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At least 19 recordsLinked to original sources
PubMed1992

SQUID: a program for the analysis and display of data from crystallography and molecular dynamics.

SQUID is a flexible computer program that allows the analysis and display of molecular coordinates from crystallography, NMR, and molecular dynamics. The program can also display two-dimensional and three-dimensional data using many graph types, as well as perform array processing of data with numerous intrinsic functions. Graphics are based on the use of "move" and "draw" instructions, allowing easy development of new device drivers, including vector plotters.

Computer Graphics↗
PubMed1992

Assessment of resolution in biological electron crystallography.

The resolution of images or density maps produced by electron microscopy and electron crystallography can be objectively defined in terms of the spatial frequency of the highest resolution diffraction spot, or Fourier coefficient, included in the data processing. In practice, this objective definition of resolution is expected to be too optimistic if the amplitudes of the highest resolution structure factors are too weak, if the population of high resolution reflections is too sparse, or if the signal-to-noise ratio of the high resolution data is too low. Calculated examples are presented here which illustrate how the apparent resolution in images of a membrane protein, bacteriorhodopsin, can be reduced from a nominal value of 3.5 A by weak amplitudes, sparse data or high noise levels. These calculations provide concrete examples which can serve as a guide when estimating whether the objective definition of image resolution is likely to correspond to a practical, structurally useful estimate of image resolution.

Bacteriorhodopsins↗
PubMed1992

Application of crystallography to the design of antiviral agents.

A historical review of x-ray crystallography introduces basic concepts and describes the potential of this science to the rational design of antiviral agents. Following a brief introduction to the study of antiviral compounds that inhibit early stages of rhino- and enteroviral infections, the impact of structural studies on rational drug design is discussed in relation to known viral structures.

Antiviral Agents↗
PubMedDate not supplied

X-ray crystallography of the binding of the bacterial cell wall trisaccharide NAM-NAG-NAM to lysozyme.

Hen egg white lysozyme was the first enzyme whose structure was determined by X-ray crystallography. The proposed mechanism based on this structure involves the distortion of the saccharide residue (2-acetamido-2-deoxy-D-muramic acid, NAM) in the natural substrate (an alternating beta (1 leads to 4) linked oligomer of 2-acetamido-2-deoxy-D-glucose (NAG) and NAM residues) bound to site D in the binding cleft. The importance of substrate distortion has prompted numerous enzymatic, chemical, theoretical, and physical studies, but there is little direct crystallographic evidence on the conformation of a NAM residue bound at site D. We now present the X-ray structure of the non-hydrolysed trisaccharide NAM-NAG-NAM bound in subsites B, C, D. Our interpretation of the 2.5-A resolution difference map does not involve distortion of this residue in site D. Comparison with the structure of the delta-lactone derived from tetra N-acetylchitotetraose (NAG)3NAL) bound to lysozyme suggests we may be looking at a Michaelis complex.

Binding Sites↗
PubMed1992

3D structure determination from electron-microscope images: electron crystallography of staurolite.

Resolution of better than 2 A has been obtained in many crystals by high-resolution electron microscopy. Although this resolution is sufficient to resolve interatomic spacings, structures are traditionally interpreted by comparing experimental images with contrast calculations. A drawback of this method is that images are 2D projections in which information is invariably obscured by overlap of atoms. 3D electron crystallography, developed by biophysicists to study proteins, has been used to investigate the crystal structure of staurolite. Amplitudes and phases of structure factors are obtained experimentally from high-resolution images (JEOL ARM 1000 at the National Center for Electron Microscopy at LBL), taken in different directions from thin regions where dynamic scattering is minimal. From images in five orientations (containing 59 independent reflections to a resolution of 1.38 A), a 3D electron potential map is constructed which resolves clearly all cations (Al, Si, Fe, including those with partial occupancy) and all O atoms. This method has great potential in crystal structure determinations of small domains in heterogeneous crystals which are inaccessible to X-ray analysis. It is estimated that 3D structure determinations should be possible on regions only about ten unit cells wide and should resolve not only atom positions but also site occupancies. The method is also applicable to space-group determination.

Chemical Phenomena↗
PubMed1979

Configuration at C-25 in 3 alpha, 7 alpha, 12 alpha-trihydroxy-5 beta-cholestan-26-oic acid by X-ray crystallography.

The two diastereoisomers at carbon-25 of 3 alpha, 7 alpha, 12 alpha-trihydroxy-5 beta-cholestan-26-oic acid, a key intermediate in the biosynthetic pathway of cholic acid, were obtained in pure form by a combination of fractional crystallization and thin-layer chromatography. The configuration at C-25 of these two isomers was established by X-ray crystallography as 25S for one diastereoisomer (mp 199-201 degrees C) and 25R for the other (mp 180-182 degrees C). These findings permit us to determine, unequivocally, the configuration of this naturally occurring C27-bile acid in man and other animals and to establish the stereospecificity of the microsomal and mitochondrial omega-hydroxylation pathway for the side-chain oxidation of cholesterol to bile acids.

Cholestanols↗
PubMed1990

The tryptophan synthase multienzyme complex: exploring structure-function relationships with X-ray crystallography and mutagenesis.

The bifunctional tryptophan synthase alpha 2 beta 2 complex that catalyzes the final two reactions in tryptophan biosynthesis is a classic example of a multienzyme complex that "channels" a metabolic intermediate (indole) between two active sites. The three-dimensional structure of the alpha 2 beta 2 complex from Salmonella typhimurium reveals that the four polypeptide subunits are arranged in an extended alpha beta beta alpha order forming a complex 150 A long. The active sites of the neighboring alpha and beta subunits are separated by about 30 A and appear to be connected by a tunnel, which may facilitate the intramolecular transfer of indole. The active site of the alpha subunit, which is centrally located near one end of an eight-fold alpha/beta barrel structure, contains the sites of most of the missense mutations which were identified as key residues by Yanofsky and colleagues in early genetic studies. Site-directed mutagenesis is being used to replace residues found in the active sites of the alpha and beta subunits in order to probe the mechanism of catalysis. Recombinant DNA technology should also be useful in analyzing protein-protein interaction, protein folding and the channeling phenomenon.

Crystallography↗
PubMed1976

Applications of synchrotron radiation to protein crystallography: preliminary results.

X-ray diffraction photographs of protein single crystals have been obtained using synchrotron radiation produced by an electron-positron storage ring. The diffracted intensities observed with this unconventional source are a factor of at least 60 greater than those obtained with a sealed x-ray tube using the same crystal and instrumental parameters. Diffraction data have been collected by the precession method to higher resolution and using smaller protein crystals than would have been possible with a conventional source. The crystal decay rate in the synchrotron beam for several proteins appears to be substantially less than that observed with Ni-filtered Cu radiation. The tunable nature of the source (which allows selective optimization of anomalous contributions to the scattering factors) and the low angular divergence of the beam make the source very useful for single crystal protein diffraction studies.

Asparaginase↗
PubMed1992

Cytochrome P450cam: crystallography, oxygen activation, and electron transfer.

Several crystal structures of various substrate and inhibited complexes of the camphor monoxygenase, cytochrome P450cam from Pseudomonas putida, are now available. These structures, together with mutagenesis, biochemical, and biophysical studies, have allowed for a detailed penetration into the problem of how P450s activate molecular oxygen, control stereoselectivity, and transfer electrons. This review will provide a summary of the crystallographic work in light of what these structures have taught us about P450 function.

Amino Acid Sequence↗
PubMed1992

Dynamical scattering and electron crystallography--Ab initio structure analysis of copper perbromophthalocyanine.

Electron diffraction intensity data were collected at 1200 kV from thin epitaxially oriented crystals of copper perbromophthalocyanine (C32Br16CuN8) in a projection down molecular columns. Measured cell constants for the projection with cmm symmetry are d100 = 17.88 (9), b = 26.46 (15) A. The structure was determined by Fourier refinement after three heavy-atom positions were identified in an initial potential map. In addition to the copper and halogens, all light-atom positions were found. Although the final R value for all data is 0.41, n-beam dynamical calculations for crystal thicknesses corresponding to the estimated sample dimension account for the observed amplitudes that deviate most from their kinematical values.

Crystallography↗