solutions of polyethylene glycol 4000. The crystals are tetragonal pyramids, space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2; the axes are a = 125 A and c = 282 A.

Crystallization↗
PubMed1987

Crystallization and preliminary x-ray investigation of sarcoplasmic calcium-binding protein from Nereis diversicolor.

Crystals of sarcoplasmic calcium-binding proteins from Nereis diversicolor have been grown from solutions of ammonium sulfate. The crystals are monoclinic, space group P2(1); the axes are a = 43.65 (1), b = 56.05 (1), c = 65.77 (1) A, and beta = 92.58 (2) degrees. The crystals are quite stable to x-rays and diffract beyond 2.5 A resolution. The asymmetric unit contains two protein molecules.

Animals↗
PubMed1987

Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin.

The crystal structure of human ubiquitin has been solved by x-ray diffraction methods and refined by standard procedures to a conventional crystallographic R factor of 0.176 at 1.8-A resolution (Vijay-Kumar, S., Bugg, C.E., and Cook, W.J. (1987) J. Mol. Biol. 194, 525-538). Crystals of yeast and oat ubiquitin have been grown using human ubiquitin crystals as seeds. Diffraction data for yeast and oat ubiquitin have been collected to a resolution of 1.9 and 1.8 A, respectively. Difference Fourier electron-density maps reveal that the structures of yeast and oat ubiquitin are quite similar to human ubiquitin. All the amino acid changes are clustered in two small patches on one surface of the molecule. This surface is probably not involved in conjugation with proteins destined for ATP-dependent proteolysis.

Computer Simulation↗
PubMed1987

Structure of ubiquitin refined at 1.8 A resolution.

The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.5 degrees, respectively. A total of 58 water molecules per molecule of ubiquitin are included in the final model. The last four residues in the molecule appear to have partial occupancy or large thermal motion. The overall structure of ubiquitin is extremely compact and tightly hydrogen-bonded; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns.

Amino Acid Sequence↗
PubMed1987

Crystallization and preliminary x-ray investigation of thymidine phosphorylase from Escherichia coli.

Crystals of thymidine phosphorylase from Escherichia coli have been grown from solutions of ammonium sulfate. The crystals are tetragonal, space group P4(1)2(1)2 or P4(3)2(1)2; the axes are a = 132.0 (1) and c = 67.2 (1) A. The crystals are quite stable to x-rays and diffract beyond 2.6-A resolution. The molecule is a dimer and utilizes the 2-fold symmetry of the space group, resulting in one subunit per asymmetric unit.

Escherichia coli↗
PubMed1987

Crystallization and preliminary X-ray investigation of uridine phosphorylase from Escherichia coli.

Crystals of uridine phosphorylase from Escherichia coli K12 have been grown from solutions of polyethylene glycol 4000. The crystals are trigonal, space group R3; the hexagonal axes are a = 154.4 A and c = 49.4 A. The crystals are quite stable to x-rays and diffract beyond 2.6 A resolution. It appears that the molecule is a hexamer with a subunit molecular weight of 27,500 and utilizes the 3-fold symmetry of the space group, resulting in two subunits/asymmetric unit.

Crystallization↗
PubMed1985

Crystallization and preliminary x-ray investigation of purine-nucleoside phosphorylase from Escherichia coli.

Crystals of purine-nucleoside phosphorylase from Escherichia coli have been grown from solutions of ammonium sulfate. The crystals are hexagonal with space group P6(1)22 or P6(5)22; the axes are alpha = 106.5 A and c = 241.3 A. The crystals are moderately stable to x-rays and diffract beyond 3.0-A resolution. It appears that the molecule, which is a hexamer, utilizes the 2-fold symmetry of the space group, resulting in three subunits/asymmetric unit.

Chemical Phenomena↗
PubMed1985

Three-dimensional structure of ubiquitin at 2.8 A resolution.

The three-dimensional structure of ubiquitin has been determined at 2.8 A resolution. X-ray diffraction data for the native protein and derivatives were collected with an automated diffractometer. Phases were obtained by use of a single isomorphous mercuric acetate derivative. The molecule contains a pronounced hydrophobic core. Prominent secondary structural features include three and one-half turns of alpha-helix, a mixed beta-sheet that contains four strands, and seven reverse turns. The histidine, tyrosine, and two phenylalanine residues are located on the surface of the molecule.

Amino Acid Sequence↗
PubMed1985

Crystal structure and conformation of the cyclic tetramer of a repeat tripeptide of elastin, cyclo(L-valyl-L-prolylglycyl)4.

X-ray diffraction data were used to determine the crystal structure of cyclo-(L-Val-L-Pro-Gly)4, the cyclic tetramer of a repeat tripeptide of elastin. The crystals are monoclinic, space group C2, with a = 29.639(3), b = 7.099(1), c = 20.325 (2) A, and beta = 130.4(4) degrees. The structure was solved by direct methods and refined by least squares to R = 0.082 for 2603 observed reflections. The cyclic dodecapeptide contains two beta (II) turns. Hydrophilic and hydrophobic channels that run parallel to the b axis are formed by the stacking of cyclic peptides on twofold axes.

Amino Acid Sequence↗
PubMed1984

Preliminary X-ray investigation of variant-2 scorpion toxin from Centruroides sculpturatus Ewing. Evidence of a reversible transition between crystal forms.

Crystals of Variant-2 scorpion toxin have been grown using seeding techniques from 30% 2-methyl-2,4-pentanediol at pH 9.2 and T = 4 degrees C. These crystals display a temperature-dependent, reversible phase transition near room temperature. The apparent space group for the high-temperature form is P3121 or P3221 with a = 48.8(1) A and c = 43.7(1) A, and with one molecule per asymmetric unit. At lower temperature, the crystals undergo a phase transition in which the space group remains the same but with c' (approximately equal to 2c) = 86.1(1) A. In addition, the low-temperature form displays several weak, diffuse reflections that correspond to a tripling of the a axis. The high-temperature form diffracts beyond 1.8-A resolution and appears to be suitable for a complete structural study.

Animals↗
PubMed1984

Crystallization and preliminary X-ray investigation of acid protease from Cladosporium.

Crystals of Cladosporium acid protease have been grown from solutions of polyethylene glycol. The crystals are orthorhombic, space group, P212121, with alpha = 136.5(7) A, b = 109.4(5) A, and c = 87.7(4) A. There are four acid protease molecules/asymmetric unit. The crystals are quite stable to x-rays and diffract beyond 3.0-A resolution.

Aspartic Acid Endopeptidases↗