Biomedical subjects

C E Bugg

Publications and source records attributed to C E Bugg.

At least 55 records · Page 3Linked to original sources

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↗

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 a protein neurotoxin from the sea anemone Anthopleura xanthogrammica.

Neurotoxic protein AX-I isolated from the sea anemone Anthopleura xanthogrammica has been crystallized. Two crystal forms were obtained. One form is tetragonal, space group P41 or P43 , with cell dimensions a = b = 40.74(2) A and c = 34.13(3) A. The second crystal form is hexagonal, space group P622 , with cell dimensions a = b = 72.23(2) A and c = 39.16(2)A. Density measurements indicate that the tetragonal crystals contain one toxin molecule/asymmetric unit. Both crystal forms diffract to high resolution.

Animals↗

PubMed1984

Aggregation patterns of bile salts: crystal structure of calcium cholate chloride heptahydrate.

Crystals of calcium cholate chloride heptahydrate, CaC24H39O7Cl . 7H2O, are monoclinic, space group P2(1), with a = 11.918(2), b = 8.636(1), c = 15.302(3) A, beta = 97.93(3) degrees, V = 1559.9(8) A3, and Z = 2. A trial structure was obtained by Patterson and Fourier techniques and was refined by full-matrix least-squares calculations using absorption corrected CuK-alpha diffractometer data. The final R index is 0.047. The crystal structure contains bilayer-type arrangements, with hydrophobic portions of cholate rings sandwiched between layers of polar groups that are interacting with calcium ions and water molecules. The calcium ion is coordinated to five water molecules and to the two carboxylate oxygen atoms of the cholate residue. Two additional water molecules are involved only in crystal packing through the formation of hydrogen bonds. Cholate-cholate hydrophobic interactions involve contacts between the hydrocarbon portions of the carboxylate sidechains and the A and B rings. This results in a staggered packing pattern that is nearly identical to that found in crystals of sodium cholate and rubidium deoxycholate. Similar bilayer aggregation patterns may also be involved in the formation of bile salt micelles in aqueous media. The characteristic bilayer packing arrangement can accommodate a variety of cation-binding patterns, as evidenced by the finding that calcium, sodium, and rubidium ions interact with the polar faces of the bilayers in different ways. The carboxylate sidechain displays two different conformations in the crystal structure of calcium cholate chloride heptahydrate. Variation in sidechain conformation may be of importance in the adjustment required to accommodate different cation coordination schemes.

Bile Acids and Salts↗

PubMed1983

Structure of variant-3 scorpion neurotoxin from Centruroides sculpturatus Ewing, refined at 1.8 A resolution.

The three-dimensional structure of the variant-3 protein neurotoxin from the scorpion Centruroides sculpturatus Ewing has been determined by X-ray diffraction data. The initial model for the 65-residue protein was obtained at 3 A resolution by multiple-isomorphous-replacement methods. The structure was refined at 1.8 A resolution by restrained difference-Fourier methods, and by free-atom, block-diagonal least-squares. Considering the 4900 reflections for which d = 1.8-7 A and Fo greater than 2.5 sigma (Fo), the final R-index is 0.16 for the restrained model, and 0.14 for the free-atom model. Average estimated errors in atomic co-ordinates are about 0.1 A. The refined structure includes 492 protein atoms; one molecule of 2-methyl-2,4-pentanediol, which is tightly bound in a hydrophobic pocket on the surface of the protein; and 72 additional solvent sites. The major secondary structural features are two and a half turns of alpha-helix and a three-strand stretch of antiparallel beta-sheet. The helix is connected to the middle strand of the beta-sheet by two disulfide bridges, and a third disulfide bridge is located nearby. Several loops extend out of this dense core of secondary structure. The protein displays several reverse turns and a highly contorted proline-rich, COOH-terminal segment. One of the proline residues (Pro59) assumes a cis-conformation. The structure involves 44 intramolecular hydrogen bonds. The crystallographic results suggest two major corrections in the published primary structure; one of these has been confirmed by new chemical sequence data. The protein displays a large flattened surface that contains a high concentration of hydrophobic residues, along with most of the conserved amino acids that are found in the scorpion neurotoxins.

Amino Acid Sequence↗

PubMed1983

The three dimensional structure of sheep liver 6-phosphogluconate dehydrogenase at 2.6 A resolution.

The three-dimensional structure of sheep liver 6-phosphogluconate dehydrogenase has been determined at 2.6 A resolution by X-ray crystallographic studies. The amino acid sequence of the enzyme is now known and can be fitted to a modified electron density map. Use of 6 A electron density maps and the results of chemical modification experiments allows description of the active site and identification of residues which may be implicated in the binding of co-enzyme and substrate.

Animals↗

PubMed1983

NMR studies of the variant-3 neurotoxin from Centruroides sculpturatus Ewing.

We report a preliminary high-resolution proton nuclear magnetic resonance characterization of the variant-3 toxin from the scorpion Centruroides sculpturatus Ewing (range Southwestern USA). This toxin assumes a well defined folded conformation in aqueous solutions at room temperature and undergoes reversible thermal denaturation. A number of amide hydrogens exhibit exchange life times varying from several minutes to several hours. A few tentative assignments of the low field aromatic CH resonances has been made on the basis of 2D-COSY and NOE experiments. The upfield shifts exhibited by Trp-47 suggest a unique microenvironment for this residue. The NMR data suggest that there is some degree of correlation between the solution structure of the variant-3 toxin and its crystallographic structure. Our studies provide a basis for a detailed elucidation of the structure-function relationships of these interesting scorpion toxins which bind to the sodium channels of excitable membranes and delay sodium current inactivation.

Amino Acid Sequence↗

PubMed1982

The crystal structure of pea lectin at 6-A resolution.

The three-dimensional crystal structure of the mitogenic lectin from the green pea (Pisum sativum) has been determined at 6-A resolution by x-ray diffraction methods. Pea lectin was isolated by use of affinity chromatography and was crystallized from polyethylene glycol solutions. Crystals of pea lectin are orthorhombic, space group P212121, and diffract to at least 1.2-A resolution. The unit cell dimensions are a = 50.85(5), b = 61.23(5), and c = 137.3(2) A. The calculated mass of protein per asymmetric unit is 49,000 daltons, and the crystals are 44% solvent by volume. There are two pea lectin monomers per crystallographic asymmetric unit. Diffractometer data were collected from a native crystal and from a single site uranyl heavy atom derivative crystal. The position of the uranium atom, determined from three-dimensional Patterson maps, was refined by least squares techniques (R index - 0.46 for centric data). A three-dimensional electron density map was calculated by use of phases determined by isomorphous-replacement and anomalous-dispersion contributions. The boundaries of the pea lectin molecule are clearly visible in the map. The molecule appears to be a dimer, roughly peanut-shaped, formed by the close association of the two monomer units. In shape and size, it bears a striking resemblance to the concanavalin A dimer, in which monomers combine to form a dimer-wide contiguous antiparallel pleated sheet.

Chromatography, Affinity↗

PubMed1982

The three-dimensional structure of scorpion neurotoxins.

The crystal and molecular structure of a toxin from the scorpion Centruroides sculpturatus has been solved by standard x-ray crystallographic methods at 3 A resolution. Subsequently the 3 A model has been refined and the resolution has been extended to 1.8 A using the gradient-curvature method. The final reliability index of 0.17 The structure has two and a half turns of alpha-helix, a three-strand stretch of antiparallel beta-sheet and several beta-turns. Three of the four disulfide bridges are found in close interaction with the alpha-helix and beta-sheet structures in what constitutes a very rigid part of the molecule. Examination of available scorpion toxin sequences reveals several sections containing invariant and/or semiinvariant amino acids. Many of these residues are found clustered on a rather large flat surface which is also clearly more hydrophobic than other areas on the molecule. These observations suggest that this surface may play a role in the biological action of scorpion toxins. Secondary structure predictions calculated using the method of Dufton and Hider agree well with the x-ray structure. This is also true for other scorpion toxins and reinforces the idea that scorpion toxins are a family of structurally related proteins.

Amino Acid Sequence↗

PubMed1981

Conformational flexibility in single-stranded oligonucleotides: crystal structure of a hydrated calcium salt of adenylyl-(3'--5')-adenosine.

The crystal and molecular structure of a hydrated calcium salt of adenylyl-(3'--5')-adenosine(ApA) was determined from X-ray diffraction data collected on an automated diffractometer. Crystals of the salt are orthorhombic, space group P21212, with a = 30.614 (3), b = 17.894 (2), and c = 5.373 (1) A. The structure was solved by a combination of Patterson and direct methods and refined by least squares. The final value of the R index is 0.08. The 5'-terminal adenosine residue has a C(2')-endo ribose and assumes a syn conformation, which is stabilized by an O(5')-H...N(3) hydrogen bond within the nucleoside. The 3'-terminal nucleoside has a C(3')-endo ribose and is in the anti conformation. Both omega and omega', the torsion angles within the phosphodiester group, are approximately 60 degrees. Adenine bases from adjacent anions are joined by pairs of N(6)-H...N(1) hydrogen bonds and are stacked with symmetry-related bases. The calcium ion is bound to the dinucleoside phosphate by a direct interaction with the phosphate group and by outer-sphere, ligand-mediated interactions with O(2') of the 5'-terminal nucleoside and N(7) of the 3'-terminal nucleoside. This tridentate interaction of the ApA anion with the calcium coordination sphere probably enhances the stability of the observed ApA conformation. When combined with other crystallographic studies of ApA conformations, the crystal structure of this calcium salt provides additional evidence that dinucleoside phosphates have considerable conformational flexibility.

Adenosine Monophosphate↗

PubMed1981

Crystallization and preliminary X-ray investigation of human erythrocytic purine nucleoside phosphorylase.

Crystals of human erythrocytic purine nucleoside phosphorylase have been grown from solutions of ammonium sulfate. The crystals are trigonal, space group R32; the hexagonal axes are a = 143.8(2) and c = 165.1(2) A. The crystals are moderately stable to x-rays and diffract beyond 3.0 A resolution. The experimental density of the crystals indicates that the molecular weight of the protein is 94,000. The three subunits are not related by crystallographic symmetry.

Crystallization↗

PubMed1980

Crystallization and preliminary X-ray investigation of calmodulin.

Crystals of rat testis calmodulin, a multifunctional Ca2+-binding protein have been grown from solutions of 2-methyl-2,4-pentanediol. The crystals are triclinic, space group P1, with a = 29.79(4) A, b = 53.74(7) A, c = 24.78(3) A, alpha = 93.46(2)degrees, beta = 96.98(2)degrees, and gamma = 89.05(3)degrees. There is 1 calmodulin molecule per unit cell. The crystals are quite stable to x-rays and diffract beyond 2.5 A resolution.

Animals↗

PubMed1980

Three-dimensional structure of a protein from scorpion venom: a new structural class of neurotoxins.

The three-dimensional crystal structure of variant-3 toxin from the scorpion Centruroides sculpturatus Ewing has been determined at 3 A resolution. Phases were obtained by use of K2PtCl4 and K2IrCl6 derivatives. The most prominent secondary structural features are two and a half turns of alpha-helix and a three-strand stretch of antiparallel beta-sheet, which runs parallel to the alpha-helix. The helix is connected to the middle strand of the beta-sheet by two disulfide bridges; a third disulfide bridge is located nearby. Several loops extend out of this dense core of secondary structure. The largest loop is joined to the COOH terminus of the molecule by the fourth disulfide bridge. The overall shape of the molecule resembles a right-hand fist: the alpha-helix runs along the knuckles of the fist; the beta-sheet lies along the second and third joints of the fingers; the thumb is defined by two short loops that are composed of residues 16-21 and residues 41-46; the wrist corresponds to the COOH-terminal stretch of residues 52-65 and a loop composed of residues 5-14; and the second joint of the little finger is near the NH2 terminus of the molecule. The alpha-carbon backbone displays a large flat surface that lies along the second joints of the fingers and the heel of the hand in the fist model. Several of the conserved residues in the scorpion neurotoxins are clustered on this surface, which may play a role in interactions of scorpion toxins with sodium channels of excitable membranes.

Hydrogen Bonding↗

PubMed1980