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Biomedical subjects

M van Heel

Publications and source records attributed to M van Heel.

51 records · Page 3Linked to original sources
PubMed1988

Molecular shape of Lumbricus terrestris erythrocruorin studied by electron microscopy and image analysis.

The molecular structure of erythrocruorin (hemoglobin) from Lumbricus terrestris has been studied by electron microscopy of negatively stained particles. Over 1000 molecular projections were selected from a number of electron micrographs and were then classified by multivariate statistical image-processing techniques. The two main groups of top and side views were each subdivided into smaller classes with significantly different features. About half of the top-view projections exhibit perfect hexagonal symmetry at the current resolution of about 2.0 nm, while the other top views lack this symmetry, probably as a result of tilting of the molecules relative to the carbon support film. The side views were separated into two 'families', each associated with the two different stable side-view positions the molecules can take. From these narrow stable side-views, the two families of projections are, again, generated by tilting. The symmetry properties of the three non-tilted projections show that Lumbricus erythrocruorin has a pointgroup D6 (622) symmetry rather than D3 (32).

Animals↗
PubMed1988

Packing of the 30 nm chromatin fiber in the human metaphase chromosome.

The human genetic material is packed hierarchically within the metaphase chromosome: the DNA molecule together with histone proteins form 11 nm diameter nucleosomes, which are then ordered into the 30 nm thick chromatin fiber. Little is known about the packing of this fiber within the chromosome. We have developed a tracking algorithm with which we followed its path within a three-dimensional reconstruction of a human chromosome computed from a series of electron micrographic projections. Fiber segments were seen to form loops of 100-350 nm diameter. Our observations indicate that these loops--which themselves show no preferred orientation--are organised into regions of roughly 200 nm axial extent.

Chromatin↗
PubMed1988

Biological macromolecules explored by pattern recognition.

Electron microscopy represents a very direct method for determining the structure of biological macromolecules, and complements both the well-established technique of X-ray crystallography (c.f. Blundell and Johnson, 1976) and the still in-its-infancy field of structure prediction (Kolata, 1986, Blundell et al., 1987). Our research has involved establishing a precise methodology based on computerised image analysis and pattern recognition to enhance the visibility of statistically significant structural features in electron images of isolated macromolecules. Our newly developed technique of angular reconstitution enables us to orient in three dimensions the commonly occurring projection forms of the macromolecules and thus perform a 3D reconstruction. In this paper, we describe the steps involved in determining the structure of a biological macromolecule by electron microscopy and image analysis, including pattern recognition and three dimensional reconstruction.

Image Processing, Computer-Assisted↗
PubMed1987

Three-dimensional reconstruction of a human metaphase chromosome from electron micrographs.

A complete human metaphase chromosome has been reconstructed from a series of electron microscopical projections obtained by tilting the specimen stage at 3 degree intervals from -60 to +60 degrees. The reconstructed structure is about 3.0 microns long, 1.6 micron wide, and 0.8 micron thick. The mass distribution was fairly homogeneous within the chromatids and neither a hollow nor a dense core was observed. The distribution and course of fibers observed are most consistent with a looping model of chromosome structure.

Algorithms↗
PubMed1987

Characteristic views of prokaryotic 50S ribosomal subunits.

Multivariate statistical analysis and classification techniques are powerful tools in sorting noisy electron micrographs of single particles according to their principal features, enabling one to form average images with an enhanced signal-to-noise ratio and a better reproducible resolution. We apply this methodology here to determining the characteristic views of the large (50S) ribosomal subunits from the eubacterium Escherichia coli and the archaebacteria Methanococcus vannielii, Sulfolobus solfataricus, and Halobacterium marismortui. Average images were obtained of the subunit in the common crown and kidney projections, but views of the particle in orientations intermediate between these two extremes were also elucidated for all species. These averages show reproducible detail of up to 2.0 nm resolution, thus enabling the visualization and interspecies comparison of many structural features as a first step toward comparing the actual three-dimensional structures. Our results disprove evolutionary lineages recently postulated on the basis of electron microscopical images of ribosomal subunits.

Archaea↗
PubMed1985

Characteristic views of E. coli and B. stearothermophilus 30S ribosomal subunits in the electron microscope.

Large sets of electron microscopic images of the 30S ribosomal subunits of Bacillus stearothermophilus (914 molecules) and Escherichia coli (422 molecules) were analysed with image processing techniques. Using computer alignment and a new multivariate statistical classification scheme, three predominant views of the subunit were found for both species. These views, which together account for approximately 90% of the population of images, were determined to a reproducible resolution of up to 1.7 nm, thus elucidating many new structural details. The angular spread of the molecular orientations around the three main stable positions is remarkably small (less than 8 degrees). Some of the current models for the small ribosomal subunit are incompatible with our new results.

Escherichia coli↗
PubMed1984

Multivariate statistical classification of noisy images (randomly oriented biological macromolecules).

Multivariate Statistical Analysis (MSA) methods have recently been introduced for analyzing images of biological macromolecules [Van Heel and Frank, Ultramicroscopy 6 (1981) 187]. With these techniques, the significant characteristics of each molecular image can be expressed in merely 2 to 8 factorial coordinate values rather than in the typical 64 X 64 = 4096 pixel grey values that originally described the image. This very large reduction in total amount of data facilitates the understanding of the general behavior of a set of molecular images in terms of classes or of general trends in the data set. The (artificial) intelligence of the procedure, however, lies in the decision-making or classification phase. The theory and philosophy of multivariate statistical classification are reviewed using generalized metrics. Problem-dependent classification rationales are proposed. A set of computer-generated "randomly oriented molecular images" are used to test the classification schemes. This model experiment is a step towards 3D structure analysis of macromolecules based on large numbers of (noisy) electron microscopical images of randomly oriented biological macromolecules.

Animals↗
PubMed1981

Use of multivariate statistics in analysing the images of biological macromolecules.

We have developed a new technique of analysis that allows automatic classification of molecule images according to subtle differences. Computer alignment and multivariate statistical methods were used to analyze electron micrographic images of horseshoe crab hemocyanin half-molecules. The molecule projections fell into four distinct classes related to four different positions of the molecule on the grid. Averages obtained for each images subset are interpreted in terms of a three-dimensional model arrangement for the four subunits forming the half-molecule.

Animals↗
PubMedDate not supplied

Structure of Lumbricus terrestris hemoglobin at 30 A resolution determined using angular reconstitution.

The three-dimensional (3D) structure of the giant hemoglobin of the common earthworm Lumbricus terrestris was determined from cryomicroscopical images of a vitrified molecular solution. From about 5000 molecular images, the best-fit 3D structure was calculated using recently developed analysis techniques. Multivariate statistical analysis data compression and automatic classification were used to find the characteristic projection images of the oligomer. The angular reconstitution approach was then applied to find the Euler angle orientations of these characteristic views. The Lumbricus hemoglobin molecule has an overall D6 (622) point-group symmetry and is found to have a local threefold symmetry axis within the 1/12th subunit. This additional symmetry appears to predict the presence of 36 abcd globin tetramers in the Lumbricus hemoglobin or a total of 144 heme chains for the whole oligomer. A distinct doughnut-shaped structure is elucidated in the center of the molecule. This central subunit, representing around 10% of the protein volume, may consist of non-heme-containing linker chains found generally in giant annelid hemoglobins.

Animals↗
PubMedDate not supplied

A new generation of the IMAGIC image processing system.

One of the aims of modern microscopy is to quantify two-, three-, or even four-dimensional phenomena in biology, medicine, and material sciences. The requirements imposed on software by such data processing are exemplified by the design considerations of the IMAGIC-5 software system. This system includes facilities for multivariate statistical analysis of large data sets, for correlation averaging of two-dimensional crystals, and for three-dimensional reconstruction of macromolecular structures. The molecules may be arranged as two-dimensional crystals, as helices, or as single particles with arbitrary pointgroup symmetry. IMAGIC's novel angular reconstitution approach allows for the rapid determination of three-dimensional structures of uncrystallized molecules to high resolution. The general organization, user interaction strategy, file structure, and extendibility of IMAGIC are discussed and illustrated with some practical examples.

Animals↗
PubMedDate not supplied

Invariant classification of molecular views in electron micrographs.

Biological macromolecules can exhibit many different orientations in electron microscopical preparations. In particular in vitreous-ice-embedded specimens, the number of different views can be high. Existing techniques of analysis require the alignment of the molecular views relative to one or more reference images with cross-correlation ("matched filtering") techniques and are somewhat unsatisfactory because of the high noise level and the large number of different views in such images. We here propose a method in which first rotation-, translation- and mirror-invariant functions are derived from the large set of input images. These functions are subsequently classified automatically using multivariate statistical classification techniques. The different molecular views in the images can therewith be found without bias, provided that a statistically significant number of copies of the views are present in the data set. The basic ideas are exemplified with realistic model data.

Fourier Analysis↗
PubMedDate not supplied

TYSON: robust searching, sorting, and selecting of single particles in electron micrographs.

We here present TYSON, a new program for automatic and semi-automatic particle selection from electron micrographs. TYSON employs a three-step strategy of searching, sorting and selecting single particles. In the first step, TYSON finds the positions of potential particles by one of three different methods: local averaging, template matching or local variance. The practical merits and drawbacks of these methods are discussed. In the second step, these potential particles are automatically sorted according to their probability of being true positives. Many criteria are provided for this sort. In the final -interactive- step, whole categories of poorly fitting false positives can be removed with a single mouse-click. We present results obtained using cryo-EM micrographs of both spherical virus particles and asymmetric particles. The procedures are fast and use of TYSON allowed, for example, some 20,000 particles to be selected in a single working day.

Algorithms↗