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PubMed1990

Conformational stability of P22 tailspike proteins carrying temperature-sensitive folding mutations.

The thermostable tailspike endorhamnosidase of Salmonella phage P22 provides a model system for comparing the role of amino acid sequences in determining the intracellular folding pathway with their role in stabilizing the mature structural protein. Complete Raman band assignments are given here for the native form of the tailspike trimer in aqueous solution. Once correctly folded and assembled, the wild-type and two well-characterized mutant proteins, tsfIle258----Leu and tsfGly323----Asp, exhibit the same secondary structure in solution, consisting predominantly of beta-strand (56 +/- 5%) and turns (17 +/- 2%). Raman bands that are sensitive indicators of hydrogen-bonding interactions of tyrosine (phenolic OH) and tryptophan (indole NH) are unchanged between 30 and 80 degrees C in both wild type and tsf mutants. Similarly, Raman bands that are sensitive to changes in the hydrophobic environment of nonpolar side chains exhibit no significant temperature dependence in wild type and tsf mutants. In contrast, these conformational features are greatly altered by chemical denaturation of the tailspike with lithium halide and guanidine hydrochloride. In the chemically denatured tailspike, the beta-strand structure is substantially converted to irregular or "random coil" conformation. These findings confirm conclusions from physiological studies that the three-dimensional structures of the tsf mutants, once stabilized at permissive temperatures, are equivalent to the native structure of the wild type, and this structure is maintained at temperatures far above those that block the folding of the chain into the final native conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2005

Aggregates of the chlorophyll-binding protein IsiA (CP43') dissipate energy in cyanobacteria.

In many natural habitats, growth of cyanobacteria may be limited by a low concentration of iron. Cyanobacteria respond to this condition by expressing a number of iron-stress-inducible genes, of which the isiA gene encodes a chlorophyll-binding protein known as IsiA or CP43'. IsiA monomers assemble into ring-shaped polymers that encircle trimeric or monomeric photosystem I (PSI), or are present in supercomplexes without PSI, in particular upon prolonged iron starvation. In this report, we present steady-state and time-resolved fluorescence measurements of isolated IsiA aggregates that have been purified from an iron-starved psaFJ-minus mutant of Synechocystis PCC 6803. We show that these aggregates have a fluorescence quantum yield of approximately 2% compared to that of chlorophyll a in acetone, and that the dominating fluorescence lifetimes are 66 and 210 ps, more than 1 order of magnitude shorter than that of free chlorophyll a. Comparison of the temperature dependence of the fluorescence yields and spectra of the isolated aggregates and of the cells from which they were obtained suggests that these aggregates occur naturally in the iron-starved cells. We suggest that IsiA aggregates protect cyanobacterial cells against the deleterious effects of light.

Bacterial Proteins↗
PubMed2004

CbpA, a DnaJ homolog, is a DnaK co-chaperone, and its activity is modulated by CbpM.

The DnaK chaperone system, consisting of DnaK, DnaJ, and GrpE, remodels and refolds proteins during both normal growth and stress conditions. CbpA, one of several DnaJ analogs in Escherichia coli, is known to function as a multicopy suppressor for dnaJ mutations and to bind nonspecifically to DNA and preferentially to curved DNA. We found that CbpA functions as a DnaJ-like co-chaperone in vitro. CbpA acted in an ATP-dependent reaction with DnaK and GrpE to remodel inactive dimers of plasmid P1 RepA into monomers active in P1 DNA binding. Additionally, CbpA participated with DnaK in an ATP-dependent reaction to prevent aggregation of denatured rhodanese. The cbpA gene is in an operon with an open reading frame, yccD, which encodes a protein that has some homology to DafA of Thermus thermophilus. DafA is a protein required for the assembly of ring-like particles that contain trimers each of T. thermophilus DnaK, DnaJ, and DafA. The E. coli YccD was isolated because of its potential functional relationship to CbpA. Purified YccD specifically inhibited both the co-chaperone activity and the DNA binding activity of CbpA, suggesting that YccD modulates the activity of CbpA. We named the product of the yccD gene CbpM for "CbpA modulator."

Adenosine Triphosphate↗
PubMed1997

The formation of intramolecular disulfide bridges is required for induction of the Sindbis virus mutant ts23 phenotype.

The Sindbis virus envelope protein spike is a hetero-oligomeric complex composed of a trimer of glycoprotein E1-E2 heterodimers. Spike assembly is a multistep process which occurs in the endoplasmic reticulum (ER) and is required for the export of E1 from the ER. PE2 (precursor to E2), however, can transit through the secretory pathway and be expressed at the cell surface in the absence of E1. Although oligomer formation does not appear to be required for the export of PE2, there is evidence that defects in E1 folding can affect PE2 transit from the ER. Temperature-sensitive mutant ts23 of Sindbis virus contains two amino acid substitutions in E1, while PE2 and capsid protein have the wild-type sequence; however, at the nonpermissive temperature, both E1 and PE2 are retained within the ER and can be isolated in protein aggregates with the molecular chaperone GRP78-BiP. We previously demonstrated that the temperature sensitivity for ts23 was lost as oligomer formation took place at the permissive temperature, suggesting that temperature sensitivity is initiated early in the process of viral spike assembly (M. Carleton and D. T. Brown, J. Virol. 70:952-959, 1996). Experiments described herein investigated the defects in envelope protein maturation that occur in ts23-infected cells and which result in retention of both envelope proteins in the ER. The data demonstrate that in ts23-infected cells incubated at the nonpermissive temperature, E1 folding is disrupted early after synthesis, resulting in the rapid incorporation of both E1 and PE2 into disulfide-stabilized aggregates. Furthermore, the aberrant E1 conformation which is responsible for induction of the ts phenotype requires the formation of intramolecular disulfide bridges formed prior to E1 association with PE2 and the completion of E1 folding.

Animals↗
PubMed2006

Association and dissociation of the cell puncturing complex of bacteriophage T4 is controlled by both pH and temperature.

The tail lysozyme, gp5, of bacteriophage T4 is a trimeric protein and all the subunits are nicked between Ser351 and Ala352 during assembly through processing. When subsequently heated, the resulting (gp5*)(3) (gp5C)(3) (the asterisk "*" denotes that the intact pre-gp5 trimer has been nicked) dissociates into three gp5* (three independent N-terminal monomeric peptides, that carry lysozyme moieties at the C-termini of gp5*), and a C-terminal trimeric beta-helical structure (gp5C)(3). The interaction between gp27 and gp5* during infection is sundered by reducing pH. This dissociation would be physiologically relevant because the lysozyme moieties should be free in the periplasm (where the pH is low) and would digest the peptidoglycan layer, thereby enabling the tail tube to contact the inner membrane, and probably help to form a pore for DNA injection.

Bacteriophage T4↗
PubMed2000

Roles of matrix, p2, and N-terminal myristoylation in human immunodeficiency virus type 1 Gag assembly.

Human immunodeficiency virus type 1 Gag protein is cotranslationally myristoylated at the N terminus and targeted to the plasma membrane, where virus particle assembly occurs. Particle assembly requires the ordered multimerization of Gag proteins, yet there is little direct evidence of intermediates of the reaction or of the domains that lead to each stage of the oligomerization process. In this study, following the expression in insect cells of C-terminally truncated Gag proteins and their purification, both the multimeric nature of each Gag protein and the ability to form Gag virus-like particles (VLP) were analyzed. Our results show that (i) the matrix (MA) domain forms a trimer and contributes to a similar level of oligomerization of the assembly-competent Gag; (ii) the p2 domain, located at the capsid/nucleocapsid junction, is essential for a higher order of multimerization (>1,000 kDa); (iii) the latter multimerization is accompanied by a change in Gag assembly morphology from tubes to spheres and results in VLP production; and (iv) N-terminal myristoylation is not required for either of the multimerization stages but plays a key role in conversion of these multimers to Gag VLP. We suggest that the Gag trimer and the > 1,000-kDa multimer are intermediates in the assembly reaction and form before Gag targeting to the plasma membrane. Our data identify a minimum of three stages for VLP development and suggest that each stage involves a separate domain, MA, p2, or N-terminal myristoylation, each of which contributes to HIV particle assembly.

Animals↗
PubMed2001

Molecular organization of a recombinant subviral particle from tick-borne encephalitis virus.

The tick-borne encephalitis (TBE) flavivirus contains two transmembrane proteins, E and M. Coexpression of E and the M precursor (prM) leads to secretion of recombinant subviral particles (RSPs). In the most common form of these RSPs, analyzed at a 19 A resolution by cryo-electron microscopy (cryo-EM), 60 copies of E pack as dimers in a T = 1 icosahedral surface lattice (outer diameter, 315 A). Fitting the high-resolution structure of a soluble E fragment into the RSP density defines interaction sites between E dimers, positions M relative to E, and allows assignment of transmembrane regions of E and M. Lateral interactions among the glycoproteins stabilize this capsidless particle; similar interactions probably contribute to assembly of virions. The structure suggests a picture for trimer association under fusion-inducing conditions.

Cryoelectron Microscopy↗
PubMed1995

TCR alpha-CD3 delta epsilon association is the initial step in alpha beta dimer formation in murine T cells and is limiting in immature CD4+ CD8+ thymocytes.

The present study has examined the molecular events leading to formation of alpha beta dimers in normal murine thymocytes and mature T cells. We demonstrate that TCR assembly proceeds by initial association of TCR alpha with CD3 delta epsilon proteins and by association of TCR beta with CD3 gamma epsilon proteins to form alpha delta epsilon and beta gamma epsilon trimers; these trimers then associate to form alpha delta epsilon-beta gamma epsilon complexes, within which alpha-beta disulfide bond formation occurs. We also show that TCR-associated protein (TRAP) associates uniquely with CD3 gamma epsilon pairs and that formation of beta gamma epsilon trimers occurs subsequent to TRAP dissociation. Importantly, we document that the assembly step that is quantitatively limiting in CD4+ CD8+ thymocytes is the initial association of TCR alpha with CD3 delta epsilon chains, which appears necessary to protect nascent TCR alpha proteins from accelerated degradation within the ER of immature thymocytes.

Animals↗
PubMedDate not supplied

Blue native PAGE as a useful method for the analysis of the assembly of distinct combinations of nicotinic acetylcholine receptor subunits.

Oligomerization of complete and incomplete combinations of rat muscle-type nicotinic acetylcholine receptor (nAChR) subunits in Xenopus oocytes was studied by blue native PAGE and compared with acetylcholine-activated current in these cells. The rank order of expression level judged by current was alpha 1 beta 1 gamma delta >> alpha 1 beta 1 gamma > alpha 1 beta 1 delta > alpha 1 gamma delta >> alpha 1 delta >> alpha 1 gamma. alpha 1 and alpha 1 beta 1 were not functional. Protein complexes incorporating a heptahistidyl-tagged alpha 1 subunit were chromatographically purified from digitonin extracts of oocytes and resolved by blue native PAGE. In the absence of any co-expressed nAChR subunit, the majority of alpha 1 formed aggregates. Co-expression of beta 1 had no effect on alpha 1 aggregation, whereas both gamma and delta diminished alpha 1 aggregation in favor of discrete oligomers: alpha 1 formed tetramers together with gamma and dimers, trimers, and tetramers together with delta. When alpha 1 gamma was complemented with beta 1 to form a functional alpha 1 beta 1 gamma receptor, a small amount of a pentamer was found besides a prominent alpha 1-His7 beta 1 gamma trimer. Expression of the functional alpha 1 beta 1 delta receptor yielded marked amounts of a pentamer besides dimers and trimers. These results are discussed in terms of the assembly model of Green and Claudio (Cell 74, 57-69, 1994), substantiating that blue native PAGE is suited for the investigation of ion channel assembly.

Animals↗
PubMed2005

Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia.

Schmid metaphyseal chondrodysplasia (SMCD) is a dominantly inherited cartilage disorder caused by mutations in the gene for the hypertrophic cartilage extracellular matrix structural protein, collagen X (COL10A1). Thirty heterozygous mutations have been described, about equally divided into two mutation types, missense mutations, and mutations that introduce premature termination signals. The COL10A1 mutations are clustered (33/36) in the 3' region of exon 3, which codes for the C-terminal NC1 trimerization domain. The effect of COL10A1 missense mutations have been examined by in vitro expression and assembly assays and cell transfection studies, which suggest that a common consequence is the disruption of collagen X trimerization and secretion, with consequent intracellular degradation. The effect of COL10A1 nonsense mutations in cartilage tissue has been examined in two patients, demonstrating that the mutant mRNA is completely removed by nonsense mediated mRNA decay. Thus for both classes of mutations, functional haploinsufficiency is the most probable cause of the clinical phenotype in SMCD.

Child↗
PubMed1996

The transcriptional form of the phosphoprotein of vesicular stomatitis virus is a trimer: structure and stability.

The phosphoprotein (P) of vesicular stomatitis virus was previously shown to assemble into a homomultimer upon phosphorylation by casein kinase II. It thus acquired transcriptional activity, including the ability to bind to the other two transcriptional components, the polymerase L and the N-RNA template. This multimer has now been found to be a trimer using a His-tag dilution method. Trimer stability was assessed using a variation of this method, by measuring the rate of exchange of monomers between preformed tagged and untagged trimers at different values of pH and ionic strength. Exchange rates increased with increasing ionic strength and were similar at pH 6, 8, and 10, but the trimer was completely dissociated at pH 4. This suggests that the trimer is stabilized by electrostatic interactions, probably involving carboxylate and guanidino groups. Addition of viral L protein stabilized the P trimers, completely preventing subunit exchange under transcription conditions. The association constants (Kass) for trimerization of partially active D and A substitution mutants were also determined by His-tag dilution and found to correlate well with transcriptional activity, further confirming that the active species is the trimer. Circular dichroism spectra were identical for phosphorylated and unphosphorylated wild-type P protein and for D and A mutants known to be predominantly trimeric and monomeric, respectively.

Alanine↗
PubMed1989

Polymorphism in the assembly of polyomavirus capsid protein VP1.

Polyomavirus major capsid protein VP1, purified after expression of the recombinant gene in Escherichia coli, forms stable pentamers in low-ionic strength, neutral, or alkaline solutions. Electron microscopy showed that the pentamers, which correspond to viral capsomeres, can be self-assembled into a variety of polymorphic aggregates by lowering the pH, adding calcium, or raising the ionic strength. Some of the aggregates resembled the 500-A-diameter virus capsid, whereas other considerably larger or smaller capsids were also produced. The particular structures formed on transition to an environment favoring assembly depended on the pathway of the solvent changes as well as on the final conditions. Mass measurements from cryoelectron micrographs and image analysis of negatively stained specimens established that a distinctive 320-A-diameter particle consists of 24 close-packed pentamers arranged with octahedral symmetry. Comparison of this unexpected octahedral assembly with a 12-capsomere icosahedral aggregate and the 72-capsomere icosahedral virus capsid by computer graphics methods indicates that similar connections are made among trimers of pentamers in these shells of different size. The polymorphism in the assembly of VP1 pentamers can be related to the switching in bonding specificity required to build the virus capsid.

Capsid↗
PubMed1991

Interaction of phosphoinositide cycle intermediates with the plasma membrane-associated clathrin assembly protein AP-2.

Several components of the phosphoinositide cycle have been found to interact specifically and at physiological concentrations with the plasma membrane-associated clathrin assembly (adaptor) protein AP-2. These include phosphatidylinositol 4,5-bisphosphate and inositol 1,4,5-trisphosphate, which are present at the plasma membrane, as well as other polyphosphoinositols. ATP and other polyphosphate molecules complete with the polyphosphoinositols, however, they are at least 80-fold less potent. Also, the effect of ATP, unlike the polyphosphoinositols, is blocked by physiological concentrations of Mg2+. Photoaffinity labeling of AP-2 by [alpha-32P]8-azidoadenosine 5'-triphosphate and its competition by polyphosphoinositols has been used to identify the alpha subunit of the AP-2 complex as the site of specific interaction with the polyphosphoinositols and to confirm direct ultrafiltration binding experiments. Proteolytic dissection of the labeled AP-2 demonstrated that binding occurred exclusively on the N-terminal portion of the alpha subunit. Interaction of purified AP-2 with sub-microM concentrations of polyphosphoinositols has inhibitory effects on a novel AP-2 self-association described in the accompanying paper (Beck, K. A., and Keen, J. H., J. Biol. Chem. 266, 4437-4441), and at higher concentrations on the binding of AP-2 to dissociated clathrin trimers as well as AP-2-mediated clathrin coat assembly. Review of the literature shows that several physiological stimuli that are known to result in increased coat pit formation in intact cells correlate with increased phosphoinositide turnover. These in vivo correlations and the in vitro observations reported here suggest that coated membrane and phosphoinositide cycles may be interdependent within cells.

Adaptor Proteins, Vesicular Transport↗
PubMed1997

A tetramer of the Flp recombinase silences the trimers within it during resolution of a Holliday junction substrate.

Recombination catalyzed by the Flp site-specific recombinase involves breakage and joining of four DNA strands between two target substrates. The reaction is carried out in two steps of pairwise strand exchanges by a DNA-protein assembly in which four Flp monomers act cooperatively to execute strand cleavage and joining. Two models for recombination have been proposed. In the trimer model, the two active sites required for each step are assembled from three Flp monomers. In the tetramer (or dimer of asymmetric dimers) model, the two active sites are assembled from four Flp monomers, two monomers each contributing one active site. Experiments in which the two models challenge each other reveal that, within the Flp tetramer arranged on a Holliday junction, the two active sites required for its resolution are derived from all four, rather than three, Flp monomers. Thus, the relative protein subunit configuration of the tetramer silences the trimers within it by excluding them from assembling a functional active site pair.

DNA↗
PubMed2005

Predicting oligomeric assemblies: N-mers a primer.

Multi-protein complexes play key roles in many biological processes. However, since the structures of these assemblies are hard to resolve experimentally, the detailed mechanism of how they work cooperatively in the cell has remained elusive. Similarly, recent advances on in silico prediction of protein-protein interactions have so far avoided this difficult problem. In this paper, we present a general algorithm to predict molecular assemblies of homo-oligomers. Given the number of N-mers and the 3D structure of one monomer, the method samples all the possible symmetries that N-mers can be assembled. Based on a scoring function that clusters the low free energy structures at each binding interface, the algorithm predicts the complex structure as well as the symmetry of the protein assembly. The method is quite general and does not involve any free parameters. The algorithm has been implemented as a public server and integrated to the protein-protein complex prediction server ClusPro. Using this application, we validated predictions for trimers, tetramers (discriminating between dimer of dimers and 4-fold symmetry structures), pentamers and hexamers (discriminating between trimer of dimers, dimer of trimers, and 6-fold symmetry structures), for a total of 107 assemblies. For 85% of the multimers, the server predicts the complex structure within an average rms deviation of 2A from the full crystal. For complexes that involve more than one binding interface, the cluster size at each surface provides a strong indication as to which interface forms first. With improving scoring functions and computer power, our multimer docking approach could be used as a framework to address the more general problem of multi-protein assemblies.

Algorithms↗
PubMed1993

OmpF assembly mutants of Escherichia coli K-12: isolation, characterization, and suppressor analysis.

This paper describes a novel genetic method used to isolate mutations that alter proper assembly of OmpF in the outer membrane. The thermolabile nature of assembly intermediates allowed selection of temperature-sensitive mutations within the ompF gene. A variant allele of ompF (ompF-Dex) was used because it provided a convenient selectable phenotype (Dex+). Assembly mutants were isolated in two steps. First, amber mutations were obtained that mapped in ompF-Dex. This resulted in a Dex- phenotype. Starting with these Dex- strains, Dex+ revertants were isolated. Mutants that displayed a temperature-sensitive Dex+ phenotype were further characterized. Three such mutants possessed a single substitution within ompF that reverted the nonsense codon to a sense codon which replaced W214 with either an E or Q and Y231 with a Q residue in the mature OmpF protein. All three mutant OmpF proteins showed an assembly defect. This defect led to a substantial reduction in the amount of stable OmpF trimers with the concomitant increase of a high-molecular-weight form of OmpF which migrated at the top of the gel. Suppressor mutations were sought that corrected the assembly defect of OmpF. These extragenic suppressor mutations were mapped at 45 min on the Escherichia coli chromosome. The suppressor mutations displayed no allele specificity and were recessive to the wild-type allele. In the presence of a suppressor, mutant stable trimers appeared in an almost normal manner. The appearance of stable trimers concurred with a substantial loss of the high-molecular-weight OmpF species. At this stage, it is not clear whether the high-molecular-weight species of OmpF is a normal assembly intermediate or a dead-end assembly product. The results presented in this study raise the intriguing possibility of a chaperone-like activity for the wild-type suppressor gene product.

Alleles↗
PubMed1987

Clathrin assembly proteins: affinity purification and a model for coat assembly.

Assembly protein (AP) preparations from bovine brain coated vesicles have been fractionated by clathrin-Sepharose affinity chromatography. Two distinct fractions that possess coat assembly activity were obtained and are termed AP-1 and AP-2. The AP-1, not retained on the resin, has principal components with molecular weights of 108,000, 100,000, 47,000, and 19,000. The AP-2, bound to the resin and eluted by Tris-HCl at a concentration that parallels the latter's effect on coat disassembly, corresponds to the active complex described previously (Zaremba, S., and J. H. Keen, 1983, J. Cell Biol., 97:1339-1347). Its composition is similar to that of the AP-1 in that it contains 100,000-, 50,000-, and 16,000-mol-wt polypeptides in equimolar amounts; minor amounts of 112,000- and 115,000-mol-wt polypeptides are also present. Both are distinct from a recently described assembly protein of larger subunit molecular weight that we term AP-3. These results indicate the existence of a family of assembly proteins within cells. On incubation with clathrin both AP-1 and AP-2 induce the formation of coat structures, those containing AP-1 slightly smaller (mean diameter = 72 nm) than those formed in the presence of AP-2 (mean diameter = 79 nm); both structures have been detected previously in coated vesicle preparations from brain. Coats formed in the presence of AP-2 consistently contain approximately one molecule each of the 100,000-, 50,000-, and 16,000-mol-wt polypeptides per clathrin trimer. By low angle laser light scattering the molecular weight of native AP-2 was determined to be approximately 343,000, indicating that it is a dimer of each of the three subunits, and implying that it is functionally bivalent in clathrin binding. A model for AP-mediated coat assembly is proposed in which a bivalent AP-2 molecule bridges the distal legs or terminal domains of two clathrin trimers that are destined to occupy adjacent vertices in the assembled coat. Binding of a second AP-2 molecule locks these two trimers in register for assembly and further addition of AP-2 to free trimer legs promotes completion of the clathrin lattice. Effects of AP binding on the angle and flexibility of the legs at the hub of the trimer (the "pucker") are suggested to account for the characteristic size distributions of coats formed under varied conditions and, more speculatively, to contribute to the transformation of flat clathrin lattices to curved coated vesicles that are thought to occur during endocytosis.

Animals↗
PubMed1995

A trimeric subdomain of the simian immunodeficiency virus envelope glycoprotein.

Previous attempts to define the oligomeric state of the HIV and SIV envelope glycoproteins have yielded conflicting results. We have produced in Escherichia coli a recombinant model for the ectodomain of the SIV envelope protein gp41 and have identified a small, trimeric subdomain by proteolytic digestion of this gp41 fragment. The subdomain assembles from two peptide fragments, spanning residues 28-80 (N28-80) and residues 107-149 (C107-149) of SIV gp41. Each of these peptides contains a 4,3-hydrophobic repeat, the hallmark of coiled-coil sequences. Upon mixing, the peptides form a highly helical, trimeric complex [3(N+C)] that resists proteolysis and has a melting temperature (Tm) above 90 degrees C in physiological buffer. The N- and C-terminal fragments are antiparallel to each other in the complex, as judged by the observation that digestion of a variant recombinant protein truncated at the amino terminus yields a C-terminal fragment shortened at its carboxy terminus. The N28-80 peptide contains more positions within the heptad repeat than C107-149 that are predominantly hydrophobic, suggesting that N28-80 is buried in the interior of the complex. We propose that the complex consists of a parallel, trimeric coiled-coil of the N-terminal peptide, encircled by three C-terminal peptide helices arranged in an antiparallel fashion, and that this complex forms a core within the gp41 extracellular domain.

Amino Acid Sequence↗