Biomedical subjects

W Chiu

Publications and source records attributed to W Chiu.

At least 19 recordsLinked to original sources

PubMed1992

The thickness determination of organic crystals under low dose conditions using electron energy loss spectroscopy.

In the 3-dimensional (3-D) reconstruction of protein crystals with variable thicknesses the electron images and diffraction patterns can only be merged if the crystal thickness is known. Measurement of the thickness using the ratio of the number of inelastically scattered electrons to the number of electrons in the zero loss peak can be accomplished with parallel electron energy loss spectrometry (PEELS). A theoretical analysis of the accuracy of the technique on paraffin crystals of different thicknesses is presented. Our experimental studies with paraffin crystals show the feasibility of measuring a single layer of 47A with good accuracy under low dose and low temperature conditions. A simple experimental apparatus is proposed to obtain thicknesses from small regions of unstained protein crystals prior to collecting the 3-D data sets from the unexposed area of the same crystal.

Crystallography↗

PubMed1992

Computer-controlled spot-scan imaging of crotoxin complex crystals with 400 keV electrons at near-atomic resolution.

400 keV electrons yield a better relative image contrast than 100 keV electrons for a beam-sensitive organic crystal when spot-scan imaging is used [J. Brink and W. Chiu, J. Microscopy 161 (1991) 279]. A FORTRAN 77 program has been written to operate the spot-scan imaging system on a computer workstation under the VMS operating system which is interfaced serially to the JEOL4000 electron microscope. We demonstrate the application of this implementation by imaging crotoxin complex crystals embedded in either vitreous ice or glucose to 2.5 A resolution. The intensity strength of the structure factors of this protein crystal are different at low (> 10 A) resolution but similar at high resolution (< 10 A) for the two embedding media as expected from their scattering contrast difference. Based on our experience as judged from the electron diffraction patterns of highly tilted crystals, flat crystals embedded in glucose can be readily obtained. Furthermore, our spot-scan imaging system also has the option of correcting the focus gradient that is present in images of tilted specimens.

Computers↗

PubMed1991

Crystallographic analysis of acrosomal bundle from Limulus sperm.

The acrosomal process of Limulus sperm contains a bundle of filaments composed of actin and a 102 kDa protein in a 1:1 molar ratio. The structure of the bundle in true discharge was investigated by electron cryomicroscopy, X-ray scattering and crystallographic image analysis. A bundle can be characterized as a quasi-crystal with continuously varying views along the bundle axis. Each segment of the bundle is found to obey the symmetry of space group P1, with a = b = 147 A, c = 762 A, alpha = 90 degrees, beta = 90.6 degrees, gamma = 120 degrees. A unit cell contains a helical repeat of the filament with a selection rule following that of an actin filament. A 24 A projection map based on the h0l view was reconstructed after averaging 5300 unit cells from six electron images. Filaments in this projection are well separated and clearly display a 21 screw symmetry. This screw symmetry results from the helical parameters of the bundle filament and is found to be a non-crystallographic symmetry element present in the unit cell. Our structural analysis has led to the proposal that the assembly of a stable bundle with a defined maximum diameter can be controlled by the crystallographic packing of the twisted filaments.

Acrosome↗

PubMed1991

Desferal-Mn(III) in the therapy of diquat-induced cataract in rabbit.

In rabbit lenses subjected to oxidative stress, induced by 1 mM diquat in vitro, there were 7- to 10-fold increases (p less than 0.001) in malondialdehyde, conjugated dienes, and carbonyl dienes, indicating extensive peroxidation of cellular membrane lipids, and approximately a 60% decrease in reduced glutathione. In the presence of 0.1-5 mM Desferal-Mn(III) these changes were diminished by 50-70%. In an experimental group of 12 rabbits having diquat-induced cataract, Desferal-Mn(III) (5% w/v) applied topically as a 50-microliters eye drop four times per day and a single intraperitoneal dose of 64 mg/kg body wt daily for 5 weeks (including pretreatment for 1 week) retarded the progression of lens opacities, whereas, in a control group of 6 rabbits treated with the vehicle (0.15 M NaCl) cataract progressed to an advanced grade. Treatment with Desferal-Mn(III) also significantly diminished production of O2.- and OH. in the lens, aqueous humor, and vitreous humor, and of H2O2 in the aqueous humor and vitreous humor. It also suppressed lipid peroxidation and oxidation of protein-SH of the lens and restored lenticular glutathione and ascorbate to normal levels.

Animals↗

PubMed1991

Analysis of symmetry and three-dimensional reconstruction of thin gp32*I crystals.

Thin, multilayered crystals of gp32*I were analyzed by negative stain electron microscopy and image processing. Images of untilted crystals exhibited different projection symmetries and structural motifs. Systematic analysis of these images categorized the projections into four types. Areas producing the type 1 projection were reconstructed in three-dimensions from four tilt series containing 111 images. The three-dimensional data has excellent p121 plane group symmetry and reveals that the gp32*I molecule contains two large domains linked together by a small domain. Computer simulations utilizing projection data suggested that the type 2 and 3 projections arise from superposition of type 1 projections related by a 21 screw axis along the projection axis. The three-dimensional reconstruction was utilized in a final simulation that explained the occurrence of the fourth type of projection. This work provides a firm foundation for future high-resolution analysis of the crystal by electron cryomicroscopy.

Crystallography↗

PubMed1991

Virion structure.

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Bunyaviridae↗

PubMed1991

Structural variation of La Crosse virions under different chemical and physical conditions.

La Crosse (LAC) virions exposed to different pHs (7.3, 6.2, and 5.4) and temperatures (37 degrees, 20 degrees, and 4 degrees) were preserved in thin layers of vitreous ice and observed by electron cryomicroscopy. Our results indicate that, at lower pH, virus particles interact with each other to form aggregates. In some cases, particles could be interpreted to have fused together. At neutral pH and higher temperatures morphological changes consistent with deformation in some particles were observed. We suggest that low pH conditions are sufficient for membrane fusion events to occur with LAC virions.

Animals↗

PubMed1991

Contrast analysis of cryo-images of n-paraffin recorded at 400 kV out to 2.1 A resolution.

n-Paraffin was used as a test specimen for evaluating the relative merits of 400-kV versus 100-kV electron microscopy in recording data for electron crystallographic analysis of beam-sensitive materials. The parameter used for comparison, the relative contrast R, is the ratio of amplitudes from the computed Fourier transform of images and amplitudes from an electron diffraction pattern from the same crystal. R will thus be a measure of the contrast from an experimental image relative to that of a perfect image. Electron diffraction patterns and bright-field images were recorded at 400 kV at a specimen temperature of -167 degrees C. Using the flood-beam imaging technique the best R-value is 0.08 for all reflections in the resolution zone from 4 to 3 A. This value is equivalent to that found at 100 kV. In the resolution zone from 3 to 2A we have found R = 0.02. Using the spot-scan imaging technique, on the other hand, R was measured to be 0.42 for the reflections between 4- and 3-A resolution. This amount of relative contrast is 1.7 times that observed at 100 kV. Reflections at 3-2 A displayed an R-value of 0.05. Besides obtaining higher R-values when applying the spot-scan imaging technique at 400 kV, we observe a higher yield of images with isotropic diffraction and/or higher resolution reflections. Various contrast-attenuating factors, including the modulation transfer function of the photographic film and the cryo-holder, envelope functions for spatial and temporal coherence and lens and high-tension instabilities, the contrast transfer function and lastly the radiation damage effects, have been considered in interpreting the observed image contrast. Overall, use of 400 kV in combination with spot-scan does offer important improvements in contrast levels, which can be very useful in determining the three-dimensional structure from protein crystals.

Crystallography↗

PubMed1990

Localization of VP4 neutralization sites in rotavirus by three-dimensional cryo-electron microscopy.

Three-dimensional structures of several spherical viruses have been determined by electron microscopy and X-ray crystallography. We report here the first three-dimensional structure of the complex between an intact virus and Fab fragments of a neutralizing monoclonal antibody. The antibody is against VP4, one of the two outer capsid proteins of rotaviruses. These large icosahedral viruses cause gastroenteritis in children and young animals and account for over a million human deaths annually. VP4 in these viruses has been implicated in several important functions such as cell penetration, haemagglutination, neutralization and virulence. Here we demonstrate that the surface spikes on rotavirus particles are made up of VP4. Antigenic sites are located near the distal ends of the spikes and two Fab fragments bind to each of the sixty spikes. The mass of the spike indicates that it is a dimer of VP4. The bilobed structure at the distal end of the spike may be involved in both the attachment to the cell and in viral penetration. A novel feature in the virus-Fab complex is the structural difference between the two chemically equivalent Fab fragments on each spike, which could be indicative of variations in the Fab elbow angles.

Antibodies, Monoclonal↗

PubMed1990

Estimation of allowable errors for tilt parameter determination in protein electron crystallography.

A three-dimensional reconstruction of a thin protein crystal requires an accurate assignment of amplitudes and phases in the three-dimensional reciprocal space. This assignment depends upon the tilt parameters which are experimentally determined. A theoretical estimate is made of the tolerable error in the determination of tilt parameters as a function of resolution and crystal thickness.

Crystallization↗

PubMed1990

Cold stage design for high resolution electron microscopy of biological materials.

Both the number and range of applications of cryotechniques in transmission electron microscopy are increasing rapidly. In some cases, most notably the determination of protein structure by electron crystallography, progress has been limited by the performance of commercially available cryo stages. We review the design and performance criteria for stages which will be necessary for wide applicability in high resolution studies of biological specimens. The important criteria include an operating temperature below -140 degrees C with a low rate of contamination of the specimen, ability to tilt to 60 degrees, and perhaps most important, good resolution as judged by an effective modulation transfer function of 0.8 at 0.35 nm. Most applications also require an effective cryotransfer system. Up until now, most work in high resolution electron crystallography has been accomplished with laboratory-built stages which meet some, but not all, of these criteria. The availability of cold stages which fully meet criteria will allow the rapid expansion of high resolution studies by electron microscopy in structural biology.

Cryopreservation↗

PubMed1989

Three-dimensional structure of the HSV1 nucleocapsid.

The three-dimensional structures of full and empty capsids of HSV1 were determined by computer analysis of low dose cryo-electron images of ice embedded capsids. The full capsid structure is organized into outer, intermediate, and inner structural layers. The empty capsid structure has only one layer which is indistinguishable from the outer layer of the full capsids. This layer is arranged according to T = 16 icosahedral symmetry. The intermediate layer of full capsids appears to lie on a T = 4 icosahedral lattice. The genomic DNA is located inside the T = 4 shell and is the component of the innermost layer of the full capsids. The outer and intermediate layers interact in such a way that the channels along their icosahedral two-fold axis coincide and form a direct pathway between the DNA and the environment outside the capsid.

Capsid↗

PubMed1989

Visualization of alpha-helices in tobacco mosaic virus by cryo-electron microscopy.

We have used tobacco mosaic virus (TMV) as a test specimen, in order to develop techniques for the analysis of high-resolution structural detail in electron micrographs of biological assemblies with helical symmetry. It has previously been shown that internal details of protein structure can be visualized by processing electron micrographs of unstained specimens of extended two-dimensional crystalline arrays. However, the techniques should in principle be applicable to other periodic specimens, such as assemblies with helical symmetry. We show here that data to spacings better than 10 A can be retrieved from electron images of frozen hydrated TMV. The three-dimensional computed map agrees well with that derived from X-ray diffraction and shows the two pairs of alpha-helices forming the core of the coat subunit, the C alpha-helix and the viral RNA. The results demonstrate that it is possible to determine detailed internal structure in helical particles.

Freezing↗

PubMed1988

Crystallization and preliminary X-ray diffraction analysis of 11 S acetylcholinesterase.

The 11 S form of acetylcholinesterase from Electrophorus electricus was purified by affinity chromatography. The protein was crystallized from polyethylene glycol solutions. One crystal form proved suitable for x-ray diffraction studies. Preliminary x-ray analysis demonstrates that the space group of this crystal is F222. The unit cell dimensions are a = 141.0 +/- 0.2, b = 202.4 +/- 0.2, and c = 237.4 +/- 0.1 A. The diffraction is anisotropic, extending to at least 3.5 A along the a* and b* axes, but becoming weak beyond about 6 A along the c* axis. Crystal density measurements suggest that one complete 11 S tetramer occupies the asymmetric unit of the crystal.

Acetylcholinesterase↗

PubMed1988

Three-dimensional structural analysis of tetanus toxin by electron crystallography.

Two-dimensional crystalline arrays of native tetanus toxin have been formed at the interface between a solution of the toxin and a phospholipid monolayer containing a ganglioside. Electron crystallographic analysis has been used to study these periodic arrays. The arrays obey the symmetry of plane group p12(1), with a = 126 A and b = 84 A, and a thickness of 90 A (1 A = 0.1 nm). The three-dimensional structure of tetanus toxin in negative stain is reconstructed to a nominal resolution of 14 A from multiple tilt images. The molecule presents an asymmetric three-lobed structure and could interact with the monolayer in two possible orientations.

Crystallography↗

PubMed1988

Three-dimensional structure of rotavirus.

The three-dimensional structures of double and single-shelled simian rotavirus have been determined to a resolution of 40 A by image processing electron micrographs of unstained, unfixed virus particles embedded in vitreous ice. This study demonstrates that the icosahedral surface lattices in these structures have a triangulation number of 13 in a left-handed configuration. The double-shelled virion has a smooth outer surface with 60 slender spikes. The single-shelled virion, in contrast, exhibits a bristly surface. On the basis of these structures, the locations and number of copies of outer and inner shell proteins have been deduced. The spikes likely correspond to VP3, a hemagglutinin, while the rest of the mass density in the outer shell represents 780 molecules of VP7, a neutralization antigen. The 260 morphological units, located on all the local and strict 3-fold axes of the single-shelled virion are proposed to represent 260 trimers of VP6, which is a subgroup antigen. The regions of closed contact between the outer and the inner shells are located mainly near the local and strict 3-fold axes. A distinctive feature in the rotavirus structure is the presence of 132 large channels spanning across both the shells at all 5 and 6-co-ordinated positions linking the outermost surface with the inner core. In the transcriptionally active single-shelled virion, these channels may provide pathways for importing the metabolites required for the viral RNA transcription and exporting the newly synthesized RNA molecules for subsequent viral replication processes.

Capsid↗

PubMed1988

Containment system for the preparation of vitrified-hydrated virus specimens.

A guillotine-type quick freezing device and a bio-hazard containment box have been designed, constructed, and used to prepare vitrified-hydrated specimens of viruses in their native environment. Special design considerations include the preservation of the specimen in its natural state in vitrified ice, prevention of virus aerosols escape, and control of the potentially explosive air-coolant vapor mixtures.

Containment of Biohazards↗

PubMed1988

The characterization of structural variations within a crystal field.

The technique of correlation averaging is refined by the use of multivariate statistical analysis and classification. The refined method can deal with the presence of structural variations within a crystal field. A low-dose image of a crotoxin crystal embedded in ice is used to demonstrate that crystallographic structural parameters characterizing the different areas of such a crystal with varying structure can be extracted rigorously and reproducibly.

Analysis of Variance↗