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Biomedical subjects

G A Petsko

Publications and source records attributed to G A Petsko.

At least 181 records · Page 10Linked to original sources
PubMed1983

Structure of iron superoxide dismutase from Pseudomonas ovalis at 2.9-A resolution.

The three-dimensional structure of the iron-containing superoxide dismutase (EC 1.15.1.1) from Pseudomonas ovalis has been determined at 2.9-A resolution by the method of multiple isomorphous replacement. The molecule is a dimer of two identical subunits with the iron atom per monomer. The conformation of the enzyme is completely different from that of the eukaryotic copper-zinc superoxide dismutase. Each subunit consists of about 50% alpha-helix plus three strands of antiparallel pleated sheet. The iron atoms are coordinated by four protein ligands, one of which is the side-chain of histidine-26. Crystals of complexes with the inhibitors azide or fluoride are considerably more resistant to irradiation than those of the free enzyme. The structure of the apoprotein is identical to that of the iron-containing molecule.

Animals↗
PubMed1982

Conformational substates in a protein: structure and dynamics of metmyoglobin at 80 K.

The crystal structure of sperm whale metmyoglobin has been determined at 80 K to a resolution of 2A. The overall structure at 80 K is similar to that at 300 K except that the volume is smaller. Refinement of the structure by the method of restrained least squares (current R = 0.175) permits the assignment of isotropic atomic mean-square displacements to all nonhydrogen atoms. Comparison with the values obtained earlier at 250-300 K indicates that the protein at 80 K is more rigid. The average experimentally determined Debye-Waller factor, B, for the protein is 14A2 at 300 K and 5A2 at 80 K. Plots of backbone mean-square displacement vs. temperature show a discontinuity of slope for at least one-third of all residues. This behavior is in good agreement with the temperature dependence of the mean-square displacement of the heme iron as measured by Mössbauer absorption. The magnitudes of the smallest mean-square displacements observed at 80 K indicate that intramolecular motions can be frozen out to a surprisingly large degree. Even at 80 K, however, some atoms in myoglobin still have mean-square displacements greater than 0.1A2, thus providing evidence for conformational substates.

Animals↗
PubMed1982

Crystallization and preliminary X-ray investigation of avidin.

Hen egg-white avidin was crystallized at pH 6 from solutions containing 8-9% (w/v) poly(ethyleneglycol) 6000 as precipitant. X-ray investigation showed that the crystals are orthorhombic with cell constants a = 7.47 nm, b = 8.00 nm, c = 4.31 nm and belong to space group P21212. They contain half of a tetrameric molecule in the asymmetric unit.

Animals↗
PubMed1981

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase.

Triose phosphate isomerase is a dimeric enzyme of molecular mass 56 000 which catalyses the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate. The crystal structure of the enzyme from chicken muscle has been determined at a resolution of 2.5 A, and an independent determination of the structure of the yeast enzyme has just been completed at 3 A resolution. The conformation of the polypeptide chain is essentially identical in the two structures, and consists of an inner cylinder of eight strands of parallel beta-pleated sheet, with mostly helical segments connecting each strand. The active site is a pocket containing glutamic acid 165, which is believed to act as a base in the reaction. Crystallographic studies of the binding of DHAP to both the chicken and the yeast enzymes reveal a common mode of binding and suggest a mechanisms for catalysis involving polarization of the substrate carbonyl group.

Animals↗
PubMed1980

Structural dynamics of liganded myoglobin.

X-ray crystallography can reveal the magnitudes and principal directions of the mean-square displacements of every atom in a protein. This structural information is complementary to the temporal information obtainable by spectroscopic techniques such as nuclear magnetic resonance. Determination of the temperature dependence of the mean-square displacements makes it possible to separate large conformational motions from simple thermal vibrations. The contribution of crystal lattice disorder to the overall apparent displacement can be estimated by Mössbauer spectroscopy. This technique has been applied to high resolution x-ray diffraction data from sperm whale myoglobin in its Met iron and oxy cobalt forms. Both crystal structures display regions of large conformational motions, particularly at the chain termini and in the region of the proximal histidine. Overall, the mean-square displacement increases with increasing distance from the center of gravity of the molecule. Some regions of the heme pocket in oxy cobalt myoglobin are more rigid than the corresponding regions in Met myoglobin.

Animals↗
PubMed1979

Temperature-dependent X-ray diffraction as a probe of protein structural dynamics.

X-ray diffraction at four temperatures from 220 to 300 K coupled with crystallographic refinement yields the mean-square displacements and conformational potentials of all 1,261 non-hydrogen atoms of metmyoglobin. The results are interpreted to indicate a condensed core around the haem, semi-liquid regions towards the outside and a possible pathway for ligands. It is concluded that X-ray diffraction can provide the spatial distribution of the dynamic features of a protein.

Animals↗
PubMed1977

Protein sequencing by computer graphics.

A computer graphics system has been used to fit a putative sequence to an electron density map of a sea snake neurotoxic protein at 2.2 A resolution. The complete sequence of this small protein could be determined from the map with very little ambiguity. In two places probable errors in the published chemical sequence were detected. This is the first instance in which a complete three-dimensional structure was solved with the use of computer graphics alone, without the construction of a physical model.

Amino Acid Sequence↗
PubMed1977

Three-dimensional structure of neurotoxin a from venom of the Philippines sea snake.

The crystal structure of neurotoxin a from the venom of Philippines sea snake Laticauda semifasciata has been determined at 2.5 A resolution by x-ray diffraction. Comparison with the structure of neurotoxin b from the same source indicates that the two toxins differ only by substitution at His 26. Earlier chemical work had suggested a difference in chain length and considerable differences in amino acid composition. The difference between our a and b toxins is the same as that reported from sequence analysis for the related erabutoxins a and b from Japanese sea snake, and suggests that the Philippines toxin may be identical to erabutoxin. The replacement of His 26 by a shorter side-chain in toxin a has no effect on the structure of the rest of the molecule. In particular, the protruding loop, which we believe interacts with the acetylcholine receptor, is not affected, even though His 26 is in the loop.

Animals↗
PubMed1976

Crystal structure of elastase-substrate complex at -- 55 degrees C.

The structure of a specific acyl-enzyme intermediate in the elastase-catalysed hydrolysis of N-carbobenzoxy-L-alanyl-p-nitrophenol ester has been determined by X-ray diffraction at 3.5 A resolution. The acyl-enzyme was stabilised by cooling the crystal to --55 degrees C during substrate addition and data collection.

Binding Sites↗