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PubMed1987

Post-translational modifications of the core-specific lectin. Relationship to assembly, ligand binding, and secretion.

The rat core-specific lectin (CSL) or mannan-binding protein is synthesized and secreted by rat hepatocytes and H-4-II-E hepatoma cells. Prior to secretion proline and lysine residues with collagen-like sequences undergo hydroxylation and subsequent glycosylation of hydroxylysine to produce glucosylgalactosylhydroxylysine. Hydroxylation and subsequent glycosylation are inhibited by alpha,alpha'-dipyridyl (Colley, K. J., and Baenziger, U. U. (1987) J. Biol. Chem. 262, 10290-10295). We have used alpha,alpha'-dipyridyl to investigate the role of hydroxylation and glycosylation on interchain disulfide bond formation, assembly of subunits into high molecular weight complexes, attainment of carbohydrate and lipid binding ability, and secretion. Formation of disulfide-bonded dimers and trimers in the endoplasmic reticulum, assembly into high molecular weight complexes in the Golgi, and attainment of carbohydrate binding activity occur in either the presence or absence of these post-translational modifications. The mature fully processed form of the CSL binds hydrophobic matrices and is secreted at a slow, but linear, rate. Inhibition of proline and lysine hydroxylation and hydroxylysine glycosylation prevents CSL secretion and attainment of binding activity for hydrophobic matrices. Secretion of the lectin, although slow, appears to be an active process and may be related to the capacity to interact with membranes and/or lipids. Other proteins known to contain collagen-like sequences such as acetylcholinesterase, pulmonary surfactant apoproteins, and C1q also interact with lipids and/or membranes. The collagen-like domains of these proteins may also play a role in promoting such interactions.

2,2'-Dipyridyl↗

PubMed1996

Type-III procollagen assembly in semi-intact cells: chain association, nucleation and triple-helix folding do not require formation of inter-chain disulphide bonds but triple-helix nucleation does require hydroxylation.

Procollagen assembly is initiated within the endoplasmic reticulum by three alpha-chains associating via their C-propeptides (C-terminal propeptides). To study the requirements for the association of procollagen monomers at synthesis we have reconstituted the initial stages in the folding, assembly and modification of procollagen using semi-permeabilized cells. By translating a type-III procollagen "mini-gene' which lacks part of the triple-helical domain, we demonstrate that these cells efficiently carry out the assembly of hydroxylated, triple-helical, procollagen trimers and allow the identification of specific disulphide-bonded intermediates in the folding pathway. Mutant chains, which lack the ability to form inter-chain disulphide bonds within the C-propeptide, were still able to assemble within this system. Furthermore, characterization of the trimeric molecules formed suggested that inter-chain disulphide bonds had formed within the C-telopeptide (C-terminal telopeptide). However, when hydroxylation of prolyl and lysyl residues was inhibited no inter-chain disulphide bonds were formed in the C-telopeptide, indicating that hydroxylation is required for the initial nucleation of the triple-helical domain. Mutant chains which lacked the ability to form inter-chain disulphide bonds within the C-propeptide or the C-telopeptide could still assemble to form trimeric triple-helical molecules linked by inter-chain disulphide bonds within the N-propeptide (N-terminal propeptide). These results indicate that inter-chain disulphide bond formation within the C-propeptide or the C-telopeptide is not required for chain association and triple-helix formation.

Amino Acid Sequence↗

PubMed1981

Assembly and packing of clathrin into coats.

We present a model for the packing of clathrin molecules into the characteristic hexagons and pentagons covering coated pits and vesicles. The assembly unit is a symmetrical trimer with three extended legs. Polymerization of these units occurs in seconds under suitable conditions, giving empty polyhedral cages resembling the structures around coated vesicles. Images of small, negatively stained fragments of cages, assembled directly on electron microscope grids, reveal details of the structure, which correlate well with the predicted features of the model. There is one clathrin trimer at each polyhedral vertex, and each leg of the trimer extends along two neighboring polyhedral edges. Quasi-equivalent packing in pentagons and hexagons in polyhedra of different sizes requires a variable joint at the vertex of the molecule and a hinge in each leg. The construction of clathrin coats is remarkable for the extended fibrous contacts that each molecule makes with many others. Such contacts may confer mechanical strength combined with flexibility needed when a vesicle is pinched off from the membrane.

Clathrin↗

PubMed2005

Monodisperse oligofluorenes with keto defect as models to investigate the origin of green emission from polyfluorenes: synthesis, self-assembly, and photophysical properties.

Oligofluorenes (a trimer, pentamer, and heptamer) with one fluorenone unit in the center (OFnK: n=3, 5, or 7) were synthesized and used as models to understand the origin of the low-energy emission band in the photoluminescence and electroluminescence spectra of some polyfluorenes. All compounds form glasses with T(g) at 30 degrees C (OF3 K), 50 degrees C (OF5 K) and 57 degrees C (OF7 K). Oligomers OF5 K and OF7 K exhibit smectic liquid crystal phases that undergo transition to isotropic melts at 107 and 205 degrees C, respectively. Oligomer OF5 K could be obtained in form of single crystals. The X-ray structure analysis revealed the helical nature of the molecule and a helix reversal defect located at the central fluorenone unit. The packing pattern precludes formation of excimers. Electrochemical properties were investigated by cyclic voltammetry. The ionization potential (I(p)) and electron affinity (E(a)) were calculated from these data. Studies of the photophysical properties of OFnK in solution and thin film by steady-state and time-resolved fluorescence spectroscopic measurements suggest efficient funneling of excitation energy from the photoexcited fluorene segments to the low-energy fluorenone sites by both intra- and intermolecular hopping events whereby they give rise to green emission. Intermolecular energy transfer was investigated by using a model system composed of a highly defect free polyfluorene PF2/6 doped by OFnK. Förster-type energy transfer takes place from PF2/6 to OFnK. The energy-transfer efficiency increases predictably with increasing concentration of OFnK.

Journal Article↗

PubMed2002

Self-assembled, helically stacked anionic aggregates of 2,5,8,11-tetra-tert-butylcycloocta[1,2,3,4-def;5,6,7,8-d'e'f']bisbiphenylene, stabilized by electrostatic interactions.

Tetraanions of alkyl-substituted derivatives of cycloocta[1,2,3,4-def;5,6,7,8-d'e'f']bisbiphenylene (BPD) and their counter lithium cations self-assemble to form helically stacked assemblies, including a dimer, a trimer, and a tetramer. NMR self-diffusion measurements and unprecedented magnetic shielding effects for the sandwiched lithium cations support their aggregated nature. The D(2)-tetramer assembly is fully characterized by NMR spectroscopy, providing unequivocal evidence for a helix of four tetraanionic BPD layers with an estimated relative twist angle of about 45 degrees and interlayer spacing of ca. 4 A. The barrier for racemization through the in-plane inter-deck rotation is DeltaG(200)= 9.5 +/- 0.2 kcal mol(-1) in the dimer compared to >15 kcal mol(-1) in the tetramer.

Journal Article↗

PubMed2006

An uncharged region within the N terminus of the P2X6 receptor inhibits its assembly and exit from the endoplasmic reticulum.

ATP-gated P2X receptors are trimeric complexes formed by the homomeric or heteromeric assembly of seven different subunits. We have shown previously that, unlike all of the other P2X subunits, the P2X6 subunit cannot form homomeric receptors and when expressed alone is retained in the endoplasmic reticulum (ER) in monomeric form (J Biol Chem 280: 107591-10765, 2005). However, other studies have shown that P2X6 can form functional heteromeric receptors with P2X2 and P2X4 subunits. In this study, we used a combination of immunocytochemistry, surface biotinylation, and atomic force microscopy to investigate the assembly and trafficking of the P2X6 subunit, both alone and as part of a heteromer. We show that as a heteromer, it exits the ER and is either stably expressed at the cell surface or constitutively internalized, depending on its partner. Through the use of targeted mutation, we demonstrate that an uncharged region at the N terminus of P2X6 exerts an inhibitory effect on its assembly and export from the ER. When this region is removed, or when charge is added to it, P2X6 forms homotrimeric assemblies, undergoes complex glycosylation and is delivered to the plasma membrane, albeit less efficiently than the P2X2 receptor. The N-terminal mutants were, however, nonfunctional. Substituting the uncharged 14-amino acid N-terminal region for the equivalent region of P2X2 increased ER retention but was not sufficient to prevent the formation of functional homomeric receptors. We propose that the N terminus of the P2X6 subunit contributes to a mechanism that prevents the inappropriate export and plasma membrane expression of nonfunctional P2X receptors.

Amino Acid Sequence↗

PubMed2000

Trimerization of cell adhesion molecule L1 mimics clustered L1 expression on the cell surface: influence on L1-ligand interactions and on promotion of neurite outgrowth.

Several studies indicate that cell adhesion molecules have to be clustered on the cell surface to engage in adhesive functions. We investigated adhesive functions of clustered versus monomeric L1 extracellular parts in vitro to distinguish how clustering affects ligand binding and promotion of neurite outgrowth. Trimeric L1 was recombinantly expressed and covalently assembled by the cartilage matrix protein's coiled-coil domain. Trimeric L1 has an apparent molecular mass of approximately 380 kDa in the nonreduced form and approximately 130 kDa in the reduced form. Rotary shadowing electron micrographs of trimeric L1 revealed a rod-like shape terminating in three globular domains. Monomeric L1 assumes a horseshoe shape of domains Ig I-IV followed by a rod-like structure consisting of Ig V and VI and fibronectin type III 1-5. Circular dichroism measurements showed that the secondary structure consists of beta-sheets. Trimeric L1 binds to itself, to monomeric L1, to laminin-1, and to alpha5beta1 integrin in a concentration-dependent manner. In contrast, binding of monomeric L1 could only be saturated with itself but not with laminin-1 and with alpha5beta1 integrin. Promotion of neurite outgrowth from PC12 cells cultured on adsorbed trimeric L1 was increased by 100%, whereas on monomeric L1 the increase was only 50% over the control value. Promotion of neurite outgrowth from PC12 cells was specifically inhibited in a concentration-dependent manner by a polyclonal antibody against L1. These findings show that clustering of only three extracellular domains increases considerably L1's binding affinity to different ligands and enhances neurite outgrowth, suggesting that adhesive functions of L1 on the cell surface depend on cluster formation.

Animals↗

PubMed2005

Phenotypic analysis of human immunodeficiency virus type 1 Rev trimerization-interface mutants in human cells.

Nuclear export of unspliced and incompletely spliced human immunodeficiency virus type 1 mRNA is mediated by the viral Rev protein. Rev binds to a structured RNA motif known as the Rev-response element (RRE), which is present in all Rev-dependent transcripts, and thereby promotes entry of the ribonucleoprotein complex into the nuclear-export pathway. Recent evidence indicates that a dimerization interface and a genetically separable "trimerization" interface are required for multimeric assembly of Rev on the RRE. In this report, the effect of mutations within the trimerization interface on Rev function was examined in mammalian cells. All trimerization-defective Rev molecules had profoundly compromised Rev function and a range of localization defects was observed. However, despite the potential for formation of heterodimers between functional and non-functional Rev proteins, trimerization-defective Rev mutants were unable to inhibit wild-type Rev function in a trans-dominant-negative manner.

Active Transport, Cell Nucleus↗

PubMed1996

Clamp loading, unloading and intrinsic stability of the PCNA, beta and gp45 sliding clamps of human, E. coli and T4 replicases.

BACKGROUND: The high speed and processivity of replicative DNA polymerases reside in a processivity factor which has been shown to be a ring-shaped protein. This protein ("sliding clamp') encircles DNA and tethers the catalytic unit to the template. Although in eukaryotic, prokaryotic and bacteriophage-T4 systems, the processivity factors are ring-shaped, they assume different oligomeric states. The Escherichia coli clamp (the beta subunit) is active as a dimer while the eukaryotic and T4 phage clamps (PCNA and gp45, respectively) are active as trimers. The clamp can not assemble itself on DNA. Instead, a protein complex known as a clamp loader utilizes ATP to assemble the ring around the primer-template. This study compares properties of the human PCNA clamp with those of E. coli and T4 phage. RESULTS: The PCNA ring is a stable trimer down to a concentration below 100 nM (Kd approximately 21 nM). On DNA, the PCNA clamp slides freely and dissociates from DNA slowly (t1/2 approximately 24 min). beta is more stable in solution (Kd < 60 PM) and on DNA (t1/2 approximately 1 h) than PCNA which may be explained by its simpler oligomeric state. The T4 gp45 clamp is a much less stable trimer than PCNA (Kd approximately 250 nM) and requires association with the polymerase to stabilize it on DNA as observed previously. The consequence of this cooperation between clamp and polymerase is that upon finishing a template and dissociation of the polymerase from DNA, the gp45 clamp spontaneously dissociates from DNA without assistance. However, the greater stability of the PCNA and beta clamps on DNA necessitates an active process for their removal. The clamp loaders (RFC and gamma complex) were also capable of unloading their respective clamps from DNA in the presence of ATP. CONCLUSIONS: The stability of the different clamps in solution correlates with their stability on DNA. Thus, the low stability of the T4 clamp explains the inability to isolate gp45 on DNA. The stability of the PCNA and beta clamps predicts they will require an unloading factor to recycle them on and off DNA during replication. The clamp loaders of PCNA and beta double as clamp unloaders presumably for the purpose of clamp recycling.

Bacteriophage T4↗

PubMed1999

Molecular determinants of oligomer formation and complement fixation in mannose-binding proteins.

Rat serum mannose-binding protein (MBP-A) functions as part of the innate immune system by targetting complement toward potentially pathogenic microorganisms. In order to examine the molecular basis for complement activation, rat MBP-A has been overproduced in Chinese hamster ovary cells. Recombinant protein is post-translationally modified in the same way as the native lectin. Hydrodynamic studies indicate that MBP-A consists predominantly of covalent oligomers containing one to four copies of a subunit that comprises a trimer of polypeptides. These oligomers are non-interconverting and do not assemble into higher order structures at concentrations in excess of those normally found in serum. Disulfide bonds formed between cysteine residues at the N-terminal end of the collagen-like domain link polypeptides to form covalent oligomers. Analysis of wild-type MBP-A and MBP-A containing the substitution Cys6 --> Ser suggests that polypeptides within each trimeric structural unit are mostly linked by disulfide bonds between cysteine residues at positions 13 and 18 arranged in an asymmetrical configuration. Disulfide bonds involving Cys6 connect polypeptides within separate trimers. Analysis of chimeras between MBP-A and rat liver MBP (MBP-C) indicates that residues within the N-terminal region of the collagenous domain and the cysteine-rich domain of MBP-A enable assembly of trimers into higher order oligomers. The activity of MBP-A in a hemolytic complement fixation assay using mannan-coated sheep erythrocytes was approximately 20-fold greater than the activity of MBP-C. Analysis of the MBP chimeras and isolated oligomers of MBP-A reveals that the larger oligomers are more efficient at complement activation. These data indicate that the overall complement fixing activity of MBP-A is a function of the individual molecular activities of oligomers and their relative abundance within the serum.

Amino Acid Sequence↗

PubMed2003

Crystal structure of the collagen alpha1(VIII) NC1 trimer.

Collagen VIII is a major component of Descemet's membrane and is also found in vascular subendothelial matrices. The C-terminal non-collagenous domain (NC1) domain of collagen VIII, which is a member of the C1q-like protein family, forms a stable trimer and is thought to direct the assembly of the collagen triple helix, as well as polygonal supramolecular structures. We have solved the crystal structure of the mouse alpha1(VIII)(3) NC1 domain trimer at 1.9 A resolution. Each subunit of the intimate NC1 trimer consists of a ten-stranded beta-sandwich. The surface of the collagen VIII NC1 trimer presents three strips of partially exposed aromatic residues shown to interact with the non-ionic detergent CHAPS, which are likely to be involved in supramolecular assemblies. Equivalent strips exist in the NC1 domain of the closely related collagen X, suggesting a conserved assembly mechanism. Surprisingly, the collagen VIII NC1 trimer lacks the buried calcium cluster of the collagen X NC1 trimer. The mouse alpha1(VIII) and alpha2(VIII) NC1 domains are 71.5% identical in sequence, with the differences being concentrated on the NC1 trimer surface. A few non-conservative substitutions map to the subunit interfaces near the surface, but it is not obvious from the structure to what extent they determine the preferred assembly of collagen VIII alpha1 and alpha2 chains into homotrimers.

Amino Acid Sequence↗

PubMed1995

Alternative mechanisms of CAK assembly require an assembly factor or an activating kinase.

We have cloned a mouse cDNA that encodes p36, a novel subunit of the CDK-activating kinase (CAK). p36 contains a C3HC4 zinc-binding domain or RING factor and is associated both with a TFIIH-bound form of CAK and with a free trimeric form. p36 promotes the assembly of CDK7 and cyclin H in vitro, stabilizing the transient CDK7-cyclin H complex. Stabilization and activation of CAK by p36 is independent of the phosphorylation state of T170, the conserved activating residue of CDK7. Assembly of active CDK7-cyclin H dimers can also occur through an alternative p36-independent pathway that requires phosphorylation of T170 by a CAK-activating kinase, or CAKAK. Thus, CDK7-cyclin H complex formation can be achieved by multiple mechanisms.

Amino Acid Sequence↗

PubMed2004

Evidence for assembly of prions with left-handed beta-helices into trimers.

Studies using low-resolution fiber diffraction, electron microscopy, and atomic force microscopy on various amyloid fibrils indicate that the misfolded conformers must be modular, compact, and adopt a cross-beta structure. In an earlier study, we used electron crystallography to delineate molecular models of the N-terminally truncated, disease-causing isoform (PrP(Sc)) of the prion protein, designated PrP 27-30, which polymerizes into amyloid fibrils, but we were unable to choose between a trimeric or hexameric arrangement of right- or left-handed beta-helical models. From a study of 119 all-beta folds observed in globular proteins, we have now determined that, if PrP(Sc) follows a known protein fold, it adopts either a beta-sandwich or parallel beta-helical architecture. With increasing evidence arguing for a parallel beta-sheet organization in amyloids, we contend that the sequence of PrP is compatible with a parallel left-handed beta-helical fold. Left-handed beta-helices readily form trimers, providing a natural template for a trimeric model of PrP(Sc). This trimeric model accommodates the PrP sequence from residues 89-175 in a beta-helical conformation with the C terminus (residues 176-227), retaining the disulfide-linked alpha-helical conformation observed in the normal cellular isoform. In addition, the proposed model matches the structural constraints of the PrP 27-30 crystals, positioning residues 141-176 and the N-linked sugars appropriately. Our parallel left-handed beta-helical model provides a coherent framework that is consistent with many structural, biochemical, immunological, and propagation features of prions. Moreover, the parallel left-handed beta-helical model for PrP(Sc) may provide important clues to the structure of filaments found in some other neurodegenerative diseases.

Amino Acid Sequence↗

PubMed2006

Columnar assembly of cyclic beta-amino acid functionalized with pyranose rings.

A novel cyclic trimer and tetramer of protected beta-glycamino acids were synthesized and investigated on conformation and assembly formation. A characteristic point of these cyclic beta-glycamino acids is their better solubility than other cyclic beta-amino acids due to the pyranose rings. Thus, the assembling process of the cyclic molecules could be examined by CD or NMR spectroscopy. FT-IR and NMR measurements and geometry optimization revealed a highly symmetric and planar conformation for each cyclic beta-peptide with all-trans amide groups. The amide groups in the cyclic peptides took a vertical orientation against the cyclic skeleton to be suitably arranged for intermolecular hydrogen bonds, which should promote formation of molecular assembly in a columnar structure through molecular stacking. These cyclic beta-peptides were successfully crystallized to yield rod-shaped molecular assemblies in nanometer sizes. Evidence for the columnar structure in the crystals was obtained by electron diffraction analysis, which showed a layer spacing of ca. 4.8 A. Interestingly, the molecular assembly of the cyclic trimer showed a high aspect ratio, width less than 40 nm, and length more than 2 mum, suggesting stable molecular stacking in the column.

Amino Acids↗

PubMed1992

Early assembly pathways of type I collagen.

A method was developed for computing the free energy (delta Fi) of aggregates of type I collagen. The method was based on a treatment of Matheson and Flory describing phase equilibria of rigid rod polymers. It included a polymer-solvent interaction term that depended on near neighbor transfer energies. Extrahelical portions of the molecule were assigned local interaction energies differing from that assigned to the helix. Free energies of reaction for successive steps along assembly pathways (delta Fi-i+1) were computed. When allowance was made for specific pairing between extrahelical and helical domains, the so-called D-staggered (D = 670 A) alignment of molecules was preferred, as opposed to a nonstaggered, or nematic, alignment. Based on delta Fi-i+1 alone, it appeared that 1D-staggered oligomers arise first in assembly, followed later by addition of molecules in 4D alignment. Neither 4D dimers nor 4D-8D trimers were predicted to be major intermediates in assembly. This result is contrary to previous hypotheses. When energies of activation were included in the analysis, the prediction was less certain, and specific circumstances were identified in which 4D dimers and 4D-8D trimers were the earliest aggregated species in assembly.

Collagen↗

PubMed2002

Condensin architecture and interaction with DNA: regulatory non-SMC subunits bind to the head of SMC heterodimer.

Condensin and cohesin are two protein complexes that act as the central mediators of chromosome condensation and sister chromatid cohesion, respectively. The basic underlying mechanism of action of these complexes remained enigmatic. Direct visualization of condensin and cohesin was expected to provide hints to their mechanisms. They are composed of heterodimers of distinct structural maintenance of chromosome (SMC) proteins and other non-SMC subunits. Here, we report the first observation of the architecture of condensin and its interaction with DNA by atomic force microscopy (AFM). The purified condensin SMC heterodimer shows a head-tail structure with a single head composed of globular domains and a tail with the coiled-coil region. Unexpectedly, the condensin non-SMC trimers associate with the head of SMC heterodimers, producing a larger head with the tail. The heteropentamer is bound to DNA in a distributive fashion, whereas condensin SMC heterodimers interact with DNA as aggregates within a large DNA-protein assembly. Thus, non-SMC trimers may regulate the ATPase activity of condensin by directly interacting with the globular domains of SMC heterodimer and alter the mode of DNA interaction. A model for the action of heteropentamer is presented.

Adenosine Triphosphatases↗

PubMed1991

Rotavirus morphogenesis: domains in the major inner capsid protein essential for binding to single-shelled particles and for trimerization.

A cell-free system containing rotavirus subviral particles (SVPs), rabbit reticulocyte lysate, and [35S]methionine was programmed to synthesize viral protein by the addition of messenger RNA (mRNA). Electrophoretic analysis of single-shelled particles recovered from the system by CsCl centrifugation showed that newly made VP6 assembled into the particles in vitro. Electrophoretic analysis also showed that the newly made VP6 which bound to single-shelled particles in vitro was arranged in trimeric units. To identify the domain within VP6 essential for assembly into single-shelled particles, amino- and carboxyl-truncated species of VP6 were assayed for the ability to associate with single-shelled particles in the cell-free system. The truncated proteins were introduced into the system by adding VP6 mRNAs containing 5'- and 3'-terminal deletions. The terminally deleted mRNAs were prepared using SP6 RNA polymerase to transcribe portions of cDNAs of the rotavirus SA11 gene for VP6 (gene 6). Analysis of the ability of truncated VP6 to associate with single-shelled particles showed that a domain essential for assembly resides at the carboxyl-end of VP6 located between amino acid residues 251 and 397. To contrast the domain for assembly with that for trimerization, amino- and carboxyl-truncated species of VP6 were also examined by electrophoretic assay for the ability to trimerize in vitro. The results showed that the domain for trimerization resides near the center of VP6 located between amino acid residues 105 and 328. Comparison of the domains for assembly and trimerization showed that they are unique but may overlap. The fact that some truncated species of VP6, although able to bind to single-shelled particles were unable to form trimers in vitro, suggests that trimerization of VP6 is not prerequisite for the assembly of single-shelled particles.

Animals↗

PubMed2006

Rational design of a reversible pH-responsive switch for peptide self-assembly.

Peptide TZ1H, based on the heptad sequence of a coiled-coil trimer, undergoes fully reversible, pH-dependent self-assembly into long-aspect-ratio helical fibers. Substitution of isoleucine residues with histidine at the core d-positions of alternate heptads introduces a mechanism by which self-assembly is coupled to the protonation state of the imidazole side chain. Circular dichroism spectroscopy, transmission electron microscopy, and microrheology techniques revealed that the self-assembly of TZ1H coincides with a distinct coil-helix conformational transition that occurs within a narrow pH range near the pKa of the imidazole side chains of the core histidine residues.

Amino Acid Sequence↗