Single-particle approaches in the analysis of small 2D crystals of the mitochondrial channel VDAC.

It has been difficult to obtain better than moderate resolution in analysis of electron microscopic images of small, 2D crystals with variable lattice parameters, e.g., crystals of the channel VDAC generated by phospholipase treatment of outer mitochondrial membranes. We demonstrate that applying single-particle analysis methods to correlation-averaged images can lead to significant improvements in the attainable resolution. Application of a soft-edged fitted mask passing only the central unit cell, and excluding the positionally variable adjacent unit cells, allows improved alignment and more sensitive multivariate statistical analysis, needed to guide intelligent merging of data from different crystals.

Introduction to electron crystallography.

This introduction describes the contributions to this topical issue, and in some cases gives observations on the importance and implications of these articles. Subsequently, there is a discussion of the phase problem and its solution using the unitary equation. This equation, which is true for all known scattering processes, provides a firm theoretical basis for the direct methods of phasing.

Solution of the phase problem in crystallography and application to dynamical electron diffraction.

Unitarity, a fundamental principle of scattering theory, leads to the prediction of an essentially unique set of phases for the scattering amplitude from a complete knowledge of the differential cross section or, in the case of a crystal, from the diffracted intensities. The Sayre equation and all the direct methods of phasing following there from are derived as a special case of unitarity for zero excitation error. Dynamical and kinematical scattering are considered, and the relationship between them, S = exp(i tau nzK), is obtained. Applications to the case of electron diffraction including for non-zero excitation error are discussed.

The Sayre equation in electron crystallography.

The Sayre equation was evaluated as a technique for phase refinement in electron crystallography. Atomic-resolution electron diffraction data from copper perchlorophthalocyanine were assigned phase values from the Fourier transforms of various experimental electron micrographs, including one at 2.3 A, containing errors due to lens astigmatism. In each case, an atomic-resolution structure could be found after Fourier refinement. In addition, it was possible to begin with a basis set derived from symbolic addition for phase extension. Such a source of phases was also found to be useful for extending zonal electron diffraction sets from six polymer crystals, even though there was considerable overlap of atomic positions in the projection down the chain axes. Other tests of the Sayre equation were made with zonal protein data sets (bacteriorhodopsin, halorhodopsin) to evaluate what difficulties are to be expected when direct phasing techniques are to be used in macromolecular electron crystallography. Comparison to known values indicated that the low-resolution range (e.g. to 6 A) was reasonably stable for phase extension from a 10-15 A resolution image. Only when a minimum in average intensity was approached (near 5 A) did the direct extension encounter serious difficulties. If this minimum was treated as a "phase node" to generate two possible solutions, a model more similar to the true phase set was found. In general, this rather simple convolutional technique for phase extension seems to be particularly suitable for a variety of electron crystallographic applications.

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.

Electron crystallography at atomic resolution: ab initio structure analysis of copper perchlorophthalocyanine.

High-voltage (1200 kV) electron diffraction intensities from approximately 100 A thick crystals of copper perchlorophthalocyanine are used to determine the molecular packing at atomic resolution, thus greatly exceeding the structure detail observed by electron microscopy. Initial crystallographic phases were determined by direct methods often used in X-ray crystallography, i.e., locating the positions of heavy (Cl and Cu) atoms in the structure. All other atom positions were found in subsequent Fourier refinement (final R = 0.28). Calculated bond distances and angles are similar to those found in the earlier X-ray crystal structure of the unchlorinated parent compound.

Characterization of electrode dissolution products on the high-voltage electron microscope.

Deposits left by electrodes and biocompatibility test specimens implanted in brain or peripheral nerve were characterized by X-ray microprobe analysis, electron diffraction and stereoscopic imaging using a high-voltage electron microscope. Examination of thick (1-micron) sections of neural tissue confirmed that the electron-dense bodies found adjacent to electrode positions consist of elements originating in the implant material (with the exceptions of the S and Se found in association with Ag). These elements have no long-range order, suggesting they are complexed with biological molecules. In some cases the deposits appear to be caused by pulsing the electrode with current, while in other cases the deposits are corroded or abraded from the electrode or are otherwise not associated with the neuroprosthetic functioning of the implant.

Progress in element analysis on a high-voltage electron microscope.

X-Ray microprobe (XMA) and electron energy-loss (EELS) spectrometers have been installed on the high-voltage electron microscope (HVEM). The probe size has been measured and background reduction is in progress for XMA and EELS as are improvements in electron optics for EELS and sensitivity measurements. XMA is currently useful for qualitative analysis and has been used by several investigators from our laboratory and outside laboratories. However, EELS background levels are still too high for meaningful results to be obtained. Standards suitable for biological specimens are being measured, and a library for quantitative analysis is being compiled.

Reproducibility of electron diffraction intensity data obtained from hydrated microcrystals of rat hemoglobin.

Analysis of electron diffraction patterns from rat hemoglobin taken at 200 kV on a wet stage yields intensity data to a resolution of 2-3 A which are as reproducible as those from typical X-ray diffraction. Some crystals were so similar that the differences in measured intensities were insignificant (R = 0.056), but in other cases real differences between crystals were observed (R = 0.33). Dynamic scattering was insignificant under our diffraction conditions; however, exposures to electron doses as low as 10(-2) e/A2 produced detectable changes in measured intensities. Limits to the reproducibility of the data are set by radiation damage and errors in microdensitometry.

A novel chemical modification of delta 5-3-ketosteroid isomerase occurring during its 3-oxo-4-estren-17 beta-yl acetate-dependent photoinactivation.

The chemical change responsible for the 3-oxo-4-estren-17 beta-yl acetate-dependent photoinactivation of delta 5-3-ketosteroid isomerase has been identified by amino acid analysis and amino acid sequencing. Amino acid analysis of the enzyme and its photoinactivated derivative shows that photoinactivation is accompanied by loss of nearly 1 residue of aspartic acid/polypeptide chain and an increase in nearly 1 residue of alanine. Edman degradation of a peptide comprising residues 31 to 48 from native isomerase showed the presence of aspartic acid at residue 38. When the corresponding peptide from photoinactivated enzyme was sequenced, residue 38 was revealed to be alanine.

Effect of protein concentration on the molecular weight of delta5-3-ketosteroid isomerase.

The molecular weight of delta-5-3-ketosteroid isomerase from Pseudomonas testosteroni was determined by means of sedimentation equilibrium and exclusion chromatography over a wide range of enzyme concentrations in 0.2 M potassium phosphate buffer, pH 7.0. In addition, the sedimentation constant of the enzyme was determinded over an extended range of concentrations. The enzyme was found to have a molecular weight of 26,000 plus or equal to 1,000, suggesting that it is a dimer of identical or similar 13,400 molecular weight polypeptide chains. In the ultracentrifuge this dimeric species was found to undergo aggregation at enzyme concentrations above 2 mg per ml and dissociation at enzyme concentrations below 0.05 mg per ml. Exclusion chromatography studies indicate that under the conditions of chromatography the oligomeric enzyme is partially dissociated at enzyme concentrations in the range 0.2 to 0.002 mug per ml. These results suggest that under conditions of enzyme assay in 0.2 M potassium phosphate buffer, pH 7.0, isomerase is in a monomeric state of aggregation.