Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase

A method for the flexible docking of high-resolution atomic structures into lower resolution densities derived from electron microscopy is presented. The atomic structure is deformed by an iterative process using combinations of normal modes to obtain the best fit of the electron microscopical density. The quality of the computed structures has been evaluated by several techniques borrowed from crystallography. Two atomic structures of the SERCA1 Ca-ATPase corresponding to different conformations were used as a starting point to fit the electron density corresponding to a different conformation. The fitted models have been compared to published models obtained by rigid domain docking, and their relation to the known crystallographic structures are explored by normal mode analysis. We find that only a few number of modes contribute significantly to the transition. The associated motions involve almost exclusively rotation and translation of the cytoplasmic domains as well as displacement of cytoplasmic loops. We suggest that the movements of the cytoplasmic domains are driven by the conformational change that occurs between nonphosphorylated and phosphorylated intermediate, the latter being mimicked by the presence of vanadate at the phosphorylation site in the electron microscopy structure.     

Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological “nanomachines” it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 μm in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.     

Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization

The complexities of X-ray crystallography and NMR spectroscopy for large protein complexes, and the comparative ease of approaches such as electron microscopy mean that low-resolution structures are often available long before their atomic resolution equivalents. To help bridge this gap in knowledge, we present 3SOM: an approach for finding the best fit of atomic resolution structures into lower-resolution density maps through surface overlap maximization. High-resolution templates (i.e. partial structures or models for multi-subunit complexes) and targets (lower-resolution maps) are initially represented as iso-surfaces. The latter are used first in a fast search for transformations that superimpose a significant portion of the target surface onto the template surface, which is quantified as surface overlap. The vast search space is reduced by considering key vectors that capture local surface information. The set of transformations with the highest surface overlap scores are then re-ranked by using more sophisticated scores including cross-correlation. We give a number of examples to illustrate the efficiency of the method and its restrictions. For targets for which partial complexes are available, the speed and performance of the method make it an attractive complement to existing methods, as many different hypotheses can be tested quickly on a single processor.     

Herpetomonas samuelpessoai: electron microscopy and cytochemistry of electron-dense granules.

Herpetomonas samuelpessoai has membrane-bound electrondense granules in its cytoplasm. The electron density independs on postfixation with osmium tetroxide and is enhanced by uranyl acetate staining. The granules contain iron, have basic proteins cytochemically detected by the silver ammoniacal method, and have a peroxidase activity as detected by the diaminobenzidine method. Some of the granules also have acid phosphatase activity. It is suggested that the granules may represent either lysosomes or a storage form of tetrapyrrole derivatives which are essential for the growth and metabolism of most Trypanosomatidae.     

Reprint of “Stereology meets electron tomography: towards quantitative 3D electron microscopy” [J. Struct. Biol. 159 (2007) 443–450]

Stereological tools are the gold standard for accurate (i.e., unbiased) and precise quantification of any microscopic sample. The past decades have provided a broad spectrum of tools to estimate a variety of parameters such as volumes, surfaces, lengths, and numbers. Some of them require pairs of parallel sections that can be produced by either physical or optical sectioning, with optical sectioning being much more efficient when applicable. Unfortunately, transmission electron microscopy could not fully profit from these riches, mainly because of the large depth of field. Hence, optical sectioning was a long-time desire for electron microscopists.This desire was fulfilled with the development of electron tomography that yield stacks of slices from electron microscopic sections. Now, parallel optical slices of a previously unimagined small thickness (2–5 nm axial resolution) can be produced. These optical slices minimize problems related to overprojection effects, and allow for direct stereological analysis, e.g., volume estimation with the Cavalieri principle and number estimation with the optical disector method.Here, we demonstrate that the symbiosis of stereology and electron tomography is an easy and efficient way for quantitative analysis at the electron microscopic level. We call this approach quantitative 3D electron microscopy.     

Polymorphism and ultrastructural organization of prion protein amyloid fibrils: an insight from high resolution atomic force microscopy

Amyloid fibrils were produced from the full-length mouse prion protein (PrP) under solvent conditions similar to those used for the generation of synthetic prions from PrP 89-230. Analysis of the ultrastructure by atomic force microscopy revealed extremely broad polymorphism in fibrils formed under a single growth condition. Fibrils varied with respect to the number of constitutive filaments and the manner in which the filaments were assembled. PrP polymerization was found to show several peculiar features: (i) the higher-order fibrils/ribbons were formed through a highly hierarchical mechanism of assembly of lower-order fibrils/ribbons; (ii) the lateral assembly proceeded stepwise; at each step, a semi-stable fibrillar species were generated, which were then able to enter the next level of assembly; (iii) the assembly of lower into higher-order fibrils occurred predominantly in a vertical dimension via stacking of ribbons on top of each other; (iv) alternative modes of lateral association co-existed under a single growth condition; (iv) the fibrillar morphology changed even within individual fibrils, illustrating that alternative modes of filament assembly are inter-convertible and thermodynamically equivalent. The most predominant fibrillar types were classified into five groups according to their height, each of which was divided in up to three subgroups according to their width. Detailed analysis of ultrastructure revealed that the fibrils of the major subtype (height 3.61(+/-0.28)nm, width 31.1(+/-2.0)nm) were composed of two ribbons, each of which was composed of two filaments. The molecular volume calculations indicated that a single PrP molecule occupied a distance of approximately 1.2 nm within a single filament. High polymorphism in fibrils generated in vitro is reminiscent of high morphological diversity of scrapie-associated fibrils isolated from scrapie brains, suggesting that polymorphism is peculiar for polymerization of PrP regardless of whether fibrils are formed in vitro or under pathological conditions in vivo.     

Hymenolepis microstoma: tegumentary disks.

The distribution and concentration of disk-like tegumentary bodies were studied in adult Hymenolepis microstoma using electron microscopy. Two sets of tissue were examined. In the first set, the tissue was post-fixed with osmic acid and stained with uranyl acetate and bismuth subnitrate or with potassium permanganate. In the second set, osmium exposure was avoided and the tissue was stained with either phosphotungstic acid or potassium permanganate. The staining revealed that the electron-opaque disk is composed of a dense central core that is surrounded by an electron-lucid region. Electron-opaque and electron-transparent bodies were found to be present at constant concentrations in the tegument of the immature, mature, and gravid regions. Also, it was found that postfixation with osmic acid concealed the presence of numerous stacks of electron-opaque bodies in the tegument. The stacks of disks have a tendency to be aligned perpendicular to the tegument surface.     

Cathodoluminescence-emitting lipid droplets in rat testis: a study by analytical color fluorescence electron microscopy

Cathodoluminescence (CL) from lipid droplets (LDs) in the rat testis was examined by analytical color fluorescence electron microscopy. The results show that (1) the Cl at wavelengths of 320 nm (CL320) and 450 nm (CL450) is derived from cholesterol esters and a mixture of lipids including vitamin A esters, respectively; (2) CL320 in the LDs of Leydig cells sharply decreases on postnatal day 21, while CL320 and CL450 in the LDs of Sertoli cells begin to be detectable; (3) the CL450-emitting LDs in seminiferous tubules, whose distributional patterns display cyclic changes during the spermatogenic cycle, are involved in spermatogenesis; and (4) the intensity of CL as well as the distributional patterns of CL-emitting LDs in testicular cells change after hypophysectomy, vitamin-A deficiency, and treatment with ethylene dimethane sulfonate and testosterone propionate. This study demonstrates that analytical color fluorescence electron microscopy is a useful tool for in-vivo observation of some specific compounds which cannot be visualized by other methods.     

Cytogenetic applications of high resolution secondary ion imaging microanalysis: detection and mapping of tracer isotopes in human chromosomes.

Analytical imaging by secondary ion mass spectrometry (SIMS) using a state-of-the-art scanning ion microprobe enables the detection and mapping of tracer isotopes in human metaphase chromosomes. The stimulated mitosis of cells cultured in media containing labelled nucleosides, typically 14C-labelled thymidine or adenosine, and BrDU, yields chromosomes that have incorporated the labelled molecule in their constituent DNA. The label is subsequently detected and localized by SIMS imaging. The relative label signal intensities of sister chromatids can be quantified. The occurrence of sister chromatid exchanges (SCE) can be detected. The distribution of specific nucleosides can be directly mapped. This is non-uniform along the chromatids, giving rise to characteristic banding patterns (SIMS bands) that seem to correspond to the well known G- or Q-bands resulting from conventional staining methods. The study of a number of cytogenetic problems is expected to benefit from the use of this new method of approach, similar in principle, but potentially more sensitive and capable of higher spatial resolution than autoradiography.     

The development of the macrogamete and oocyst wall in Eimeria maxima: immuno-light and electron microscopy

We have identified, and followed the development of three macrogamete organelles involved in the formation of the oocyst wall of Eimeria maxima. The first were small lucent vacuoles that cross-reacted with antibodies to the apple domains of the Toxoplasma gondii microneme protein 4. They appeared early in development and were secreted during macrogamete maturation to form an outer veil and were termed veil forming bodies. The second were the wall forming bodies type 1, large, electron dense vacuoles that stained positively only with antibodies raised to an enriched preparation of the native forms of 56 (gam56), 82 (gam82) and 230 kDa (gam230) gametocyte antigens (termed anti-APGA). The third were the wall forming bodies type 2, which appeared before the wall forming bodies type 1 but remain enclosed within the rough endoplasmic reticulum and stained positively with antibodies raised to recombinant versions of gam56 (anti-gam56), gam82 (anti-gam82) and gam230 (anti-gam230) plus anti-APGA. At the initiation of oocyst wall formation, the anti-T. gondii microneme protein 4 positive outer veil detached from the surface. The outer layer of the oocyst wall was formed by the release of the contents of wall forming bodies type 1 at the surface to form an electron dense, anti-APGA positive layer. The wall forming bodies type 2 appeared, subsequently, to give rise to the electron lucent inner layer. Thus, oocyst wall formation in E. maxima represents a sequential release of the contents of the veil forming bodies, wall forming bodies types 1 and 2 and this may be controlled at the level of the rough endoplasmic reticulum/Golgi body.     

Inflammation with restricted lysosomal proteolysis during early ascites carcinoma invasion of mouse parietal peritoneum. A medium and high-voltage electron microscopic and cytochemical study

A carcinoma invasion system (Krebs-2 and Ehrlich tetraploid ascites tumors invading mouse peritoneum) was studied by high-voltage electron microscope (HVEM) stereoscopy, conventional (medium voltage) electron microscopy (MVEM), and cytochemistry. Tumor cells entered areas of peritoneum (mainly parietal) only where mesothelial cells were damaged and where there was inflammation of the underlying stroma. The initial invasion was different from that of most other invading carcinomas in that there was minimal breakdown of basal lamina and collagen. Neither tumor cells, inflammatory leukocytes nor peritoneal fibroblasts showed significant secondary lysosome production or release of intracellular or extracellular acid phosphatase. Morphological and cytochemical criteria suggest that in some invading carcinomas, as with non-tumor migrating cells such as leukocytes, widespread proteolysis due to diffusion of proteases is not a prerequisite for invasion of stromal connective tissue.     

Structural study of translating 70 S ribosomes from Escherichia coli: I. Electron microscopy

Translating 70 S ribosomes of Escherichia coli either in the pre-translocation or in the post-translocation state have been prepared by using the cell-free translation system in poly(U)—S—S—Sepharose columns [Methods Enzymol. (1979) 59, 382–398]. Electron microscopy study of the preparations has demonstrated that: (1) the mutual orientation of the ribosomal subunits in the translating ribosomes is the same as proposed by Lake for routine 30 S·50 S couples [J. Mol. Biol. (1976) 105, 111–130]; (2) the L7/L12 stalk of the 50 S subunit sticks out from the 70 S particle and does not join the 30 S subunit; (3) pre-translocation and post-translocation state ribosomes do not differ in mutual orientation of the subunits and in the position of the L7/L12 stalk, within the limits of electron microscopy resolution.     

The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions

The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.     

Cellular prion protein electron microscopy: attempts/limits and clues to a synaptic trait. Implications in neurodegeneration process

Prion diseases are caused by an infectious agent constituted by a rogue protein called prion (PrP^Sc) of neuronal origin (PrP^c) and are exemplified by Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in cattle. Considerable efforts have been made to understand the cerebral damage caused by these diseases but a clear comprehensive view cannot be achieved without defining the neurophysiological function of PrP^c. This lack of information is in part attributable to our ignorance of the precise localization of PrP^c in the brain neuronal cell. One relevant option to explore this aspect is to undertake PrP immunohistochemistry at the electron-microscopy level, knowing that this challenge raises major technical constraints. In describing the attempts and restrictions of the various approaches used, we review here the efforts that have been invested in this particular field of prionology. The common result emerging from these contributions is that the synapse could be the site at which PrP^c exerts its critical activity. This location suggests, in the perspective of synaptic regulation, that PrP^c can be assigned multiple biological functions and supports the novel concept that prion-like changes are involved in long-term memory formation. The synaptic trait of PrP^c and PrP^Sc suggests that synapse loss is the key event in neuronal death. Interestingly, synaptic alterations are also considered to be predominant in the pathophysiological mechanism in Alzheimer, Parkinson and Huntington diseases. All these brain disorders, characterized by the formation of a specific amyloid protein of synaptic origin, can be classified under the heading of amyloidogenic synaptopathies.     

Trypanosoma cruzi: isolation and characterization of membrane and flagellar fractions.

A cell fractionation procedure for obtaining membrane and flagellar fractions was developed using Trypanosoma cruzi epimastigote forms. The cells, swollen in an hypotonic medium, were disrupted in the presence of a nonionic detergent, and fractions were isolated by differential centrifugation. The flagellar fraction, pelleted in 10 min at 10,000g, was further purified on a sucrose gradient. The membrane fraction was obtained by centrifugation of the supernatant at 27,000g for 30 min. Electron microscopy of the isolated fractions demonstrated a high degree of purity of each fraction. The membrane fraction showed homogeneous vesicles with low ribosome content. In frozen-etched preparations, the distribution of intramembranous particles on the vesicles was similar to that of the plasma membrane of intact cells. Enzymatic assays indicated that the membrane and flagellar fractions had low contamination with mitochondria and lysosomes. 5′-Nucleotidase activity was not detected in the membrane fraction; Mg²⁺-dependent ATPase activity was slightly enhanced, although, the enzyme was not sensitive to Na⁺, K⁺, and Ca²⁺ ions. The membrane fraction showed about five times the adenylyl cyclase activity of the whole homogenate. Gel immunodiffusion revealed the whole antigen of T. cruzi extracted by formamide to be identical to the membrane fraction when both were tested against rabbit anti- T. cruzi (epimastigote) immune serum.     

Bombesin-like immunoreactivity in eosinophils. A light and electron microscopic study: effect of fixatives and cross-reactivity with various compounds.

Eosinophils immunopositive for bombesin tetradecapeptide were detected by means of light and electron microscopy in human and rat gastrointestinal tract and pulmonary tissue. This immunoreaction was only evidenced after the use of acetic acid-containing fixative such as Bouin's fluid. The dependence of this immunostaining on fixatives and time course were extensively studied. This immunoreaction promotes mainly one epitope probably associated with the C-terminal sequence. This epitope seems also to be present in other neuropeptides such as substance P (SP) and, to a lesser extent in chemotactic factors like formyl peptide (fMLP) or eosinophil chemotactic factor of anaphylaxis (ECF-A). At the electron microscopic level, the immunopositivity was associated with eosinophil membranes.     

Fasciola hepatica: an electron microscope autoradiographic study of protein synthesis and secretion by gut cells in tissue slices.

A loop technique for electron microscope autoradiographic studies on slices of Fasciola hepatica is described, and used to study the synthesis of protein-containing bodies by gut cells of the fluke. Slices were pulse labeled with tritiated tyrosine, methionine, leucine, and phenylalanine, and, after appropriate chase periods in unlabeled medium, were fixed with formaldehyde and prepared for electron microscopy by a procedure involving ethylene glycol dehydration. Labeled amino acids were found to be incorporated into protein, or glyoprotein, in the gut cells of the slices by a GER-Golgi complex mediated mechanism similar to that which occurs in vertebrate tissues. The precursors appeared to enter the cells across their basal and lateral plasma membranes and mature secretory bodies were discharged at the cell apex.     

Trypanosoma cruzi: location of a specific antigen on the surface of bloodstream trypomastigote and culture epimastigote forms.

The nature of surface antigens of culture epimastigote and bloodstream trypomastigote forms of Trypanosoma cruzi was investigated by light and electron microscopy using indirect immunofluorescence and peroxidase labeling techniques and antisera against unique, common, and contaminant antigens. A specific antigen, identified by monospecific rabbit antiserum (anti-component 5 antiserum), is the major constituent of the cell surface and flagellar membrane of both the culture epimastigote and bloodstream trypomastigote forms. Antigens of heterologous stercorarian trypanosomes (Trypanosoma rangeli) and of culture medium proteins could not be detected on the cell surface of culture epimastigote forms and bloodstream trypomastigote forms.     

Crystal structure of human epidermal kallikrein 7 (hK7) synthesized directly in its native state in E. coli: insights into the atomic basis of its inhibition by LEKTI domain 6 (LD6)

Human kallikrein 7, a major protease of human skin, has been synthesized directly in its native conformation in Escherichia coli by forcing the secretion of the newly synthesized polypeptide into the bacterial periplasm. The procedure yields a stable kallikrein 7 with highly specific activity that is inhibited efficiently by its specific inhibitor LEKTI domain 6. The protein was crystallized, and its three-dimensional structure was solved in the absence of protease inhibitors. The structure obtained agrees with that reported recently for human tissue kallikrein 7 crystallized in the presence of protease inhibitors from a preparation obtained in a baculovirus protein expression system. A model of the interaction between the protease and its inhibitor is proposed on the basis of both the three-dimensional structure of human tissue kallikrein 7 reported here and that of the LEKTI domain 6 solved previously by NMR.