Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Trimer assembly”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed2005

Novel type of enzyme multimerization enhances substrate affinity of oat beta-glucosidase.

Oat beta-glucosidase in plastid hydrolyzes avenacosides to C26-desgluco-avenacosides to combat against fungal infections. The enzyme has a unique quaternary protein structure of a three-dimensionally radiated assembly of long fibrillae. We elucidated the fibrillar assembly of oat type 1 beta-glucosidase by means of cryo-electron microscopy, enzyme kinetics and chemical modification. It was assembled by linear stacking of hollow trimeric units and the resulting fibril had a long central tunnel connecting to the outer medium via regularly distributed side fenestrations. The enzyme active sites were located within the central tunnel. This unique multimer assembly increased enzyme affinity to avenacosides, in vivo substrates, and may function to discriminate avenacosides from many other kinds of beta-glucoside in oat. The fibrillar multimer of oat beta-glucosidase is a novel quaternary protein structure for enzyme supramolecular assembly that may have a functional role in the regulation of enzyme affinity.

Avena↗
PubMed1995

The alpha chain of the AP-2 adaptor is a clathrin binding subunit.

We have utilized a rabbit reticulocyte lysate coupled transcription-translation system to express the large subunits of the clathrin associated protein-2 (AP-2) complex so that their individual functions may be studied separately. Appropriate folding of each subunit into N-terminal core and C-terminal appendage domains was confirmed by limited proteolysis. Translated beta 2 subunit bound to both assembled clathrin cages and immobilized clathrin trimers, confirming and extending earlier studies with preparations obtained by chemical denaturation-renaturation. Translated alpha a exhibited rapid, reversible and specific binding to clathrin cages. As with native AP-2, proteolysis of alpha a bound to clathrin cages released the appendages, while cores were retained. Further digestion revealed a approximately 29-kDa alpha a clathrin-binding fragment that remained tightly cage-associated. Translated alpha a also bound to immobilized clathrin trimers, although with greater sensitivity to increasing pH than the translated beta 2 subunit. Clathrin binding by both the alpha and beta subunits is consistent with a bivalent cross-linking model for lattice assembly (Keen, J. H. (1987) Cell Biol. 105, 1989). It also raises the possibility that the alpha-clathrin interaction may have other consequences, such as modulation of lattice stability or shape, or other alpha functions.

Adaptor Proteins, Vesicular Transport↗
PubMed1996

SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins.

Little is known about either the process of periplasmic protein folding or how information concerning the folding state in this compartment is communicated. We present evidence that SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, is involved in the maturation and assembly of LamB. LamB is a trimeric outer membrane porin for maltodextrins as well as the bacteriophage lambda receptor in Escherichia coli. We demonstrate that SurA is involved in the conversion of unfolded monomers into a newly identified intermediate in LamB assembly, which behaves as a folded monomer. The absence of SurA blocks the assembly pathway and leads to accumulation of species prior to the folded monomer. These species also accumulate when the stress sigma factor sigmaE is induced by LamB overexpression. We suggest that accumulation of species prior to the generation of folded monomer is a stress signal sensed by sigmaE.

Amino Acid Isomerases↗
PubMed2005

Duplex molecular strands based on the 3,6-diaminopyridazine hydrogen bonding motif: amplifying small-molecule self-assembly preferences through preorganization and iterative arrangement of binding residues.

Structural parameters obtained through single-crystal X-ray diffraction analysis of the one-dimensional H-bonding motif expressed by 3,6-diaminopyridazine are applied to the design of related monomeric, dimeric, and trimeric duplex molecular strands. The mode of assembly and the interstrand affinity of the oligomers are established in solution by (1)H NMR dilution experiments, isothermal titration calorimetry (ITC), and vapor pressure osmometry. Single-crystal X-ray crystallographic analysis of the dimeric diaminopyridazine 2a corroborates the intended duplex mode of assembly. Binding free energy per unimer (-DeltaG degrees /n) increases upon extension from monomer to dimer to trimer, signifying a positive cooperative effect. Micromolar binding affinity (K(d) = 1.25 +/- 0.1 microM) was determined for the duplex trimer by ITC in 1,2-dichloroethane at 20 degrees C. These data provide further insight into the structural and interactional features of synthetic duplex oligomers required for high-affinity, high-specificity binding and define new recognition elements for use in nanoscale assembly.

Journal Article↗
PubMed2006

High fidelity self-sorting assembling of meso-cinchomeronimide appended meso-meso linked Zn(II) diporphyrins.

In noncoordinating solvents, meso-cinchomeronimide appended Zn(II) porphyrin 2 forms a cyclic trimer, while diporphyrins 7 exhibit high-fidelity self-sorting assembling to form discrete cyclic trimer, tetramer, and pentamer with large association constants from 7(in-in), 7(in)(-)(out), and 7(out-out), respectively, through almost perfect discrimination of enantiomeric and conformational differences of the meso-cinchomeronimide substituents. In the latter self-sorting processes, the dihedral angles dictated by the two pyridyl nitrogen atoms control the size of the aggregates; the trimer from 7(in-in), the tetarmer from 7(in)(-)(out), and the pentamer from 7(out-out). Cyclic structures of (2)(3) and (R-7(out-out))(5) have been determined by single-crystal X-ray diffraction analysis.

Biomimetic Materials↗
PubMed1994

Molecular structure of pulmonary surfactant protein D (SP-D).

Previous studies have shown that pulmonary surfactant protein D (SP-D) is composed of a 43-kDa polypeptide with a short NH2-terminal domain, a collagen sequence, and a COOH-terminal C-type lectin domain. In the present studies, ultrastructural and biochemical techniques were used to examine the quaternary structure of native rat SP-D (rSP-D). Electron microscopy of freeze-dried preparations demonstrated a highly homogeneous population of molecules with four identical rod-like arms (46 nm in length), each with an 8-9-nm diameter globular terminal expansion. The arms, which are similar in diameter to the type I collagen helix (approximately 4 nm), emanate from the central "hub" in two pairs that closely parallel each other for their first 10 nm. This structure is consistent with hydrodynamic studies that predict an highly asymmetric and extended molecule (f/f0 = 3.26) with a large Stokes radius (Rs = 18 nm). Pepsin digestion gave glycosylated, trimeric collagenous fragments (43 +/- 4 nm, 17 kDa/chain). Trimeric subunits containing intact triple helical domains were also liberated from SP-D dodecamers by sulfhydryl reduction under non-denaturing conditions. Digestion of rSP-D with bacterial collagenase generated a COOH-terminal carbohydrate binding fragment and a smaller peptide (approximately 12 kDa, unreduced) that contains interchain disulfide bonds. Electron microscopy also demonstrated higher orders of multimerization, with as many as 8 molecules associated at the hub. These studies demonstrate that SP-D is assembled as homopolymers of four identical trimeric subunits, that interactions between the amino-terminal domains of the trimers are stabilized by interchain disulfide bonds, and that SP-D molecules can associate to form complex multimolecular assemblies.

Amino Acid Sequence↗
PubMed2000

Purified recombinant rotavirus VP7 forms soluble, calcium-dependent trimers.

Rotavirus is a major cause of severe, dehydrating childhood diarrhea. VP7, the rotavirus outer capsid glycoprotein, is a target of protective antibodies and is responsible for the calcium-dependent uncoating of the virus during cell entry. We have purified, characterized, and crystallized recombinant rhesus rotavirus VP7, expressed in insect cells. A critical aspect of the purification is the elution of VP7 from a neutralizing monoclonal antibody column by EDTA. Gel filtration chromatography and equilibrium analytical ultracentrifugation demonstrate that, in the presence of calcium, purified VP7 trimerizes. Trimeric VP7 crystallizes into hexagonal plates. Preliminary X-ray analysis suggests that the crystal packing reproduces the hexagonal component of the icosahedral lattice of VP7 on triple-layered rotavirus particles. These data indicate that the rotavirus outer capsid assembles from calcium-dependent VP7 trimers and that dissociation of these trimers is the biochemical basis for EDTA-induced rotavirus uncoating and loss of VP7 neutralizing epitopes.

Animals↗
PubMed2001

Identification of phospholipids as new components that assist in the in vitro trimerization of a bacterial pore protein.

The in vitro trimerization of folded monomers of the bacterial pore protein PhoE, into its native-like, heat- and SDS-stable form requires incubations with isolated cell envelopes and Triton X-100. The possibility that membranes could be isolated that are enriched in assembly factors required for assembly of the pore protein was now investigated. Fractionation of total cell envelopes of Escherichia coli via various techniques indeed revealed the existence of membrane fractions with different capacities to support assembly in vitro. Fractions containing mainly inner membrane vesicles supported the formation of trimers that were associated with these membrane vesicles. However, only a proportion of these trimers were heat- and SDS-stable and these were formed with slow kinetics. In contrast, fractions containing mainly outer membrane vesicles supported formation of high amounts of heat-stable trimers with fast kinetics. We identified phospholipids as active assembly components in these membranes that support trimerization of folded monomers in a process with similar characteristics as observed with inner membrane vesicles. Furthermore, phospholipids strongly stimulate the kinetics of trimerization and increase the final yield of heat-stable trimers in the context of outer membranes. We propose that lipopolysaccharides stabilize the assembly competent state of folded monomers as a lipochaperone. Phospholipids are involved in converting the folded monomer into new assembly competent intermediate with a short half-life that will form heat-stable trimers most efficiently in the context of outer membrane vesicles. These results provide biochemical evidence for the involvement of different lipidic components at distinct stages of the porin assembly process.

Centrifugation, Density Gradient↗
PubMed2004

Pressure dissociation studies provide insight into oligomerization competence of temperature-sensitive folding mutants of P22 tailspike.

Several temperature-sensitive folding (tsf) mutants of the tailspike protein from bacteriophage P22 have been found to fold with lower efficiency than the wild-type sequence, even at lowered temperatures. Previous refolding studies initiated from the unfolded monomer have indicated that the tsf mutations decrease the rate of structured monomer formation. We demonstrate that pressure treatment of the tailspike aggregates provides a useful tool to explore the effects of tsf mutants on the assembly pathway of the P22 tailspike trimer. The effects of pressure on two different tsf mutants, G244R and E196K, were explored. Pressure treatment of both G244R and E196K aggregates produced a folded trimer. E196K forms almost no native trimer in in vitro refolding experiments, yet it forms a trimer following pressure in a manner similar to the native tailspike protein. In contrast, trimer formation from pressure-treated G244R aggregates was not rapid, despite the presence of a G244R dimer after pressure treatment. The center-of-mass shifts of the fluorescence spectra under pressure are nearly identical for both tsf aggregates, indicating that pressure generates similar intermediates. Taken together, these results suggest that E196K has a primary defect in formation of the beta-helix during monomer collapse, while G244R is primarily an assembly defect.

Bacteriophage P22↗
PubMed2002

Trimerization of the amino propeptide of type IIA procollagen using a 14-amino acid sequence derived from the coiled-coil neck domain of surfactant protein D.

The folding of a collagen triple helix usually requires the presence of additional sequences that contribute to the association and correct alignment of the collagen chains. We recently reported that the C-terminal neck and lectin domains of a collagenous C-type lectin, rat pulmonary surfactant protein D (SP-D), are sufficient to drive the trimerization of a heterologous type IIA procollagen amino propeptide sequence. However, the conformation of the resulting trimeric IIA propeptide and the specific contributions of the SP-D sequence to trimerization were not elucidated. In the present study, we show that trimerization of the fusion protein is associated with correct folding of the collagen helix within the IIA propeptide domain (as assessed by circular dichroism) and that the constituent chains are hydroxylated. Chemical cross-linking and analytical ultracentrifugation showed that the IIA amino-propeptide retains its trimeric configuration even after proteolytic removal of the SP-D domains. By contrast, IIA amino-propeptides synthesized without fusion to the neck or lectin domains are assembled exclusively as monomers. To localize the trimerization sequence, mutant chimeric cDNA constructs were designed containing premature termination codons within the coiled-coil neck domain. A short, 14-amino acid sequence corresponding to the first two heptad repeats of the neck domain was sufficient to drive the trimeric association of the IIA amino-propeptide alpha-chains. However, deletion of the collagen domain resulted in the secretion of monomers. These studies demonstrate that two heptad repeats are sufficient for trimeric association of the propeptide but indicate that cooperative interactions between the coiled-coil and collagen domains are required for the formation of a stable helix.

Amino Acid Sequence↗
PubMed2001

Renal fibrosis: collagen composition and assembly regulates epithelial-mesenchymal transdifferentiation.

Type IV collagen is a major component of basement membranes and it provides structural and functional support to various cell types. Type IV collagen exists in a highly complex suprastructure form and recent studies implicate that protomer (the trimeric building unit of type IV collagen) assembly is mediated by the NC1 domain present in the C-terminus of each collagen alpha-chain polypeptide. Here we show that type IV collagen contributes to the maintenance of the epithelial phenotype of proximal tubular epithelial cells, whereas type I collagen promotes epithelial-to-mesenchymal transdifferentiation (EMT). In addition, the recombinant human alpha1NC1 domain inhibits assembly of type IV collagen NC1 hexamers and potentially disrupts the deposition of type IV collagen, facilitating EMT in vitro. Inhibition of type IV collagen assembly by the alpha1NC1 domain up-regulates the production of transforming growth factor-beta1 in proximal tubular epithelial cells, an inducer of EMT. These results strongly suggest that basement membrane architecture is pivotal for the maintenance of epithelial phenotype and that changes in basement membrane architecture potentially lead to up-regulation of transforming growth factor-beta1, which contributes to EMT during renal fibrosis.

Animals↗
PubMed1997

The C-propeptide domain of procollagen can be replaced with a transmembrane domain without affecting trimer formation or collagen triple helix folding during biosynthesis.

The folding and assembly of procollagen occurs within the cell through a series of discrete steps leading to the formation of a stable trimer consisting of three distinct domains: the N-propeptide, the C-propeptide and the collagen triple helix flanked at either end by short telopeptides. We have established a semi-permeabilized cell system which allows us to study the initial stages in the folding and assembly of procollagen as they would occur in the intact cell. By studying the folding and assembly of the C-propeptide domain in isolation, and a procollagen molecule which lacks the C-propeptide, we have shown that this domain directs the initial association event and is required to allow triple helix formation. However, the essential function of this domain does not include triple helix nucleation or alignment, since this can occur when the C-propeptide is substituted with a single transmembrane domain. Also the telopeptide region is not involved in triple helix nucleation; however, a minimum of two hydroxyproline-containing Gly-X-Y triplets at the C-terminal end of the triple helix are required for nucleation to occur. Thus, the C-propeptide is required solely to ensure association of the monomeric chains; once these are brought together, the triple helix is able to nucleate and fold to form a correctly aligned triple helix.

Amino Acid Sequence↗
PubMed2002

A structure for the trimeric MHC class II-associated invariant chain transmembrane domain.

The major histocompatibility complex (MHC)-associated invariant chain (Ii) contains a single transmembrane domain that forms trimers. Ii is involved in the assembly of the MHC and antigen presentation, and is thus central to the function of the immune system. Here, we show by attenuated total reflectance, Fourier transform infrared (ATR-FTIR) spectroscopy that the transmembrane domain is alpha-helical and we provide a structural model of the transmembrane domain obtained by a combination of site-specific infrared dichroism and molecular dynamics (MD) simulations. This work resolves the backbone structure of a transmembrane peptide by multiple (13)C=(18)O labelling at ten different residues. A second purely computational approach, based on MD simulations of Ii transmembrane homologous sequences, yields a similar structure that is consistent with our experimental results. The structure presented forms a left-handed coiled coil with an average helix tilt of 13(+/-6) degrees; the residue Gln47 implicated in trimer formation forms strong interhelical contacts, Thr50 points to the inside of the trimeric coil and forms a network of hydrogen bonds.

Amino Acid Sequence↗
PubMed2006

Direct observation of oligomeric species formed in the early stages of amyloid fibril formation using electrospray ionisation mass spectrometry.

Numerous debilitating human disorders result from protein misfolding and amyloid formation. Despite the grave nature of these maladies, our understanding of the structural mechanism of fibril assembly is limited. Of paramount importance is the need to identify and characterize oligomeric species formed early during fibril assembly, so that the nature of the initiating assembly mechanism can be revealed and species that may be toxic to cells identified. However, the transient nature of early oligomeric species, combined with their heterogeneity and instability, has precluded detailed analysis to date. Here, we have used electrospray ionisation mass spectrometry (ESI-MS), complemented by analytical ultracentrifugation (AUC) and measurements of thioflavin-T fluorescence, to monitor the early stages of assembly of amyloid-like fibrils formed from human beta-2-microglobulin (beta2m) in vitro. We show that worm-like fibrils that form with nucleation-independent kinetics assemble by a mechanism consistent with monomer addition, with species ranging from monomer to > or = 13-mer being identified directly and uniquely as transient assembly intermediates. By contrast, only monomers, dimers, trimers and tetramers are observed during nucleated growth, which leads to the formation of long straight fibrils. The results highlight the unique power of non-covalent ESI-MS to identify protein assembly intermediates in complex heterogeneous systems and demonstrate its great potential to identify and characterise individual species formed early during amyloid assembly.

Alzheimer Disease↗
PubMed1996

Preliminary crystallographic studies of bacteriophage T4 fibritin confirm a trimeric coiled-coil structure.

Fibritin, a 52-kDa product of gene wac of bacteriophage T4, forms fibrous "whiskers" that connect to the phage tail and facilitate the later stages of phage assembly. Preliminary experiments suggest that fibritin is a trimer, and its predominant central part has a parallel alpha-helical coiled-coil structure. To investigate the oligomerization and function of fibritin, we have designed and studied two related deletion mutants, denoted M and E, that consist of its last 75 and 120 amino acids, respectively. Both proteins contain part of the coiled-coil region and the 29 amino acid carboxy-terminal domain essential for the trimerization of fibritin. The proteins are expressed as a soluble product in an Escherichia coli system. We have obtained crystals of fibritins M and E. Complete native X-ray diffraction data sets have been collected to 1.85 and 2.7 A resolution, respectively. The crystals have space group P3 with a=44.3 A, c=91.3 A (fibritin M) and R32 with a=41.2 A, b=358.7 A (fibritin E) in the hexagonal setting. Symmetry and packing considerations show that fibritin is a triple coiled coil.

Amino Acid Sequence↗
PubMed2000

Assembly of spikes into coronavirus particles is mediated by the carboxy-terminal domain of the spike protein.

The type I glycoprotein S of coronavirus, trimers of which constitute the typical viral spikes, is assembled into virions through noncovalent interactions with the M protein. Here we demonstrate that incorporation is mediated by the short carboxy-terminal segment comprising the transmembrane and endodomain. To this aim, we used the virus-like particle (VLP) system that we developed earlier for the mouse hepatitis virus strain A59 (MHV-A59) and which we describe now also for the unrelated coronavirus feline infectious peritonitis virus (FIPV; strain 79-1146). Two chimeric MHV-FIPV S proteins were constructed, consisting of the ectodomain of the one virus and the transmembrane and endodomain of the other. These proteins were tested for their incorporation into VLPs of either species. They were found to assemble only into viral particles of the species from which their carboxy-terminal domain originated. Thus, the 64-terminal-residue sequence suffices to draw the 1308 (MHV)- or 1433 (FIPV)-amino-acid-long mature S protein into VLPs. Both chimeric S proteins appeared to cause cell fusion when expressed individually, suggesting that they were biologically fully active. This was indeed confirmed by incorporating one of the proteins into virions which thereby acquired a new host cell tropism, as will be reported elsewhere.

Amino Acid Sequence↗
PubMed1993

The canine parvovirus empty capsid structure.

The structure of empty canine parvovirus capsids shows that residues 37 to the carboxy-terminal residue 584 (VP2 numbering) are ordered in each of the 60 subunits. The central structural motif of each subunit is the eight-stranded antiparallel beta-barrel that has been found in many other virus structures. Five beta-hairpin turns form a beta-cylindrical structure at each icosahedral 5-fold axis. The N-terminal glycine-rich sequence can be accommodated within this cylinder without excessive steric hindrance, consistent with the electron density distribution. By far the largest conformational differences between the full and empty virus were found in the region where some ordered DNA has been observed to bind in canine parvovirus full particles. Extensive interactions among 3-fold related subunits indicate that a trimeric subunit might be a viral assembly intermediate.

Amino Acid Sequence↗
PubMed1995

Mutations in three subdomains of the carboxy-terminal region of collagen type X account for most of the Schmid metaphyseal dysplasias.

We have used the polymerase chain reaction and single strand conformation polymorphism (SSCP) methods to analyse the COL10A1 gene, which encodes collagen type X, in DNA samples from patients with metaphyseal dysplasia type Schmid (SMCD) and other related forms of metaphyseal dysplasia. Five cases of SMCD were sporadic and three others were familial. Abnormal SSCP profiles were observed in six instances. In two families, the altered pattern segregated with the phenotype. The heterozygous mutations corresponded to a glycine substitution by glutamic acid at position 595 and to an asparagine substitution by lysine at position 617. In one sporadic case, the sequence studies demonstrated that the individual was heterozygous for a single base deletion (del T 1908) that produced a premature stop codon. Three additional mutations were single base substitutions that affected highly conserved residues at positions 597, 644 and 648. In two additional individuals with SMCD, in two patients with unclassifiable forms of metaphyseal dysplasia, and in one family with epiphyso-metaphyseal dysplasia, SSCP analysis detected neutral polymorphisms in the entire coding sequence of the gene but no mutations. Our results demonstrate that mutations in the carboxy-terminal region of collagen X are specific for the SMCD phenotype. Mutations appear to be clustered into three small subdomains: one of them is rich an aromatic residues, the second includes the putative N-linked oligosaccharide attachment site and the third contains mostly hydrophilic residues. The absence of clinical variability between patients carrying heterozygous single base substitutions or small deletions suggests that, in both instances, the mutant collagen chains either fail to be incorporated into stable trimers or disturb type X collagen assembly.

Base Sequence↗