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Oligomers of hexa-peri-hexabenzocoronenes as "super-oligophenylenes": synthesis, electronic properties, and self-assembly.

Hexa-peri-hexabenzocoronene (HBC) is a remarkable polycyclic aromatic hydrocarbon and is often called "superbenzene" because of its similarity to benzene. In this article we present the facile synthesis of oligomers of HBC, up to trimers (3, 4, 5a-c) with different modes of connection. UV-vis and fluorescence spectroscopy studies reveal that the oligomers are electronically decoupled. This arises from the small atomic orbital coefficients of the bridge-head carbon atoms, the large torsion angle between the HBC units, and the large distance of interacting transition dipoles due to the size of the HBC chromophore. For comparison, a methylene-bridged HBC dimer 6, so-called "superfluorene", was prepared. The induced planarity improves pi-conjugation and suppresses the geometrical relaxation of the backbone upon electronic excitation, leading to a prominent 0-0 transition band in the fluorescence spectra. The self-assembly of the oligomers and of superfluorene 6 was studied by wide-angle X-ray diffraction (WAXD) in the bulk state, and ordered columnar stacking occurs in the HBC dimer 3, p-HBC trimer 4, and superfluorene 6. Measurements of shear-aligned samples show that, despite increasing aspects ratio by linear entrainment of disks, the anitropic element that is subject to alignment by shear is the supramolecular columns.

Journal Article↗

A bifunctional fusion protein containing the maltose-binding polypeptide and the catalytic chain of aspartate transcarbamoylase: assembly, oligomers, and domains.

The in vivo synthesis of many target proteins or polypeptides has been enhanced dramatically and their purification facilitated through the use of gene fusion techniques which lead to the expression of fusion proteins. This approach was used to characterize the product formed in Escherichia coli encoded by a DNA construct comprising malE, the gene encoding maltose binding protein, linked to a small 30 nucleotide region which, in turn, was linked to pyrB, the gene encoding the catalytic (c) chains of aspartate transcarbamoylase (ATCase). The resulting fusion protein, MBP-C, was produced in excellent yield and readily purified in two steps because of its binding to an amylose column and displacement by maltose. The complex was studied by both sedimentation velocity and sedimentation equilibrium and shown to be a trimer of c chains with one MBP linked covalently to each chain. Treatment of the fusion protein with factor Xa cleaved each chain at the tetrapeptide encoded by the linker region yielding purified MBP with a minor modification at the C-terminus and the catalytic (C) trimer of ATCase. The MBP-C complex was fully active as an enzyme and could be reversibly denatured in 6 M urea. Scanning calorimetry studies on the fusion protein demonstrated that the MBP domain melted at the same temperature as did the purified protein. Similarly, the Tm for the C trimer in the complex was identical to the value for C trimer isolated from ATCase. Moreover, the thermal stability of the C trimer in the MBP-C complex was greatly enhanced by the addition of the bisubstrate ligand, N-(phosphonacetyl)-L-aspartate (PALA), just as observed with purified C trimer. Analogous denaturation experiments with varying concentrations of guanidine-HCl indicated that the fusion protein was denatured at much lower concentration of denaturant than observed for C trimer. These experiments demonstrate that the linker between the two structural genes encodes a polypeptide of sufficient length to permit independent folding and assembly of each protein and permit the subsequent specific cleavage at the factor Xa recognition site, thereby yielding both active proteins.

ATP-Binding Cassette Transporters↗

Folding of beta-structured fibrous proteins and self-assembling peptides.

Natural fibrous proteins include families found in natural materials such as wool and silk; in tissue components such as collagen and elastin; or in virus and bacteriophage adhesins. They have long fascinated scientists and engineers because of their mechanical and elastic properties, and considerable efforts have been made in order to produce artificial materials inspired from these natural proteins. The understanding of their structure, folding, and assembly properties is necessary in order to achieve these objectives. However, because of their complexity, structural information is quite often extremely difficult to obtain for these proteins. In this chapter, we focus on a particular family of fibrous proteins: trimeric, beta-stranded viral adhesins. We describe folding strategies that led to the identification of stable domains that could be crystallized, and the novel structural motifs that are emerging. We also discuss self-assembling peptides derived from these motifs. Finally, we review the possibilities of designing novel macroscopic materials as well as nanoscale fibrous objects with controlled dimensions and properties based on these novel structural motifs.

Adenoviridae↗

Cotranslational endoplasmic reticulum assembly of FcepsilonRI controls the formation of functional IgE-binding receptors.

The human high affinity receptor for IgE (FcepsilonRI) is a cell surface structure critical for the pathology of allergic reactions. Human FcepsilonRI is expressed as a tetramer (alphabetagamma(2)) on basophils or mast cells and as trimeric (alphagamma(2)) complex on antigen-presenting cells. Expression of the human alpha subunit can be down-regulated by a splice variant of FcepsilonRIbeta (beta(var)). We demonstrate that FcepsilonRIalpha is the core subunit with which the other subunits assemble strictly cotranslationally. In addition to alphabetagamma(2) and alphagamma(2), we demonstrate the presence of alphabeta and alphabeta(var)gamma(2) complexes that are stable in the detergent Brij 96. The role of individual FcepsilonRI subunits for the formation of functional, immunoglobulin E-binding FcepsilonRI complexes during endoplasmic reticulum (ER) assembly can be defined as follows: beta and gamma support ER insertion, signal peptide cleavage and proper N-glycosylation of alpha, whereas beta(var) allows accumulation of alpha protein backbone. We show that assembly of FcepsilonRI in the ER is a key step for the regulation of surface expression of FcepsilonRI. The ER quality control system thus regulates the quantity of functional FcepsilonRI, which in turn controls onset and persistence of allergic reactions.

Endoplasmic Reticulum↗

Subunit assembly of giant haemoglobin from the polychaete Tylorrhynchus heterochaetus.

The subunit assembly of the giant haemoglobin of the polychaete Tylorrhynchus heterochaetus is presented. Tylorrhynchus haemoglobin consists of two types of subunits: a "monomeric" chain I and a disulphide-bonded "trimer" of chains IIA, IIB and IIC. The molar ratio of the four constituent chains was determined by statistical comparison of the accurate amino acid composition calculated from the sequence of each chain and the observed composition measured by amino acid analysis of the whole molecule. On the basis of the molar ratio and the molecular weight of each chain, deduced from the amino acid sequence, a symmetrical model for the molecular assembly of the haemoglobin was constructed. The proposed model consists of four species of chains of 192 polypeptides and has a molecular weight of 3,275,808. The minimum structural entity is a "tetramer" consisting of the "monomeric" chain and the disulphide-bonded "trimer". Each chain contains one haem.

Amino Acid Sequence↗

Role of glycoprotein PE2 in formation and maturation of the Sindbis virus spike.

Sindbis virus envelope assembly is a multistep process resulting in the maturation of a rigid, highly ordered T=4 icosahedral protein lattice containing 80 spikes composed of trimers of E1-E2 heterodimers. Intramolecular disulfide bonds within E1 stabilize E1-E1 associations required for envelope formation and maintenance of the envelope's structural integrity. The structural integrity of the envelope protein lattice is resistant to reduction by dithiothreitol (DTT), indicating that E1 disulfides which stabilize structural domains become inaccessible to DTT at some point during virus maturation. The development of E1 resistance to DTT occurs prior to the completion of E1 folding and is temporally correlated with spike assembly in the endoplasmic reticulum. From these data we have predicted that in the final stages of spike assembly, E1 intramolecular disulfides, which stabilize the structural integrity of the envelope protein lattice, are buried within the spike and become inaccessible to the reductive activity of DTT. The spike is formed prior to the completion of E1 folding, and we have suggested that PE2 (the precursor to E2) may play a critical role in E1 folding after PE2-E1 oligomer formation has occurred. In this study we have investigated the role of PE2 in E1 folding, oligomer formation, and development of E1 resistance to both protease digestion and reduction by DTT by using a Sindbis virus replicon (SINrep/E1) which allows for the expression of E1 in the presence of truncated PE2. Through pulse-chase analysis of both Sindbis virus- and SINrep/E1-infected cells, we have determined that the folding of E1 into a trypsin-resistant conformation and into its most compact and stable form is not dependent upon association of E1 with PE2. However, E1 association with PE2 is required for oligomer formation, the export of E1 from the endoplasmic reticulum, and E1 acquisition of resistance to DTT.

Dithiothreitol↗

Regulation of gephyrin assembly and glycine receptor synaptic stability.

Gephyrin is required for the formation of clusters of the glycine receptor (GlyR) in the neuronal postsynaptic membrane. It can make trimers and dimers through its N- and C-terminal G and E domains, respectively. Gephyrin oligomerization could thus create a submembrane lattice providing GlyR-binding sites. We investigated the relationships between the stability of cell surface GlyR and the ability of gephyrin splice variants to form oligomers. Using truncated and full-length gephyrins we found that the 13-amino acid sequence (cassette 5) prevents G domain trimerization. Moreover, E domain dimerization is inhibited by the gephyrin central L domain. All of the gephyrin variants bind GlyR beta subunit cytoplasmic loop with high affinity regardless of their cassette composition. Coexpression experiments in COS-7 cells demonstrated that GlyR bound to gephyrin harboring cassette 5 cannot be stabilized at the cell surface. This gephyrin variant was found to deplete synapses from both GlyR and gephyrin in transfected neurons. These data suggest that the relative expression level of cellular variants influence the overall oligomerization pattern of gephyrin and thus the turnover of synaptic GlyR.

Animals↗

Visualization of the maturation transition in bacteriophage P22 by electron cryomicroscopy.

Large-scale conformational transitions are involved in the life-cycle of many types of virus. The dsDNA phages, herpesviruses, and adenoviruses must undergo a maturation transition in the course of DNA packaging to convert a scaffolding-containing precursor capsid to the DNA-containing mature virion. This conformational transition converts the procapsid, which is smaller, rounder, and displays a distinctive skewing of the hexameric capsomeres, to the mature virion, which is larger and more angular, with regular hexons. We have used electron cryomicroscopy and image reconstruction to obtain 15 A structures of both bacteriophage P22 procapsids and mature phage. The maturation transition from the procapsid to the phage results in several changes in both the conformations of the individual coat protein subunits and the interactions between neighboring subunits. The most extensive conformational transformation among these is the outward movement of the trimer clusters present at all strict and local 3-fold axes on the procapsid inner surface. As the trimer tips are the sites of scaffolding binding, this helps to explain the role of scaffolding protein in regulating assembly and maturation. We also observe DNA within the capsid packed in a manner consistent with the spool model. These structures allow us to suggest how the binding interactions of scaffolding and DNA with the coat shell may act to control the packaging of the DNA into the expanding procapsids.

Bacteriophage P22↗

The refolding of lactate dehydrogenase subunits and their assembly to the functional tetramer.

The renaturation process of different lactate dehydrogenase isozymes (L-lactate:NAD+ oxidoreductase, EC 1.1.1.27) from their unfolded subunits was investigated using a number of techniques. (a) kinetics of activity regain, (b) the kinetics of fluorescence change of fluoresecence change of the protein tryptophans, (c) kinetics of regain of the fluorescence properties of a covalently attached fluorescence probe (fluorescein) and (d) the kinetics of assembly, by following the intermediate oligomeric species appearing in the assembly pathway from monomers to tetramers. The results indicate that the unfolded polypeptide is converted to the active oligomeric species by the following scheme: Denatured subunit I leads to partially refolded subunit II leads to folded subunit III leads to dimer IV leads to tetramer. Step I and step II are first-order where step II is rate limiting. The ligands NAD+ and NADH accelerate step II, thus converting step I to the rate-limiting process. The fact that partially folded lactate dehydrogenase subunits are capable of co-enzyme binding may indicate the possible role of these ligands in the assembly of lactate dehydrogenase in vivo. Steps III and IV were found to be fast. The intermediate formation of an enzyme dimer which then dimerizes to the tetrameric species is found to be the major assembly pathway. Only a small portion of the lactate dehydrogenase tetramer is formed through the intermediate formation of a trimer intermediate.

Animals↗

The two cysteine-rich head domains of minicollagen from Hydra nematocysts differ in their cystine framework and overall fold despite an identical cysteine sequence pattern.

Synthetic replicates of naturally occurring cysteine-rich peptides such as hormones, neurotransmitters, growth factors, enzyme inhibitors, defensins and toxins often can be oxidatively folded in high yields to their native structure in simple redox buffers. Thereby, identical cysteine patterns in the sequence were found to generate identical disulfide connectivities and homologous spatial structures despite significant variability in the non-cysteine positions. Minicollagen-1 from the nematocysts of Hydra is a trimeric protein that contains cysteine-rich domains at the N and C termini, which are involved in the assembly of an intermolecular disulfide network. Determination of the three-dimensional structures of peptides corresponding to the N-terminal and C-terminal domains by NMR spectroscopy revealed a remarkable exception from the general rule. Despite an identical cysteine pattern, the two domains of minicollagen-1 form different disulfide bridges and exhibit distinctly different folds, both of which are not found in the current structural databases. To our knowledge, this is the first case where two relatively short peptides with the abundant cysteine residues in identical sequence positions fold uniquely and with high yields into defined, but differing, structures. Therefore, the cysteine-rich domains of minicollagen constitute ideal model systems for studies of the interplay between folding and oxidation in proteins.

Amino Acid Sequence↗

Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production.

Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 A resolution. The subunit structure of ECAI is organised into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.

Aldose-Ketose Isomerases↗

Conserved quaternary structure of ligand-gated ion channels: the postsynaptic glycine receptor is a pentamer.

The postsynaptic glycine receptor of rat spinal cord is a glycosylated membrane protein that, after affinity purification, contains membrane-spanning subunits of Mr 48,000 and 58,000 and an associated peripheral polypeptide of Mr 93,000. Here, the quaternary structure of the transmembrane core of the receptor was investigated by chemically crosslinking its subunits. Upon treatment with crosslinking reagents of different side-chain specificities and lengths, a consistent set of adducts up to Mr 260,000 was detected after separation by NaDodSO4/PAGE. The observed pattern of adducts was similar irrespective of whether purified receptor protein or synaptosomal membranes were crosslinked. Compositional analysis revealed that the crosslinked adducts contained the Mr 48,000 and 58,000 subunits in varying ratios but not the peripheral Mr 93,000 polypeptide. Thus adducts of intermediate molecular weight represent dimers, trimers, and tetramers of the transmembrane subunits, whereas the major adduct of Mr 260,000 corresponds to a pentameric assembly of subunits forming the ion channel of the glycine receptor. This subunit arrangement is similar to that reported for the nicotinic acetylcholine receptor of fish electric organ and skeletal muscle. Hence, we suggest that the different ligand-gated ion channels of excitable membranes share a similar quaternary structure.

Animals↗

Assembly of human immunodeficiency virus (HIV) antigens on bacteriophage T4: a novel in vitro approach to construct multicomponent HIV vaccines.

Bacteriophage T4 capsid is an elongated icosahedron decorated with 155 copies of Hoc, a nonessential highly antigenic outer capsid protein. One Hoc monomer is present in the center of each major capsid protein (gp23*) hexon. We describe an in vitro assembly system which allows display of HIV antigens, p24-gag, Nef, and an engineered gp41 C-peptide trimer, on phage T4 capsid surface through Hoc-capsid interactions. In-frame fusions were constructed by splicing the human immunodeficiency virus (HIV) genes to the 5' or 3' end of the Hoc gene. The Hoc fusion proteins were expressed, purified, and displayed on hoc(-) phage particles in a defined in vitro system. Single or multiple antigens were efficiently displayed, leading to saturation of all available capsid binding sites. The displayed p24 was highly immunogenic in mice in the absence of any external adjuvant, eliciting strong p24-specific antibodies, as well as Th1 and Th2 cellular responses with a bias toward the Th2 response. The phage T4 system offers new direction and insights for HIV vaccine development with the potential to increase the breadth of both cellular and humoral immune responses.

AIDS Vaccines↗

Histone dimers: a fundamental unit in histone assembly.

Histone interactions which occur, at moderate ionic strengths, when several types of purified, renatured histones are mixed at equimolar ratios have been studied. The four histones H2A,H2B,H3 and H4 complex and form dimers. Histone H1 does not interact with the other four histone types and does not form dimers. Mixing of single histone species with preformed histone pairs as well as mixing of two different types of histone pairs, leads to exchange of histones among the pairs and formation of dimers. No trimers are formed. The dimers are in equilibrium with high-molecular weight histone structures. The results indicate that histone dimers may serve as a stable intermediate in histone assembly. Because each histone type (except H1) can interact with itself as well as with each of the other three histone types we suggest that each histone type should be considered as an interchangeable subunit of a multichain protein in which the dimer species is the most stable structure.

Animals↗

Self-assembled RANK induces osteoclastogenesis ligand-independently.

UNLABELLED: By immunoprecipitation assay, we showed that mouse RANK was self-assembled through its cytoplasmic domain located at position 534-539, whose domain was different form TRAF binding domains. Moreover, overexpression experiments showed that oligomeric RANK, which was self-associated, induced osteoclastogenesis ligand-independently. INTRODUCTION: TNF receptor I or II (TNF-RI or TNF-RII) is thought to induce its own trimerization by ligand binding; however, recently TNF-RI or TNF-RII was shown to form a trimer through its extracellular domain without ligand binding. RANK, which plays an important role in osteoclast differentiation, is a member of the TNF receptor family. Here, we studied the self-assembly of mouse RANK. MATERIALS AND METHODS: Self-assembly of mouse RANK was examined by immunoprecipitation assay using 293T cells that had been transfected with the full-length RANK (Full) fused to FLAG tag (Full-FLAG) and Full fused to HA tag (Full-HA) without soluble RANKL (sRANKL). To explore the binding site for self-assembly, FLAG-tagged RANK C-terminal deletion mutants, 461-, 511-, 533-, 539-, and 544-FLAG, were constructed, and immunoprecipitation was performed. To examine whether RANK overexpression induced osteoclastogenesis, osteoclast progenitors that were derived from wildtype bone marrow cells, in which RANK was overexpressed, were cultured with monocyte-macrophage colony-stimulating factor (M-CSF), and TRACP staining was performed. We examined whether overexpression of each five individual C-terminal mutants induced osteoclastogenesis in osteoclast progenitors. To study the involvement of TRAF6 in RANK-induced osteoclastogenesis, osteoclast progenitors, in which RANK was overexpressed, were cultured with M-CSF and TNF receptor-associated factor (TRAF)6 decoy peptides (T6DP) that inhibit the interaction of RANK with TRAF6. RESULTS AND CONCLUSIONS: Immunoprecipitation experiments showed that RANK was self-assembled without sRANKL. Among the five individual mutants, only 539- and 544-FLAG mutants were associated with Full-HA ligand-independently, suggesting that self-association of RANK was regulated by its cytoplasmic domain located at position 534-539. Overexpression of full-length RANK induced osteoclast differentiation, and this differentiation was suppressed by treatment with T6DP. Overexpression of RANK deletion mutants revealed that only 539- and 544-FLAG induced osteoclastogenesis. The five C-terminal mutants had the TRAF6 binding domain in their cytoplasmic regions, suggesting that ligand-independent osteoclastogenesis requires the receptor oligomerization of RANK.

Acid Phosphatase↗

Glycoprotein complexes interacting with cellulose in the "cell print" zones of the Dictyostelium discoideum extracellular matrix.

Cellulose is one of the commonest structural biopolymers. How cellulose is organized in extracellular matrices is a mystery. Here we investigate a model system, the extracellular matrix (ECM) of Dictyostelium discoideum which is composed of proteins and cellulose. A group of glycoproteins, the sheathins, which colocalize with cellulose in the ECM of D. discoideum are characterized. Sheathins are dimeric or trimeric forms of molecular mass 53-68 kDa, where the monomers are 12-35 kDa. The sheathin subunits are similar but not identical proteins. The sheathin family comprises sheathin 68, (68-kDa trimer); sheathin 62, (62-kDa dimer); sheathin 55, (55-kDa dimer), and sheathin 53, (53-kDa dimer). The subunits which assemble into the four sheathins represent at least three gene products: ShC, ShD, and ShE which are linked by disulphide bonds. Protein sequence analysis shows two of the sheathin genes encode products ShC and ShD with very similar amino terminal sequences. This group of D. discoideum ECM glycoproteins has homology with two other much larger ECM proteins of D. discoideum, ST430 and ST310, which are located in a more dispersed fashion in the ECM. Sheathins are tightly but non-covalently associated with the ECM, and this association requires strong denaturing conditions for disruption, e.g., SDS or 8 M urea. Sheathins form a component of the "cell prints" which are believed to have a role in cell-ECM interactions and slug cell migration.

Amino Acid Sequence↗

Abnormal growth plate function in pigs carrying a dominant mutation in type X collagen.

We have identified a naturally occurring, dominant mutation that causes dwarfism in domestic pigs (Sus scrofa). With a positional candidate gene approach, the dwarf phenotype was shown to be a result of a single amino acid change, G590R, in the alpha1 (X) chain of type X collagen. Type X collagen is a homotrimer of alpha1(X) chains encoded by the COL10A1 gene, which is expressed in hypertrophic chondrocytes during the process of endochondral ossification. An amino acid substitution at the equivalent position in human type X collagen, G595E, has previously been shown to cause Schmid metaphyseal chondrodysplasia (SMCD), which is a relatively mild skeletal disorder associated with dwarfism and growth plate abnormality. Consistent with the clinical phenotype of SMCD patients, radiological and histological examination of the dwarf pigs revealed metaphyseal chondrodysplasia in the long bones. Yeast-based, two-hybrid protein interaction studies and in vitro assembly experiments demonstrated that the amino acid substitution interfered with the ability of the mutated collagen molecules to engage in trimerization. This work establishes that the chondrodysplastic dwarf pigs by genetic, biochemical, radiological and histological criteria provide a valid animal model of SMCD.

Animals↗

Assembly of photosystem I. II. Rubredoxin is required for the in vivo assembly of F(X) in Synechococcus sp. PCC 7002 as shown by optical and EPR spectroscopy.

The rubA gene was insertionally inactivated in Synechococcus sp. PCC 7002, and the properties of photosystem I complexes were characterized spectroscopically. X-band EPR spectroscopy at low temperature shows that the three terminal iron-sulfur clusters, F(X), F(A), and F(B), are missing in whole cells, thylakoids, and photosystem (PS) I complexes of the rubA mutant. The flash-induced decay kinetics of both P700(+) in the visible and A(1)- in the near-UV show that charge recombination occurs between P700(+) and A(1)- in both thylakoids and PS I complexes. The spin-polarized EPR signal at room temperature from PS I complexes also indicates that forward electron transfer does not occur beyond A(1). In agreement, the spin-polarized X-band EPR spectrum of P700(+) A(1)- at low temperature shows that an electron cycle between A(1)- and P700(+) occurs in a much larger fraction of PS I complexes than in the wild-type, wherein a relatively large fraction of the electrons promoted are irreversibly transferred to [F(A)/F(B)]. The electron spin polarization pattern shows that the orientation of phylloquinone in the PS I complexes is identical to that of the wild type, and out-of-phase, spin-echo modulation spectroscopy shows the same P700(+) to A(1)- center-to-center distance in photosystem I complexes of wild type and the rubA mutant. In contrast to the loss of F(X), F(B), and F(A), the Rieske iron-sulfur protein and the non-heme iron in photosystem II are intact. It is proposed that rubredoxin is specifically required for the assembly of the F(X) iron-sulfur cluster but that F(X) is not required for the biosynthesis of trimeric P700-A(1) cores. Since the PsaC protein requires the presence of F(X) for binding, the absence of F(A) and F(B) may be an indirect result of the absence of F(X).

Bacterial Proteins↗