Ryanodine receptors (RyRs) function as the major intracellular calcium release channels in striated muscle, where they also play a central role in excitation-contraction (e-c) coupling, the signal transduction process by which neuron-induced depolarization of the muscle plasma membrane leads to release of Ca from the sarcoplasmic reticulum. Structurally, RyRs are the largest ion channels known, being composed of 4 identical large subunits (565 kDa). In situ, RyRs interact with numerous proteins that are essential for e-c coupling or regulation thereof. Some of these ligands include calmodulin, a 12-kDa FK506-binding protein (FKBP, an immunophi1 in), calsequestrin, triadin, and the dihydropyridine receptor (DHPR).

Detergent-solubilized, purified RyRs appear to retain their native structure as assessed by electron cryo-microscopy, and are amenable to three-dimensional reconstruction by single-particle image processing techniques. In Fig. 1, a solid-body representation of the reconstructed skeletal muscle RyR shows the structural complexity that is revealed at moderate resolutions (3-4 nm).

3D electron microscopy of macromolecules is now moving beyond the very successful tomographic approach of using images of a tilt-series of 2D crystals at known angles to single randomly oriented particles with less and less internal symmetry. The success of 3D reconstruction of symmetrical objects was predicated primarily on the redundancy of information due to lateral symmetry in 2D crystals, or to internal rotational symmetry in the icosahedral, helical or cylindrically symmetric particles. Such a spatially predictable redundancy permitted both a reduction in irradiation dose, to reduce radiationinduced structural alterations of the molecules, and an averaging of image noise due to the low number of electrons used and from the specimen support.

For 3D reconstruction from single particles the noise level in the images is crucial for the accurate determination of the relative orientation of the particles. In principle the central line theorem was recognized to be as applicable to asymmetric particles as it was to symmetrical viruses.

Nucleic acid polymerase structure has been studied by both X-ray and electron crystallography. To date, only the smaller, single subunit polymerases have been subjected to X-ray analysis, including the bacteriophage T7 RNA polymerase, which is the only RNA polymerase whose structure is known to atomic resolution. Lower resolution structures of several multisubunit polymerases have been determined by electron crystallography, including a mutant form of yeast RNA polymerase II which lacks subunits Rpb4 and Rpb7 (denoted A4/7 polymerase). All polymerase structures obtained by both X-ray and electron crystallography show a large cleft appropriate in size for binding duplex DNA, and further appear to contain a mobile arm allowing open and closed conformations of the cleft, presumably permitting entry and retention of DNA. Subunits Rpb4 and Rpb7 of RNA polymerase II form a dissociable subcomplex that has been implicated in the stress response and in the initiation of transcription. Human homologs of Rpb4 and Rpb7 have been identified.

Herpesviruses form an extensive family of DNA viruses, in which three subfamilies called alpha-, beta- and gammaherpesviruses, respectively, are distinguished on the basis of biological properties. In terms of overall structure, all herpesviruses conform to a common plan: the virion consists of a thick-walled capsid, ∼ 1250 Å in diameter, containing the genome, surrounded by a complex layer of proteins called the tegument (a feature unique to herpesviruses), and a lipoprotein envelope. At a more detailed level, it has not been clear whether the three subfamilies are also differentiated structurally. The molecular architecture of alphaherpesvirus capsids has been studied by cryoelectron microscopy of herpes simplex virus 1, revealing its icosahedral (T=16) surface lattice and the locations of the four abundant shell proteins. To ascertain how closely these features are emulated in a betaherpesvirus, we have studied capsids of simian cytomegalovirus (SCMV) by similar methods. By comparing the structures of nuclear capsids and cytoplasmic capsids (which have bound some tegument proteins),

Vaults are highly conserved ribonucleoprotein complexes found in thousands of copies per cell in various tissues. The major vault protein, pi 04, accounts for over 70% of the particle mass and has been recently found to be involved in cancer cell multidrug resistance. We have utilized cryoelectron microscopy (cryo-EM), and three-dimensional image reconstruction to generate a 3-D structure of the vault particle. Individual particle images were isolated using the QVIEW software package, which simultaneously performs density exclusion, planar background subtraction, and application of an elliptical mask. The IMAGIC-5 software package was used for the subsequent particle orientation and reconstruction steps (Fig. I).

A symmetry self-search test was used to measure the signal strength for a variety of point groups and the highest correlation was found for the cyclic 8-fold point group. We have utilized the sinogram correlation algorithms in IMAGIC-5 to find the Euler angles of both 1 μm and 2 μm defocus particle images.

ATP-dependent proteases play a major role in regulatory protein degradation in both prokaryotic and eukaryotic cells. ATP-dependent proteases in E. coli fall into two classes. The first class requires the interaction of structurally separate proteases with an ATPase, whereas in the second class both the protease and ATPase are formed from regions of the same polypeptide chain. We have studied the structure of several of these protein degrading complexes in E. coli and have found a remarkable similarity in the architecture of these macromolecular assemblies.

The prototypical protease of the first class has as its proteolytic component ClpP, a 14 subunit (MW 21,500) complex arranged as two lOnm-diameter stacked rings of seven subunits each. ClpP can interact with either one of two ATPases, ClpA or ClpX, each with unique substrate specificity. ClpA has two ATP-binding sites per subunit (MW 84,000), and its subunits are arranged as a 13nm (diameter) hexameric ring (MW -500,000).

Since cellular structures are rebuilt continually, protein degradation is essential for the maintenance of homeostasis. Misfolded proteins ensuing from genetic defects or environmental stress, are prone to aggregation; chaperones and proteases cooperate in minimizing such unproductive interactions. Last, but not least, protein degradation serves to terminate the lifespan of many regulatory proteins at distinct times and thus features as a key regulatory element itself. Proteins destined for degradation must be recognized and selected within the crowded environment of the cell. The stratagem of self-compartmentalization is key to controlling cellular proteolysis (1).

In recent years, a number of multisubunit proteolytic complexes have been described which possess large internal cavities or nano-compartments. This allows them to confine the proteolytic action to their interior; access to these inner compartments is usually restricted to the unfolded proteins. This, in turn, makes it necessary for these proteases to interact - either in a transient or in a permanent manner

The eukaryotic 20S proteasome (700 kDa) serves as the core complex for the breakdown of most cytosolic proteins by the ubiquitin-dependent pathway. This cylinder-shaped proteolytic assembly (17 nm long, 11 nm diameter) consists of four stacked heptameric rings that help to form a central cavity where degradation occurs. The catalytic sites are located on the cavity surface of the two middle (3 rings while the outer a rings serve as docking sites for various regulatory complexes.

PA700 (700 kDa, 20 protein subunits) is the major regulatory complex of the proteasome, forming a “cap” that attaches to either or both proteasome ends. The resulting superassembly structurally resembles the larger, more active 26S proteasome and exhibits both a higher intrinsic peptidase activity as well as a wider range of substrate specificity, including ubiquitin-tagged proteins. A second regulatory complex, the modulator (300 kDa), further stimulates the effects of PA700 at subsaturating concentrations of the activator with no detectable effect on the proteasome in the absence of PA700.

HK97 is a tailed temperate bacteriophage of E. coli that builds an icosahedral capsid using steps that include regulated assembly, proteolysis, radical conformational changes and the formation of novel covalent bonds (Fig. 1). This pathway is being exploited as a model system to explore how the formation of multiprotein complexes can be regulated by each of these mechanisms. We have identified and purified at least four intermediates (Prohead I, Prohead II, Head I and Head II) and examined them by cryo-electron microscopy and three dimensional reconstruction procedures (Fig. 2). Comparison of particle reconstructions at resolution of about 25 - 30 A have lead to major insights into the causes and purposes of the regulated changes that we have also characterized biochemically and genetically.

Prohead I consists of 420 copies of the 42 kDa gp5 capsid protein arranged as 72 blister-shaped morphological capsomers in a thick walled hollow T=7 icosahedral particle with a diameter of -470 Å.

Human α2 macroglobulin (α2M) has structural and functional properties that contribute to its uniqueness as proteinase inhibitor. It is the largest known (Mr=720,000) and the only natural proteinase inhibitor which has a broad range of reactivity and for which the reaction is irreversible. It has a vital role in the clearance of proteinases from the circulation and in regulating their activity in fibrinolysis, coagulation and complement activation.

An α2M molecule can entrap two proteinase molecules such as chymotrypsin and trypsin and can therefore be considered to contain two functional domains. Each subunit in the homotetramer has a bait region with cleavage sites for nearly all known endoproteinases and an internal thiol ester bond. A proteinase cleaves the two bait regions within both functional units leading to an activation and cleavage of the thiol ester bonds. Consequently, α2M undergoes a major structural change resulting in the irreversible entrapment of the proteinase.

Gold particles as markers in immunocytochemical procedures have undergone tremendous changes since their introduction by Faulk and Taylor (1). With the development of both small colloidal gold (<3 nm) and 1.4 nm gold clusters (Nanogold™) for immunocytochemical labeling, steric hindrance has been significantly reduced. In a comparative study using colloidal gold-anti CD3 complexes and particle sizes of 5 nm, 3 nm and less than 3 nm on surface labeling of lymphocytes there was a 1.5 fold increase in labeling density when 3 nm particles were used. There was no increase when smaller particles were used (unpublished data). In another unpublished experiment, labeling densities on an astrocytoma cell line were compared between 3nm colloidal gold-CD44 Fab’ fragments and 1.4 nm gold-CD44 Fab’ fragments. Again there was no detectable differences between particle sizes. The limiting factors remain the size of the IgG or Fab’ fragment, the ability to bind it whether by absorption or by covalent bonding without rendering it inactive and also the accessibility of the target molecule in the tissue.

The field of immunocytochemistry comprises a large body of methodologies whose purpose is to obtain spatial and temporal information about biological samples with a high degree of chemical specificity. The major differences in immunocytochemical methods are: (1) type of sample preparation (i.e., pre-embedding or post-embedding) and (2) type of detection system (i.e., chromogenic, fluorochromes, or particulate). The history of advances in immunocytochemistry can be understood, to a large extent, through the development of the various detection systems. All of these labeling systems have their appropriate applications and are in use today.

The introduction of colloidal gold as a particulate immunoprobe revolutionized immunocytochemistry, particularly at the ultrastructural level. The fact that these probes are discrete particles that are electron dense contributes to their wide acceptance. Due to the particulate nature of these probes, labeling density over a given structure or region of a cell can be determined by simple counting procedures.

Fluorescein and the 1.4 nm Nanogold cluster have been separately attached to polyclonal antibody Fab’ fragments to generate combined fluorescent and gold secondary antibody probes (1, 2), and in comparisons with Nanogold, colloidal gold and fluorescein-labeled secondary antibodies, neither label was found to be significantly compromised by the presence of the other. The proximity to a gold label with which a fluorophore retains sufficient fluorescence emission intensity to be useful is limited by non-radiative fluorescence resonance energy transfer (FRET) (3). This is a function of the degree of overlap of the fluorophore emission spectrum with the metal particle absorbtion spectrum, and of the separation of the metal particle and the fluorophore (4); for an effective dual-labeled probe, separation should be greater than the Forster distance (3), at which 50 % of excited-state decay occurs by FRET.

Molecular cloning offers an opportunity for designing constructs for expressing chimeric proteins containing incorporated reporter molecules. In this approach, molecules are identified based upon reporter molecules which are expressed within cells as a result of transfection, instead of marking them through immunolabeling, in situ hybridization, or derivative incorporation. This approach is particularly useful for studies involving integrated microscopy. Integrated microscopy allows us to assemble images of the same cell obtained with different microscopes into one comprehensive message concerning cellular functions. Integration of fluorescence and electron spectroscopic imaging is particularly promising. The main advantage of this approach relies in overcoming limitations of each type of microscopy alone i.e. in studies on living cells limitations in spatial resolution of light microscopy and in analysis of supramolecular organization, limitation of electron microscopy to frozen or fixed cells. For this purpose, special reporter molecules suitable for selected modes of microscopy have to be used.

In situ detection of specific antigens and nucleic acid sequences is possible with a variety of immunohistochemical (IHC) and in situ hybridization (ISH) methods. The drawback of conventional methodologies is their relatively low detection sensitivity. Improved detection efficiency is required in preparations containing only minute amounts of detectable antigens or only few copies of specific DNA and/or RNA sequences, which is often the case in routine paraffin cytoand histopathologic material. The use of gold as the label, followed by silver amplification (autometallography) avoids hazardous reagents and also gives an improved resolution compared to „standard” methods. Sensitivity problems may now be overcome by our specific combinations of recent technologies, utilitizing reporter molecule amplification with labeled tyramides (CARD, catalyzed reporter deposition, or tyramide signal amplification), followed by streptavidin bound to a new gold label, Nanogold™ (Nanoprobes, Stony Brook, NY), and silver acetate autometallography.

Colloidal gold is routinely used conjugated to ligands or antibodies as a label for the detection of cell structures by transmission (TEM) and scanning (SEM) electron microscopy. Silver enhancement, a procedure that amplifies the size of gold spheres, is used for light microscopic (LM) observation of colloidal gold. These techniques are valuable in localization studies but it is difficult to quantitate the level of labeling in larger volumes of tissue solely by microscopic means.

Instrumental Neutron Activation Analysis (INAA) can be used to provide a quantitative index of gold accumulation at the organ and tissue levels. Given that gold is not naturally found in the body in any substantial amount and that colloidal gold and ligand conjugates can be prepared to yield uniform bead sizes, the amount of label can be determined at the organ and tissue levels in whole animal systems.

The green fluorescent protein (GFP) has great potential as a tool for biologists because it can be used as an in vivo real time reporter of protein localization and gene expression in a variety of experimental systems. Wild type GFP, however, has several undesirable properties including low brightness, a significant lag in the development of fluorescence, complex photoisomerization, inefficient protein folding at 37°C, and poor expression in several species. To improve upon these qualities, we have combined an ultra-bright variant of GFP, GFPmutl, with a synthetic gene sequence containing codons preferentially found in highly expressed human proteins. The combination of improved fluorescence intensity and higher expression levels yields an enhanced variant (EGFP) (Table 1) that greatly increases the sensitivity of this reporter.

The natural green emission of GFP can conveniently be monitored by optics designed to detect fluorescein. There are, however, many potential applications for GFP that require additional emission colors.

The emission spectrum from bioluminescent bacteria has been observed to depend on the type of bacteria. Photobacterium phosphoreum species usually show bioluminescence maxima around 472 nm and Photobacterium leiognathi species to slightly longer wavelength. A certain strain (Yl) of Vibrio fischeri, has a yellow bioluminescence with maximum at 542 nm. These differences have been explained as due to the bioluminescence originating from the fluorescence transition of an “antenna” protein, participating in the bioluminescence reaction along with the enzyme bacterial luciferase. The bioluminescence from a number of coelenterates involves a similar participation of an antenna protein, the famous “Green-Fluorescent Protein” being the origin of the bioluminescence emission from these organisms.

The cloning and expression of GFP in heterologous systems introduced a fantastic tool for studying specific gene expression and protein localization inside living cells. However, one aspect of GFP that has not been exploited to its full potential is its use as a quantitative imaging tool. To determine its quantitative usefulness, we have addressed five points that are important in GFP imaging: detectable signal over background, photostability, pH stability of the molecule, temperature dependence of chromophore formation, and estimation and normalization of GFP levels.

To determine the quantitative limits of GFP in cells, several GFP versions (wtGFP, αGFP (F99S/M153T/V163A), S65T, EGFP (F64L/S65T), and a blue-shifted variant, EBFP (F64L/S65T/Y66H/Y145F)) were compared by imaging of GFP expressing cells or by spectroscopic measurements of purified proteins. When imaged, the GFP signals are contaminated by the naturally occurring background autofluorescence, but improved detection can be achieved for each green GFP by combination of confocal microscopy using 488 nm excitation, a rapid cut-on dichroic mirror, and a narrow bandpass emission filter (Figure l).

Green fluorescent protein (GFP) was evaluated as a non-invasive probe to quantify the rheological properties and pH of intracellular aqueous compartments. Spectroscopic studies were done on several bacterially-expressed and purified GFP mutants. GFP-S65T was brightly fluorescent in solution (ƛex 492 nm, ƛem 509 nm) with lifetime 2.9 ns and rotational correlation time ( tc ) ∼20 ns. Recovery of GFP fluorescence after photobleaching was complete with a half-time (t1/2) in aqueous saline of 30 ± 2 ms (5 μm diameter spot) giving a diffusion coefficient of 8.7 x 10-7 cm2/s. The t1/2 was proportional to solution viscosity and was dependent on spot diameter. In contrast to fluorescein, GFP photobleaching efficiency was not affected by solution O2 content, triplet state quenchers, singlet oxygen scavengers, and general radical quenchers. In solutions of higher viscosity, an additional, rapid GFP recovery process was detected and ascribed to reversible photobleaching. The t1/2 for reversible photobleaching was 1.5-5.5 ms (relative viscosity 5-250), independent of spot diameter, and not affected by O2 or quenchers.