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PubMed1990

Electron microscopy and image analysis reveal common principles of organization in two large protein complexes: groEL-type proteins and proteasomes.

In an attempt to settle the question of whether the multicatalytic proteinase or proteasome exist in all three kingdoms of life--eukaryotes, archaebacteria, and eubacteria--we have undertaken a search for them in the eubacterium Comamonas acidovorans. We have, in fact, isolated and purified a cylinder-shaped particle. However, according to various structural and biochemical criteria this turned out to be more reminiscent of the groEL protein from Escherichia coli and its homologs than to proteasomes of eukaryotic or archaebacterial origin. N-terminal sequencing provided definite proof for its belonging to this family of molecular chaperonins. Image analysis of electron micrographs revealed that the C. acidovorans groEL-like protein and proteasomes in spite of their significantly different dimensions have certain principles of organization in common.

Amino Acid Sequence↗
PubMed2004

PINdb: a database of nuclear protein complexes from human and yeast.

SUMMARY: Proteins Interacting in the Nucleus database (PINdb) is a database of protein complexes purified from the nucleus of human and yeast cells. It is compiled from the published literature and existing databases. Currently, PINdb contains mostly protein complexes that may be involved in gene transcription. To facilitate comparative analyses and identification of protein complexes, the compositional information is integrated with standardized gene nomenclature, annotation and protein sequences from public databases. The PINdb web interface provides a number of tools for (1) comparison of protein complexes, (2) search for a protein complex by its published name or by a partial list of its components and (3) browsing specific subsets or a functional classification of the complexes. Availablity: http://pin.mskcc.org

Abstracting and Indexing↗
PubMed1990

Analysis of DNA-protein complexes induced by chemical carcinogens.

DNA-protein complexes induced in intact cells by chromate have been isolated and compared with those formed by other agents such as cis-platinum. Actin has been identified as one of the major proteins that is complexed to the DNA by chromate based upon a number of criteria including, a molecular weight and isoelectric point identical to actin, positive reaction with actin polyclonal antibody, and proteolytic mapping. Chromate and cis-platinum both complex proteins of very similar molecular weight and isoelectric points and these complexes can be disrupted by exposure to chelating or reducing agents. These results suggest that the metal itself is participating in rather than catalyzing the formation of a DNA-protein complex. An antiserum which was raised to chromate-induced DNA-protein complexes reacted primarily with a 97,000 protein that could not be detected by silver staining. Western blots and slot blots were utilized to detect p97 DNA-protein complexes formed by cis-platinum, UV, formaldehyde, and chromate. Other work in this area, involving studying whether DNA-protein complexes are formed in actively transcribed DNA compared with genetically inactive DNA, is discussed. Methods to detect DNA-protein complexes, the stability and repair of these lesions, and characterization of DNA-protein complexes are reviewed. Nuclear matrix proteins have been identified as a major substrate for the formation of DNA-protein complexes and these findings are also reviewed.

Actins↗
PubMed2005

The pST44 polycistronic expression system for producing protein complexes in Escherichia coli.

Protein complexes are responsible for key biological processes, but methods to produce recombinant protein complexes for biochemical and biophysical studies are limited. We have developed a second generation Escherichia coli polycistronic expression system which improves on the modularity of our original pST39 polycistronic system. This pST44 expression system simplifies the construction of polycis-tronic plasmids, particularly of variant plasmids expressing deletion or point mutations in any subunit. To facilitate purification of the expressed complex, we have prepared a suite of 72 plasmids which allows individual subunits to be tagged at the N- or C-terminus with six permanent or cleavable peptide affinity tags. We demonstrate these new features in a detailed deletion analysis of a three protein yeast Piccolo NuA4 histone acetyltransferase complex, and in the affinity purification of a human Piccolo NuA4 complex. We also utilize the modular design to show that the order of expression of the three subunits along the polycistronic plasmid does not affect the reconstitution of the yeast Piccolo complex in E. coli.

Acetyltransferases↗
PubMed1993

Affinity purification of a somatostatin receptor-G-protein complex demonstrates specificity in receptor-G-protein coupling.

The inhibitory neuropeptide somatostatin (SRIF) initiates many of its physiological effects by binding to membrane receptors which are coupled to pertussis toxin-sensitive G-protein(s). We have solubilized such a SRIF receptor-G-protein complex and purified it using a biotinylated SRIF analog and guanine nucleotide-dependent affinity chromatography. Following [125I-Tyr11]SRIF binding to membranes from AR4-2J pancreatic acinar cells, only two detergents, dodecyl-beta-D-maltoside (D beta M) and sucrose monolaureate, extracted greater than 70% of the prebound peptide in association with receptor. The D beta M-solubilized ligand-receptor complex was extremely stable: the half-time (t1/2) for dissociation was 11 days at 4 degrees C. However, guanosine 5'-3-O-(thio)triphosphate (10 microM) elicited rapid dissociation of the [125I-Tyr11]SRIF-receptor complex (t1/2 < 30 s), and this effect was concentration-dependent (ED50 = 4.0 + 0.3 nM). [125I-Tyr11]SRIF dissociation was also stimulated by GDP (ED50 = 4.1 +/- 0.3 microM), and the potency of GDP was increased 4-fold by 30 microM AlF4-. Thus, the solubilized receptor was functionally associated with G-proteins. Cross-linking of the soluble [125I-Tyr11]SRIF-receptor complex resulted in the covalent labeling of a 70-90-kDa band, the same band that was specifically labeled in membranes. Affinity purification of the SRIF receptor-G-protein complex was accomplished by prebinding a biotinylated SRIF analog, [N-biotinyl-Leu8,D-Trp22,Tyr25]SRIF28, to membranes followed by solubilization of the ligand-receptor-G-protein complex, adsorption to streptavidin-agarose, and specific elution with 100 microM GDP, 30 microM AlF4-. G-proteins were identified in the eluate by immunoblotting with specific antipeptide antisera. Using this protocol, the G-protein subunits alpha i, alpha i-3, and beta 36 were shown to be specifically associated with the AR4-2J cell SRIF receptor. Thus, we have developed a new, generally applicable, procedure for the efficient solubilization and affinity purification of a stable SRIF receptor-G-protein complex and have characterized the specific G-protein subunits associated with pancreatic SRIF receptors.

Animals↗
PubMed2003

Members of the evolutionarily conserved PMT family of protein O-mannosyltransferases form distinct protein complexes among themselves.

Protein O-mannosyltransferases (PMTs) initiate the assembly of O-mannosyl glycans, an essential protein modification. Since PMTs are evolutionarily conserved in fungi but are absent in green plants, the PMT family is a putative target for new antifungal drugs, particularly in fighting the threat of phytopathogenic fungi. The PMT family is phylogenetically classified into PMT1, PMT2, and PMT4 subfamilies, which differ in protein substrate specificity. In the model organism Saccharomyces cerevisiae as well as in many other fungi the PMT family is highly redundant, and only the simultaneous deletion of PMT1/PMT2 and PMT4 subfamily members is lethal. In this study we analyzed the molecular organization of PMT family members in S. cerevisiae. We show that members of the PMT1 subfamily (Pmt1p and Pmt5p) interact in pairs with members of the PMT2 subfamily (Pmt2p and Pmt3p) and that Pmt1p-Pmt2p and Pmt5p-Pmt3p complexes represent the predominant forms. Under certain physiological conditions, however, Pmt1p interacts also with Pmt3p, and Pmt5p with Pmt2p, suggesting a compensatory cooperation that guarantees the maintenance of O-mannosylation. Unlike the PMT1/PMT2 subfamily members, the single member of the PMT4 subfamily (Pmt4p) acts as a homomeric complex. Using mutational analyses we demonstrate that the same conserved protein domains underlie both heteromeric and homomeric interactions, and we identify an invariant arginine residue of transmembrane domain two as essential for the formation and/or stability of PMT complexes in general. Our data suggest that protein-protein interactions between the PMT family members offer a point of attack to shut down overall protein O-mannosylation in fungi.

Evolution, Molecular↗
PubMed2000

Junctophilins: a novel family of junctional membrane complex proteins.

Junctional complexes between the plasma membrane (PM) and endoplasmic/sarcoplasmic reticulum (ER/ SR) are a common feature of all excitable cell types and mediate cross-talk between cell surface and intracellular ion channels. We have identified the junctophilins (JPs), a novel conserved family of proteins that are components of the junctional complexes. JPs are composed of a carboxy-terminal hydrophobic segment spanning the ER/SR membrane and a remaining cytoplasmic domain that shows specific affinity for the PM. In mouse, there are at least three JP subtypes: JP-1, -2, and -3. JP-2 is abundantly expressed in the heart, and mutant mice lacking JP-2 exhibited embryonic lethality. Cardiac myocytes from the mutant mice showed deficiency of the junctional membrane complexes and abnormal Ca2+ transients. Our results suggest that JPs are important components of junctional membrane complexes.

Amino Acid Motifs↗
PubMed1993

Demonstration of selective protein complexes of p53 with 73 kDa heat shock cognate protein, but not with 72 kDa heat shock protein in human tumor cells.

It has been demonstrated that p53, especially, mutant p53 (mp53), makes protein complexes with major heat shock proteins hsp72/hsc73. However, there is no direct evidence showing whether hsp72 or hsc73 could bind preferentially to p53. In the present study, using TYKnu human ovarial carcinoma cells and monoclonal antibodies reacting specifically to hsp72/hsc73, we were able to find the selective protein complex formation with p53, presumably mp53, and hsc73, but not in the case of p53 and hsp72. The p53-hsc73 protein complexes dissociate with the addition of ATP, indicating that the dissociation is dependent upon the ATP-hydrolysis. These data suggest that hsc73 rather than hsp72 plays an important role in the yet undefined mechanism of disregulated cell growth control by mp53.

Adenosine Triphosphate↗
PubMed2001

Structure prediction of protein complexes by an NMR-based protein docking algorithm.

Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the protein-protein docking problem, where the input consists of the tertiary structures of proteins A and B plus an unassigned one-dimensional 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a 'theoretical' 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental one. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. [Morelli et al. (2000) Biochemistry, 39, 2530-2537]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with four protein complexes whose three-dimensional structures are stored in the PDB data bank (Bernstein et al., 1977) and whose 1H-NMR shift assignments are available from the BMRB database. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives.

Algorithms↗
PubMed1989

Synaptonemal complex proteins.

Synaptonemal complexes were isolated from rate spermatocytes for the purpose of biochemical and morphological analysis. Several monoclonal antibodies were elicited against purified synaptonemal complexes to study the composition and assembly of these structures. Four classes of antibodies could be discriminated according to the polypeptides that they recognize on Western blots of purified synaptonemal complexes, namely antibodies recognizing (i) a 190-kDa polypeptide; (ii) a 30- and a 33-kDa polypeptide; (iii) two polypeptides with molecular weights of about 120 kDa; and (iv) polypeptides with molecular weights of 66-55 kDa. The localization of these antigens within spermatocytes was analyzed light microscopically, by means of the immunoperoxidase technique and ultrastructurally, by immunogold labelling of surface-spread spermatocytes. The 66- to 55-kDa polypeptides are not confined to synaptonemal complexes; rather, these polypeptides appear to be chromosomal components. The 190-, 30-, and 33-kDa polypeptides make part of the lateral elements of paired as well as unpaired segments of synaptonemal complexes. The 120-kDa polypeptides were localized on the inner edge of the lateral elements, specifically in paired segments of synaptonemal complexes. The distribution of the 190-, 120-, 30-, and 33-kDa polypeptides within the testis was analyzed by immunofluorescence staining of cryostat sections. All these polypeptides turned out to be specific for nuclei of zygotene up to and including diplotene spermatocytes. Only in some early spermatids could the 190-, 30-, and 33-kDa polypeptides be detected, presumably in remnants of synaptonemal complexes.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMedDate not supplied

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data.

Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to the yeast S. cerevisiae and the bacteria H. pylori. Our analysis combines protein interaction data that are available for each of the two species and orthology information based on protein sequence comparison. We develop a detailed probabilistic model for protein complexes in a single species and a model for the conservation of complexes between two species. Using these models, one can recast the question of finding conserved complexes as a problem of searching for heavy subgraphs in an edge- and node-weighted graph, whose nodes are orthologous protein pairs. We tested this approach on the data currently available for yeast and bacteria and detected 11 significantly conserved complexes. Several of these complexes match very well with prior experimental knowledge on complexes in yeast only and serve for validation of our methodology. The complexes suggest new functions for a variety of uncharacterized proteins. By identifying a conserved complex whose yeast proteins function predominantly in the nuclear pore complex, we propose that the corresponding bacterial proteins function as a coherent cellular membrane transport system. We also compare our results to two alternative methods for detecting complexes and demonstrate that our methodology obtains a much higher specificity.

Bacterial Proteins↗
PubMed1997

A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex.

All six minichromosome maintenance (MCM) proteins have DNA-dependent ATPase motifs in the central domain which is conserved from yeast to mammals. Our group purified MCM protein complexes consisting of MCM2, -4 (Cdc21), -6 (Mis5), and -7 (CDC47) proteins from HeLa cells by using histone-Sepharose column chromatography (Ishimi, Y., Ichinose, S., Omori, A., Sato K., and Kimura, H. (1996) J. Biol. Chem. 271, 24115-24122). The present study revealed that both ATPase activity and DNA helicase activity that displaces oligonucleotides annealed to single-stranded circular DNA are associated with an MCM protein complex. Both ATPase and DNA helicase activities were co-purified with a 600-kDa protein complex that is consisted of equal amounts of MCM4, -6, and -7 proteins. An immunodepletion of the MCM protein complex from the purified fraction using anti-MCM4 antibody resulted in the severe reduction of the DNA helicase activity. Displacement of DNA fragments by the DNA helicase suggested that it migrated along single-stranded DNA in the 3' to 5' direction, and the DNA helicase activity was detected only in the presence of hydrolyzable ATP or dATP. These results suggest that this helicase may be involved in the initiation of DNA replication as a DNA unwinding enzyme.

Adenosine Triphosphatases↗
PubMed1999

Human antibody responses to A and C capsular polysaccharides, IgA1 protease and transferrin-binding protein complex stimulated by infection with Neisseria meningitidis of subgroup IV-1 or ET-37 complex.

The protein sequences of the IgA1 protease, TbpA and TbpB proteins differ between meningococci representative of serogroup A, subgroup IV-1 from epidemic disease in The Gambia and serogroup C, ET-37 complex from endemic disease in Mali. The uniformity of restriction endonuclease sites was determined for the iga, tbpA and thpB genes among strains of both clonal lineages. Rare isolates had acquired a variant thpAB operon by horizontal genetic exchange but all other strains were uniform within each clonal lineage. The quantitative levels of IgG to capsular polysaccharide, IgA1 protease and TBP complex were measured in paired acute phase and convalescent phase sera from The Gambia and from Mali using antigens from the homologous clonal lineages. IgG levels to these antigens were also measured in paired sera from healthy Gambians who permanently carried meningococci in the nasopharynx or did not. The results showed that disease stimulated IgG to each antigen in Mali and to all but TBP complex in The Gambia. Similarly, higher levels of IgG were found in sera from permanent carriers than in sera from permanent non-carriers. Acute phase sera from Mali contained low levels of IgG to C capsular polysaccharide (geometric mean value of 0.3 microg ml(-1)) while such sera from The Gambia contained higher and potentially protective levels of IgG to A polysaccharide (geometric mean of 5.5 microg ml(-1)). The concentrations of IgG to TBP complex in acute phase sera were higher and IgG to IgA1 protease was even higher, suggesting that intermediate levels of IgG to these proteins do not protect against disease.

Amino Acid Sequence↗
PubMed2005

The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking.

We investigate the extent to which the conformational fluctuations of proteins in solution reflect the conformational changes that they undergo when they form binary protein-protein complexes. To do this, we study a set of 41 proteins that form such complexes and whose three-dimensional structures are known, both bound in the complex and unbound. We carry out molecular dynamics simulations of each protein, starting from the unbound structure, and analyze the resulting conformational fluctuations in trajectories of 5 ns in length, comparing with the structure in the complex. It is found that fluctuations take some parts of the molecules into regions of conformational space close to the bound state (or give information about it), but at no point in the simulation does each protein as whole sample the complete bound state. Subsequent use of conformations from a clustered MD ensemble in rigid-body docking is nevertheless partially successful when compared to docking the unbound conformations, as long as the unbound conformations are themselves included with the MD conformations and the whole globally rescored. For one key example where sub-domain motion is present, a ribonuclease inhibitor, principal components analysis of the MD was applied and was also able to produce conformations for docking that gave enhanced results compared to the unbound. The most significant finding is that core interface residues show a tendency to be less mobile (by size of fluctuation or entropy) than the rest of the surface even when the other binding partner is absent, and conversely the peripheral interface residues are more mobile. This surprising result, consistent across up to 40 of the 41 proteins, suggests different roles for these regions in protein recognition and binding, and suggests ways that docking algorithms could be improved by treating these regions differently in the docking process.

Cluster Analysis↗
PubMed2006

A survey of protein-protein complex crystallizations.

A survey of crystallization conditions was carried out for 650 published protein-protein complexes in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics (RCSB). This resulted in the establishment of a Protein Complex Crystallization Database (PCCD) and a set of configuration-space boundaries for protein-complex crystallizations. Overall, polyethylene glycol (PEG) based conditions accounted for 70-80% of all crystallizations, with PEG 3000-4000, 5000-6000 and 8000 being the most frequently used. The median values of PEG concentrations were between 10 and 20% and were inversely correlated with their molecular weights. Ammonium sulfate remained the most favorable salt precipitant, with a median concentration of 1.6 M. The crystallization pH for the vast majority of protein complexes was between 5.0 and 8.0. Overall, the boundaries for the crystallization configuration space of protein complexes appear to be more restricted than those of soluble proteins. This may reflect the limited stability and solubility of protein-protein complexes. Based on statistical analysis of the database, a sparse-matrix and a systematic buffer and pH screen were formulated to best represent the crystallization of protein complexes.

Buffers↗
PubMed1982

Effect of protein, cholesterol, and phosphatidylglycerol on the surface activity of the lipid-protein complex reconstituted from pig pulmonary surfactant.

Lipid-protein complexes reconstituted from pig surfactant lipids and proteins were investigated for surface adsorption, minimum surface tension, stability index, and surface compressibility. Lipid constituents remained unchanged with procedures for the reconstitution. An apoprotein with a nominal molecular weight of 15,000 daltons significantly accelerated the lipid-protein complex to absorb the air-water interface. A 34,000-dalton apoprotein slightly modified the surface adsorption and the surface activity when it was incorporated into the lipid-protein complex formed from lipids and 15,000-dalton apoprotein. No significant surface adsorption was found in lipid vesicles even with the same lipid constituents as in the lipid-protein complex. In the lipid-protein complex prepared by changing the content of cholesterol and phosphatidylglycerol, cholesterol affected both the minimum surface tension and the surface compressibility while phosphatidylglycerol had little effect on the surface activity of the complex.

Animals↗
PubMed2006

Decomposition of overlapping protein complexes: a graph theoretical method for analyzing static and dynamic protein associations.

BACKGROUND: Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks. RESULTS: We propose a new method for identifying and representing overlapping protein complexes (or larger units called functional groups) within a protein interaction network. We develop a graph-theoretical framework that enables automatic construction of such representation. We illustrate the effectiveness of our method by applying it to TNFalpha/NF-kappaB and pheromone signaling pathways. CONCLUSION: The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. Our results show that the proposed method opens a new avenue for the analysis of protein interaction networks.

Journal Article↗
PubMed2000

Regulation of complex formation of POB1/epsin/adaptor protein complex 2 by mitotic phosphorylation.

RalBP1 and POB1, the downstream molecules of small GTP-binding protein Ral, are involved in receptor-mediated endocytosis together with Epsin and Eps15. The regulation of assembly of the complex of these proteins was examined. RalBP1, POB1, Epsin, and Eps15 formed a complex with alpha-adaptin of AP-2 in Chinese hamster ovary cells, but the formation was reduced in mitotic phase. RalBP1, POB1, Epsin, and Eps15 were all phosphorylated in mitotic phase. The phosphorylated forms of POB1 and Epsin were recognized by the antibody MPM2, which is known to detect mitotic phosphoproteins. POB1 and Epsin were phosphorylated by p34(cdc2) kinase in vitro. Their phosphorylation sites (Ser(411) of POB1 and Ser(357) of Epsin) were determined. Phosphorylated Epsin and Epsin(S357D) formed a complex with alpha-adaptin less efficiently than wild type Epsin. Although the EH domain of POB1 bound directly to Epsin, phosphorylation of Epsin inhibited the binding. Furthermore, Epsin(S357D) but not Epsin(S357A) lost the effect of Epsin on the insulin-dependent endocytosis. These results suggest that phosphorylation of Epsin in mitotic phase inhibits receptor-mediated endocytosis by disassembly of its complex with POB1 and alpha-adaptin.

Adaptor Proteins, Vesicular Transport↗