Structural features of archaebacterial and eukaryotic proteasomes

The 26S proteasome is the central protease of the ubiquitin-dependent pathway of protein degradation. The molecule has a molecular mass of approximately 2000 kD and has a highly conserved structure in eukaryotes. The 26S proteasome is formed by a barrel-shaped 20S core complex and two polar 19S complexes. The 20S complex has C2 symmetry and is formed by four seven-membered rings of which the outer rings (-type subunits) are rotated by 25.7° relative to the inner rings while the inner rings (-type subunits) are in register. From a comparison of the activity and regulation of the 26S and 20S particles it can be deduced that the 20S particle contains the protease activity while the 19S complex contains isopeptidase, ATPase and protein unfolding activities. In this article we describe the structures of various proteasome complexes as determined by electron microscopy and discuss structural implications of their subunit sequences.     

Structural analysis of a membrane glycoprotein: Glycophorin A

Glycophorin A is the major sialoglycoprotein of the human erythrocyte membrane. Structural studies indicate that this molecule is made up of 3 domains composed of 2 hydrophilic segments which are separated by a region of 22 nonpolar amino acids. The N-terminal half of the molecule contains all the carbohydrate associated with this protein. Glycophorin A forms high-molecular-weight complexes which can be dissociated only under certain conditions. The site of subunit interaction is located within the hydrophobic segment, which serves both to mediate protein-protein and protein-lipid interactions within the bilayer membrane. Glycophorin A spans the membrane presumably as a demeric complex with the carboxyterminal ends extending into the cytoplasm of the red cell. The transmembrane nature of the polypeptide chains finds strong support from the use of specific antibody-ferritin conjugates applied to thin sections of fixed and frozen intact cells. Preliminary information on the analysis of human red cell variants which may lack some or all of the sialoglycopeptides are consistent with the presence in normal cells of a second sialoglycoprotein, provisionally labeled glycophorin B.     

Purification and Characterization of a Major Cell Surface Glycoprotein in Zajdela Ascites Hepatoma Cells Which Displays a Potent Concanavalin A Receptor Activity

A major cell surface sialoglycoprotein with Concanavalin A receptor activity has been isolated from rat Zajdela ascites hepatoma cells. The sialic acid residues of the plasma membrane glycoproteins were specifically labeled by oxidation with NaIO₄ followed by reduction with NaB³H₄. Surface-labeled glycoproteins were released by short incubations with TPCK-trypsin at 37°C and then separated by gel filtration on Sepharose 6B column. The predominantly labeled fraction, GP II₂, was then purified by chromatography on DEAE-cellulose equilibrated with 0.05 M phosphate buffer, pH 7.5, and eluted with increasing molarities of NaCl. It was shown to be homogeneous by protein and carbohydrate staining on SDS-polyacrylamide gels, isoelectric focusing, rechromatography on DEAE-cellulose and immunoelectrophoresis. It has an apparent molecular weight of 110,000 daltons. The location of GP II₂on the cell surface was confirmed by the fact that it could be labeled metabolically with, D-(³H) glucosamine and externally through the nonpenetrating periodate-NaB³H₄ system. GP II₂could not be removed from the cell surface by high salt concentrations, chelator, or chaotropic agents but was released from the membrane by detergents. This suggests that GP II₂could be an integral protein. Analysis of the carbohydrate composition of GP II₂ revealed galactose, N-acetylglucosamine, N-acetylgalactosamine, and sialic acid as major constituents and mannose as a minor one. This suggests that it contains carbohydrate chains both O- and N-linked to the polypeptide chain, most of them being O-linked. Finally, GP II₂has a potent Concanavalin A receptor activity. It inhibits the interaction between Concanavalin A and hepatoma cells and suppresses its effects on hepatoma cell proliferation.     

Human neutrophil plasma membrane. Specific labelling,topological distribution of proteins and surface antigen detection

We describe here the major protein components of a highly purified human neutrophil plasma membrane fraction analyzed by uni- and two-dimensional gel electrophoresis, as well as their glycoprotein nature as determined by PAS staining, [¹²⁵I]-Con A binding and [³H]-sodium borohydride labelling. A polypeptide of about 150kDa appeared as the main Con A binding protein. The topology of the polypeptides has also been determined by protein labelling from the outside of the cell surface by lactoperoxidase catalyzed iodination and from within the bilayer by using the hydrophobic reagent [1251]-iodonaphtylazide. The antigenic features of some cell surface polypeptides have also been determined by the use of monoclonal antibodies. In this context we have detected by immunoprecipitation in human neutrophils the antigen MAC 120, previously found in monocytes and putatively associated with antigen presenting function.Abbreviations Con A Concanavalin A - INA Iodonaphtylazide - mAB monoclonal Antibody - PAS Periodic Acid Schiff reaction - PBS Phosphate Buffered Saline - PMSF Phenylmethylsulfonil Fluoride - PPO 2,5-Diphenyloxazole     

Lectin affinity chromatography of cell surface proteins of novikoff tumor cells

Novikoff hepatocellular carcinoma cells were radioiodinated by a cell surface-specific method using lactoperoxid ase/¹²⁵I. The iodinated proteins were solubilized in 0.5% Nonidet P-40 and subjected to affinity chromatography on Sepharose-conjugated lectins (Ricinus communis agglutinins I or II, soybean agglutinin, concanavalin A, or wheat germ agglutinin) and analyzed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Almost all the iodinated proteins bound to one or more of the Sepharose-conjugated lectins, presumptive evidence that these peptides are glycosylated. Lectin affinity chromatography resolved defined subsets of iodinated glycoproteins and suggested that certain glycoproteins could be fractionated on the basis of heterogeneity of their heterosaccharide moieties. Incubation of the iodinated cells with neuraminidase resulted in increased binding of iodinated proteins to Sepharose-conjugated Ricinus communis agglutinins I and II and soybean agglutinin and decreased binding to Sepharose-conjugated wheat germ agglutinin. Binding of iodinated proteins to concanavalin A was unaffected by neuraminidase treatment of the cells. These studies demonstrate the utility of lectins for the multicomponent analysis of plasma membrane proteins.     

Structural differences in the inner part of Photosystem II between higher plants and cyanobacteria

A detailed comparison of key components in the Photosystem II complexes of higher plants and cyanobacteria was carried out. While the two complexes are overall very similar, significant differences exist in the relative orientation of individual components relative to one another. We compared a three-dimensional map of the inner part of plant PS II at 8 Å resolution, and a 5.5 Å projection map of the same complex determined by electron crystallography, to the recent 3.5–3.8 Å X-ray structures of cyanobacterial complexes. The largest differences were found in the rotational alignment of the cyt b_^559 subcomplex, and of the CP47 core antenna with respect to the D1/D2 reaction centre. Within the D1/D2 proteins, there are clear differences between plants and cyanobacteria at the stromal ends of membrane-spanning helices, even though these proteins are highly homologous. Notwithstanding these differences in the protein scaffold, the distances between the critical photosynthetic pigment cofactors seem to be precisely conserved. The different protein arrangements in the two complexes may reflect an adaptation to the two very different antenna systems, membrane-extrinsic phycobilisomes for cyanobacteria, and membrane-embedded chlorophyll a/b proteins in plants.     

Structural physiology based on electron crystallography

There are many questions in brain science, which are extremely interesting but very difficult to answer. For example, how do education and other experiences during human development influence the ability and personality of the adult? The molecular mechanisms underlying such phenomena are still totally unclear. However, technological and instrumental advancements of electron microscopy have facilitated comprehension of the structures of biological components, cells, and organelles. Electron crystallography is especially good for studying the structure and function of membrane proteins, which are key molecules of signal transduction in neural and other cells. Electron crystallography is now an established technique to analyze the structures of membrane proteins in lipid bilayers, which are close to their natural biological environment. By utilizing cryo-electron microscopes with helium cooled specimen stages, which were developed through a personal motivation to understand functions of neural systems from a structural point of view, structures of membrane proteins were analyzed at a resolution higher than 3 Å. This review has four objectives. First, it is intended to introduce the new research field of structural physiology. Second, it introduces some of the personal struggles, which were involved in developing the cryo-electron microscope. Third, it discusses some of the technology for the structural analysis of membrane proteins based on cryo-electron microscopy. Finally, it reviews structural and functional analyses of membrane proteins.     

Structural study of N-linked sugar chains of sheep erythrocyte membrane glycoproteins

Our previous study showed that non-reducing terminal galactose residues of N-linked sugar chains present in sheep erythrocyte membrane glycoproteins are important for rosette formation with T lymphoblastic cells [Ogasawara et al. (1995) Immunol Lett 48: 35–38]. As a first step to elucidate the significant structures of sugar chains involved in rosette formation, we analysed N-linked sugar chains released from the membrane glycoproteins by hydrazinolysis. The oligosaccharides were labeled with NaB3H4 and fractionated using columns of Aleuria aurantia lectin-Sepharose, MonoQ and Bio-Gel P-4. Structural analyses of oligosaccharides by sequential exoglycosidase digestion in combination with methylation analysis revealed that the membrane glycoproteins contain bi- (19%), tri- (33%), and tetraantennary (44%) complex-type oligosaccharides and that the oligosaccharides having exposed galactose residues amount to 40% of the total.     

Structural and functional studies of the response regulator HupR

HupR is a response regulator that controls the synthesis of the membrane-bound [NiFe]hydrogenase of the photosynthetic bacterium Rhodobacter capsulatus. The protein belongs to the NtrC subfamily of response regulators and is the second protein of a two-component system. We have crystallized the full-length protein HupR in the unphosphorylated state in two dimensions using the lipid monolayer technique. The 3D structure of negatively stained HupR was calculated to a resolution of approximately 23 A from tilted electron microscope images. HupR crystallizes as a dimer, and forms an elongated V-shaped structure with extended arms. The dimensions of the dimer are about 80 A length, 40 A width and 85 A thick. The HupR monomer consists of three domains, N-terminal receiver domain, central domain and C-terminal DNA-binding domain. We have fitted the known 3D structure of the central domain from NtrC1 Aquifex aeolicus protein into our 3D model; we propose that contact between the dimers is through the central domain. The N-terminal domain is in contact with the lipid monolayer and is situated on the top of the V-shaped structure. The central domain alone has been expressed and purified; it forms a pentamer in solution and lacks ATPase activity.     

Synthesis and deposition of oocyte envelopes in the Colorado beetle,Leptinotarsa decemlineata say

Summary Electron microscopical and autoradiographic methods demonstrate that the secretion vesicles (SV), which are condensed by the Golgi-complexes of the follicle cells of the Colorado beetle, contain proteins which can be labelled with ³H-leucine. The labelled proteins are transported to the oocyte during vitellogenesis. At the end of yolk deposition, a few SV, situated just above the microvilli, disintegrate and give rise to the two layers of the vitelline membrane (VM). During the laying down of the VM or perhaps at a slightly earlier stage a layer is deposited beneath the basement membrane of the follicle cells. This layer may be important in inducing the formation of the egg membranes. Once the VM has formed, the follicle cells degenerate completely. The chorionic inner layer arises from the breakdown of SV, while the chorionic outer layer is formed from the degenerated follicle cells.Dr. A. de Loof gratefully acknowledges a mandate as Aangesteld Navorser of the National Foundation of Scientific Research in Belgium. He also thanks Prof. Dr. A. Gillard for his very helpfull criticism, Dr. W. Mordue (Cambridge) for his help in correcting the language, Prof. Dr. A. Lagasse, for supplying facilities in his laboratory of EM, Mr. W. Bohyn for operating the EM and Mr. G. Maes for photography. Special thanks to Drs. G. Vrensen (Nijmegen) for the introduction in autoradiographic techniques.     

N‐glycoprotein surfaceome of human induced pluripotent stem cell derived hepatic endoderm

Using cell surface capture technology, the cell surface N‐glycoproteome of human‐induced pluripotent stem cell derived hepatic endoderm cells was assessed. Altogether, 395 cell surface N‐glycoproteins were identified, represented by 1273 N‐glycopeptides. This study identified N‐glycoproteins that are not predicted to be localized to the cell surface and provides experimental data that assist in resolving ambiguous or incorrectly annotated transmembrane topology annotations. In a proof‐of‐concept analysis, combining these data with other cell surface proteome datasets is useful for identifying potentially cell type and lineage restricted markers and drug targets to advance the use of stem cell technologies for mechanistic developmental studies, disease modeling, drug discovery, and regenerative medicine.     

Structural basis for the assembly and gate closure mechanisms of the Mycobacterium tuberculosis 20S proteasome

Mycobacterium tuberculosis (Mtb) possesses a proteasome system analogous to the eukaryotic ubiquitin‐proteasome pathway. Mtb requires the proteasome to resist killing by the host immune system. The detailed assembly process and the gating mechanism of Mtb proteasome have remained unknown. Using cryo‐electron microscopy and X‐ray crystallography, we have obtained structures of three Mtb proteasome assembly intermediates, showing conformational changes during assembly, and explaining why the β‐subunit propeptide inhibits rather than promotes assembly. Although the eukaryotic proteasome core particles close their protein substrate entrance gates with different amino terminal peptides of the seven α‐subunits, it has been unknown how a prokaryotic proteasome might close the gate at the symmetry axis with seven identical peptides. We found in the new Mtb proteasome crystal structure that the gate is tightly sealed by the seven identical peptides taking on three distinct conformations. Our work provides the structural bases for assembly and gating mechanisms of the Mtb proteasome.     

Cytochemical study of role of α-d-mannose- and β-d-galactose-containing glycoproteins in apoptosis

Recently, we found increased levels of -d-mannose- and -d-galactose-containing glycoproteins in plasma membrane of the apoptotic murine leukemia L1210 cells (Bilyy & Stoika 2003). That indicator was suggested to be a novel marker of apoptosis in L1210 cells. The aim of our present work was to reveal if these changes in glycoprotein expression can be common for apoptotic cells of different origin and for various ways of apoptosis induction. It was demonstrated that an elevated expression of plasma membrane glycoproteins rich in -d-mannose and -d-galactose did not depend on type of cell line and its tissue origin as well as on nature of apoptosis-inducing agent. We also found that an increase in membrane glycoprotein expression was dependent on concentration of apoptosis-inducing agent and was time-dependent. Changes in glycoproteins expression were detected as early as 9–12 hours after apoptosis induction. Two hours pretreatment of cells with non-labeled lectin decreased plasma membrane staining with corresponding peroxidase-labeled lectin, probably because of lectin-induced internalization of specific membrane glycoproteins. PSL-lectin-affinity procedure was developed for isolation of apoptotic cells from their mixed population with normal cells. Lectin-dependent agglutination analysis showed that this process occurs at much lower lectin dilutions in the apoptotic cells than in the non-apoptotic cells. Thus, we found that -d-mannose- and -d-galactose-containing glycoproteins can be used for lectinocytochemical detection, study and isolation of apoptotic cells.     

Radioiodination studies of the envelopes from Xenopus laevis eggs

To investigate the molecular basis of the observed morphological and biological characteristics of coelomic egg envelopes (CE), vitelline envelopes (VE), and fertilization envelopes (FE) of Xenopus laevis eggs, envelopes were radioiodinated under a variety of conditions: in situ, isolated and intact, or solubilized. The distribution of 125I in envelope components was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Each envelope type displayed unique profiles when iodinated in the intact state. A major constituent of VE, the 41,500 molecular weight component, was not labeled in the intact state, although the corresponding component of CE was heavily labeled. After dissociation of the envelope by guanidine-HCl or sodium dodecyl sulfate, all of the components could be radioiodinated. However, when the envelopes (VE and FE) were dissolved by heating and subsequently radioiodinated by lactoperoxidase, the resulting radioactivity profile was similar to that of the intact envelopes, suggesting that in the heat-dissolved envelope, the individual components retain similar structural relations as in the intact envelope. Quantitative but not qualitative differences were found between the inner and outer aspects of VE and FE. The significance of these findings is discussed in relation to what is known about the morphological, biological, and molecular properties of the envelopes.     

Boar sperm surface glycoproteins: Isolation,localization, and temporal expression during spermatogenesis

Boar sperm glycoprotein fractions were isolated by Lens culinaris hemagglutinin affinity chromatography of detergent-solubilized ejaculated spermatozoa, followed by preparative sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. In order to develop methods for further investigations of the sperm proteins, we proceeded with two of the isolated glycoproteins. Antibodies were raised in female rabbits against each of the two sperm glycoproteins. By a combination of immunosorbent chromatography, using the antibodies obtained, and preparative SDS polyacrylamide gel electrophoresis, highly purified sperm proteins were isolated. The sperm proteins were immobilized on Sepharose gel columns and specific immunoglobulin Fab fragments were enriched by affinity chromatography. The specificity of the Fab fragments was ascertained by immunoprecipitation analysis. The Fab fragments were used in indirect immunofluorescence analysis to localize the corresponding antigens on the surface of boar spermatozoa. Both antigens were exclusively confined to the postacrosomal region. Immunohistochemical staining of boar testis sections revealed that both antigens are expressed from the spermatid stage. This technique also revealed that one of the antigens congregated at the Golgi complex-acrosome region during spermatogenesis.     

Glycoprotein changes in the rat sperm plasma membrane during maturation in the epididymis.

To investigate surface glycoprotein changes during post-testicular maturation, plasma membranes were isolated from proximal caput, distal caput, and cauda epididymal rat spermatozoa. Membrane glycoproteins were identified on Western blots of SDS-PAGE fractionated samples using biotinylated lectins and Vecta-stain reagents; these were compared to glycoproteins present in cauda epididymal luminal fluid. Lens culinaris agglutinin, Pisum sativum agglutinin, peanut agglutinin, wheat germ agglutinin, Ricinus communis agglutinin, Ulaex europaeus agglutinin, and Dolichol biflorus agglutinin each bound a specific subset of the polypeptides present. Several types of glycoprotein changes were noted including their appearance, loss, alteration of staining intensity, and alteration of electrophoretic mobility. Some maturation-dependent sperm surface glycoproteins co-migrated with glycoproteins present in epididymal fluid. This approach of direct analysis of the glycoproteins in purified plasma membranes identifies a broader spectrum of maturation-related surface changes occurring within the epididymis than are noted with surface labeling procedures.     

Re-examination of the anomeric configuration of the galactose-(1–3)-galactose linkages in the asparagine-linked sugar chains of subcomponent C1q of bovine complement and calf thymocyte plasma membrane glycoproteins

The anomeric configuration of the terminal Gal1–3Gal linkages found in the asparagine-linked sugar chains of subcomponent C1q of bovine complement and of calf thymocyte plasma membrane glycoproteins were re-examined, and confirmed to be alpha by coffee bean -galactosidase digestion. This contradictory result compared to the previous assignment could be explained by the finding that even very trace amounts (0.06 mU) of -galactosidase contaminating the preparation of jack bean -galactosidase were able to cleave the Gal1–3Gal linkage.     

The lymphocyte plasma membrane: Locus of control in the immune response

Summary The lymphocyte plasma membrane is the locus of events which control the immune response. T and B lymphocytes, which mediate cellular and humoral immunity respectively, show distinctive plasma membrane morphologies and cell surface receptors. The dynamic state of these plasma membrane components is emphasized by their lateral mobility in the fluid plane of the membrane, as well as variation in their structure or expression as the lymphocyte proliferates and differentiates in response to stimulation by antigen or mitogens. The best understood membrane glycoproteins are surface membrane immunoglobulins that serve as antigen receptors on B cells, and the histocompatability-β ₂ microglobulin complex that has an immunoglobulin-like structure. Other less well defined surface structures showing modulation during the cell cycle may affect growth regulation of proliferating lymphocytes. Some of these are shared by fetal and neoplastic cells. Major theories of lymphocyte signaling are discussed, and the early events in lymphocyte activation are reviewed. While a complete model encompassing all these early events is not yet possible, the central issues can be usefully discussed in terms of receptor-transducer-effector concepts derived by strong parallels from a knowledge of hormone-membrane interactions. Presented in the formal symposium on Information Transfer in Eukaryotic Cells, at the 26th Annual Meeting of the Tissue Culture Association, Montreal, Quebec, June 2–5, 1975. Supported by: Medical Research Council of Canada and National Cancer Institute of Canada. Scholar of the Medical Research Council of Canada.     

Quantitative and qualitative changes of plasma membrane glycoproteins in the early period of liver regeneration

Alterations of cell surface glycoconjugates have been observed in many developing systems and may be important in the physiological control of growth and differentiation. Liver regeneration after partial hepatectomy is a suitable model in which to study the regulatory mechanisms of cell proliferation in vivo. We have isolated the sinusoidal plasma membrane of hepatocytes at different times after partial hepatectomy. The sialic acid content and the SDS-polyacrylamide gel electrophoresis pattern of glycoproteins were determined. A decrease of periodic acid-Schiff-profiles, a change in the binding capacities of 125I-concanavalin A, a reduction of the sialic acid content and the appearance and disappearance of specific components have been observed during the pre-replicative phase of liver regeneration. These findings during this early period are consistent with the active involvement of the plasma membrane glycoproteins in the transition of cells to the proliferative state.