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PubMed1994

Spin label EPR study of lipid solvation of supramolecular photosynthetic protein complexes in thylakoids.

Lipid-protein association in the chloroplast membrane and its various thylakoid fractions from higher plants, namely pea and maize, rich in Photosystem I (PSI) and Photosystem II (PSII), respectively, were studied using EPR spectroscopy of spin-labelled lipid molecules. All the EPR spectra consisted of two spectral components corresponding to bulk fluid lipids and solvation lipids motionally restricted at the hydrophobic surface of membrane proteins. Spin-labelled stearic acid and phosphatidylglycerol exhibited marked selectivity towards the supramolecular protein complexes of both PSI and PSII although to different extent. In addition, lipid-protein titration experiments are described for partially delipidated PSII-enriched membrane fractions of pea chloroplasts, incorporating unlabelled egg phosphatidylcholine prior to or after the incorporation of spin-labelled lipids. Two sets of solvation sites were resolved by timed labelling experiments and a significant result of these studies was that a well-defined population of solvation sites (approx. 100 mol lipids/820 kDa protein) was rapidly exchanged by laterally diffusing membrane lipids, while other solvation sites (approx. 50 mol lipids/820 kDa protein) were exchanged much slower or not exchanged at all.

Chloroplasts↗
PubMed2002

Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes.

Analysis of the spatial arrangement of protein and water atoms that form polar interactions with ribose has been performed for a structurally non-redundant dataset of ATP, ADP and FAD-protein complexes. The 26 ligand-protein structures were separated into two groups corresponding to the most populated furanose ring conformations (N and S-domains). Four conserved positions were found for S-domain protein-ligand complexes and five for N-domain complexes. Multiple protein folds and secondary structural elements were represented at a single conserved position. The following novel points were revealed: (i) Two complementary positions sometimes combine to describe a putative atomic spatial location for a specific conserved binding spot. (ii) More than one third of the interactions scored were water-mediated. Thus, conserved spatial positions rich in water atoms are a significant feature of ribose-protein complexes.

Adenosine Diphosphate↗
PubMed2003

Two-dimensional Blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates: a proteomics approach.

Identification and characterization of multi-protein complexes is an important step toward an integrative view of protein-protein interaction networks that determine protein function and cell behavior. The limiting factor for identifying protein complexes is the method for their separation. Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. To date, BN-PAGE has only been applicable to purified material. Here, we show that dialysis permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE. We visualized different multi-protein complexes by immunoblotting including forms of the eukaryotic proteasome. Complex dynamics after gamma interferon stimulation of cells was studied, and an antibody shift assay was used to detect protein-protein interactions in BN-PAGE. Furthermore, we identified defined protein complexes of various proteins including the tumor suppressor p53 and c-Myc. Finally, we identified multi-protein complexes via mass spectrometry, showing that the method has a wide potential for functional proteomics.

Animals↗
PubMed2004

Towards functional proteomics of membrane protein complexes in Synechocystis sp. PCC 6803.

The composition and dynamics of membrane protein complexes were studied in the cyanobacterium Synechocystis sp. PCC 6803 by two-dimensional blue native/SDS-PAGE followed by matrix-assisted laser-desorption ionization time of flight mass spectrometry. Approximately 20 distinct membrane protein complexes could be resolved from photoautotrophically grown wild-type cells. Besides the protein complexes involved in linear photosynthetic electron flow and ATP synthesis (photosystem [PS] I, PSII, cytochrome b6f, and ATP synthase), four distinct complexes containing type I NAD(P)H dehydrogenase (NDH-1) subunits were identified, as well as several novel, still uncharacterized protein complexes. The dynamics of the protein complexes was studied by culturing the wild type and several mutant strains under various growth modes (photoautotrophic, mixotrophic, or photoheterotrophic) or in the presence of different concentrations of CO2, iron, or salt. The most distinct modulation observed in PSs occurred in iron-depleted conditions, which induced an accumulation of CP43' protein associated with PSI trimers. The NDH-1 complexes, on the other hand, responded readily to changes in the CO2 concentration and the growth mode of the cells and represented an extremely dynamic group of membrane protein complexes. Our results give the first direct evidence, to our knowledge, that the NdhF3, NdhD3, and CupA proteins assemble together to form a small low CO2-induced protein complex and further demonstrate the presence of a fourth subunit, Sll1735, in this complex. The two bigger NDH-1 complexes contained a different set of NDH-1 polypeptides and are likely to function in respiratory and cyclic electron transfer. Pulse labeling experiments demonstrated the requirement of PSII activity for de novo synthesis of the NDH-1 complexes.

Adenosine Triphosphate↗
PubMed1992

[The LPS-protein complex from the outer membrane of Francisella tularensis].

LPS-protein complex containing proteins of 15 kD, 17 kD and 19 kD was isolated from F. tularensis outer membrane by solving with sodium deoxycholate with the subsequent gel filtration on Sephacryl S-200. Protein of 17 kD constituted the main protein component of the complex. The LPS-protein ratio of this complex was 1:1. Proteins contained in LPS-protein complex have mainly the alpha-spiral structure. In the absence of detergent these proteins and LPS formed micelles with molecular weight exceeding 10(7) D. LPS-protein complex was shown to have a protective effect in mice infected with F. tularensis virulent strain 503.

Animals↗
PubMed1994

Insulin and other growth factors induce binding of the ternary complex and a novel protein complex to the c-fos serum response element.

Rapid, transient induction of c-fos transcription follows treatment of cells with insulin and other growth factors. This is mediated through the serum response element (SRE), which binds the serum response factor (SRF), as well as accessory factors such as p62 ternary complex factor. Using a gel shift assay we found that formation of the ternary complex increased transiently within 2 min of insulin or phorbol ester treatment of several insulin-sensitive cell lines. However, mutations that prevented formation of this ternary complex did not inhibit insulin- or phorbol ester-stimulated induction of c-fos transcription in these cell lines. We also identified a novel SRF-containing multiprotein complex that forms on the SRE within 2 min following insulin, phorbol ester, or other growth factor treatment. Formation of this novel complex, called band 3, occurred rapidly and transiently, with a time course parallel to the induction of c-fos transcription. Band 3 also formed with gamma-actin and zif268/3 SRE probes. Methylation and carboxy ethylation interference analysis, as well as extensive SRE mutagenesis, suggest that only the SRF directly contacts the SRE in forming band 3. Formation of this novel complex appears to involve protein-protein interactions between SRF and other nuclear protein(s) that may play a role in growth factor stimulation of c-fos transcription.

3T3 Cells↗
PubMed2005

Identification of functional modules in protein complexes via hyperclique pattern discovery.

Proteins usually do not act isolated in a cell but function within complicated cellular pathways, interacting with other proteins either in pairs or as components of larger complexes. While many protein complexes have been identified by large-scale experimental studies, due to a large number of false-positive interactions existing in current protein complexes 10, it is still difficult to obtain an accurate understanding of functional modules, which encompass groups of proteins involved in common elementary biological function. In this paper, we present a hyperclique pattern discovery approach for extracting functional modules (hyperclique patterns) from protein complexes. A hyperclique pattern is a type of association pattern containing proteins that are highly affiliated with each other. The analysis of hyperclique patterns shows that proteins within the same pattern tend to present in the protein complex together. Also, statistically significant annotations of proteins in a pattern using the Gene Ontology suggest that proteins within the same hyperclique pattern more likely perform the same function and participate in the same biological process. More interestingly, the 3-D structural view of proteins within a hyperclique pattern reveals that these proteins physically interactwith each other. In addition, we show that several hyperclique patterns corresponding to different functions can participate in the same protein complex as independent modules. Finally, we demonstrate that a hyperclique pattern can be involved in different complexes performing different higher-order biological functions, although the pattern corresponds to a specific elementary biological function.

Algorithms↗
PubMed1981

Circular dichroism of bacteriochlorophyll a in light harvesting bacteriochlorophyll protein complexes from Chromatium vinosum.

Bacteriochlorophyll (Bchl) protein complexes containing light harvesting (LH) Bchls were isolated from Chromatium vinosum, and their CD spectra were measured in the near-infrared region. These isolated Bchl protein complexes retained the CD signals of LH Bchls that were observed in situ in chromatophores. The CD spectrum of fraction A (containing B890) consisted of paired positive and negative bands (a double CD) having a zero-crossing at 800 nm and a single negative band at around 900 nm attributed to the B890. For low 850 fraction B (B800 and B850), a double CD having a zero-crossing at 795 nm and a single negative band at around 850 nm attributed to the B850 were found. High 850 fraction B exhibited a double CD having a zero-crossing at 795 nm, a negative band at around 860 nm and a positive band at around 840 nm. For fraction C (B800 and B820), a double CD having a zero-crossing at 795 nm and a single negative band at around 830 nm, which was attributed to the B820, were found. The double CD was attributed to the B800 in fractions A, B, and C. There was no additional CD besides the CD of the isolated Bchl protein complexes in the CD spectra of chromatophores.

Bacterial Chromatophores↗
PubMed1993

The VPS16 gene product associates with a sedimentable protein complex and is essential for vacuolar protein sorting in yeast.

The Saccharomyces cerevisiae vacuolar protein sorting mutant, vps16, exhibits pleiotropic defects in vacuolar protein targeting and vacuole morphology. To understand the role of the VPS16 gene in vacuolar protein sorting and organelle assembly, a vps16 ts mutant was used to clone the wild-type gene. DNA sequence analysis identified a single open reading frame within a vps16 complementing DNA fragment, capable of encoding a protein of 92,000 Da. Hydrophobicity analysis indicates that the Vps16 protein (Vps16p) is hydrophilic and contains no obvious signal sequence or membrane spanning domains. Gene disruption experiments have shown that VPS16 is not essential. delta vps16 cells exhibit, 1) a severe defect in vacuolar protein sorting; 2) a ts growth defect; 3) a grossly abnormal vacuole morphology, no normal vacuole compartment(s) is present; and 4) a defect in alpha-factor processing. A trpE-Vps16 fusion protein has been used to generate polyclonal antiserum. This antiserum detects an unglycosylated protein of 90,000 Da. Subcellular fractionation studies indicate that the vast majority of the VPS16 gene product is associated with a particulate cell fraction. This association is resistant to detergent and salt extractions, but Vps16p can be extracted with 6 M urea and alkali buffer. In addition, overexpression of Vps16p appears to saturate the association sites available in this sedimentable structure. These data indicate that Vps16p may be specifically associated with a large protein complex, or with a limited number of sites on cytoskeletal elements of the cell.

Amino Acid Sequence↗
PubMed2005

Hemextin AB complex, a unique anticoagulant protein complex from Hemachatus haemachatus (African Ringhals cobra) venom that inhibits clot initiation and factor VIIa activity.

During injury or trauma, blood coagulation is initiated by the interaction of factor VIIa (FVIIa) in the blood with freshly exposed tissue factor (TF) to form the TF.FVIIa complex. However, unwanted clot formation can lead to death and debilitation due to vascular occlusion, and hence, anticoagulants are important for the treatment of thromboembolic disorders. Here, we report the isolation and characterization of two synergistically acting anticoagulant proteins, hemextins A and B, from the venom of Hemachatus haemachatus (African Ringhals cobra). N-terminal sequences and CD spectra of the native proteins indicate that these proteins belong to the three-finger toxin family. Hemextin A (but not hemextin B) exhibits mild anticoagulant activity. However, hemextin B forms a complex (hemextin AB complex) with hemextin A and synergistically enhances its anticoagulant potency. Prothrombin time assay showed that these two proteins form a 1:1 complex. Complex formation was supported by size-exclusion chromatography. Using a "dissection approach," we determined that hemextin A and the hemextin AB complex prolong clotting by inhibiting TF.FVIIa activity. The site of anticoagulant effects was supported by their inhibitory effect on the reconstituted TF.FVIIa complex. Furthermore, we demonstrated their specificity of inhibition by studying their effects on 12 serine proteases; the hemextin AB complex potently inhibited the amidolytic activity of FVIIa in the presence and absence of soluble TF. Kinetic studies showed that the hemextin AB complex is a noncompetitive inhibitor of soluble TF.FVIIa amidolytic activity, with a Ki of 50 nm. Isothermal titration calorimetric studies showed that the hemextin AB complex binds directly to FVIIa with a binding constant of 1.62 x 10(5) m(-1). The hemextin AB complex is the first reported natural inhibitor of FVIIa that does not require a scaffold to mediate its inhibitory activity. Molecular interactions of the hemextin AB complex with FVIIa/TF.FVIIa will provide a new paradigm in the search for anticoagulants that inhibit the initiation of blood coagulation.

Amino Acid Sequence↗
PubMed1998

A general RNA-binding protein complex that includes the cytoskeleton-associated protein MAP 1A.

Association of mRNA with the cytoskeleton represents a fundamental aspect of RNA physiology likely involved in mRNA transport, anchoring, translation, and turnover. We report the initial characterization of a protein complex that binds RNA in a sequence-independent but size-dependent manner in vitro. The complex includes a approximately 160-kDa protein that is bound directly to mRNA and that appears to be either identical or highly related to a approximately 1600-kDa protein that binds directly to mRNA in vivo. In addition, the microtubule-associated protein, MAP 1A, a cytoskeletal associated protein is a component of this complex. We suggest that the general attachment of mRNA to the cytoskeleton may be mediated, in part, through the formation of this ribonucleoprotein complex.

Animals↗
PubMed2005

Single-step Strep-tag purification for the isolation and identification of protein complexes from mammalian cells.

Identification of protein complexes is the key to understanding cellular functions. In this study, we present a novel method for the identification of multiprotein complexes from mammalian cells. By using the Strep-tag affinity chromatography method, enabling fast and simple one-step purification, coupled with competitive elution under physiological conditions, we successfully purified a PP2A holoenzyme protein complex from a cultured mammalian cancer cell line. We identified, by mass spectrometry, both known and novel interacting proteins for PP2A, and demonstrate that the purified PP2A complex is functional. The benefits and potential applications of the Strep-tag method for protein complex purification are discussed.

Amino Acid Sequence↗
PubMed2004

Interconversion between dimers and monomers of endogenous mitochondrial F1-inhibitor protein complexes and the release of the inhibitor protein. Spectroscopic characteristics of the complexes.

The F1-inhibitor protein complex (F1-IP) was purified from heart submitochondrial particles. Size exclusion chromatography of the endogenous complex showed that it contains dimers (D) and monomers (M) of F1-IP. Further chromatographic analysis showed that D and M interconvert. At high protein concentrations, the interconversion reaction is shifted toward the D species. The release of the inhibiting action of IP is faster at low than at high protein concentrations. During activation of F1, the M species accumulates through a process that is faster than the release of IP from F1. These findings indicate that the activation of F1-IP involves the transformation of D into M, which subsequently loses IP. The spectroscopic characteristics of D, M, and free F1 show that the binding of IP and dimerization modifies the fluorescence intensity of tyrosine residues and that of the single tryptophan of F1 which is far from the IP binding site.

Animals↗
PubMed2004

Developing chick embryos express a protein which shares homology with the nuclear pore complex protein Nup88 present in human tumors.

Nup88 is a nuclear pore complex protein which is overexpressed in a variety of human tumors of the stomach, colon, liver, pancreas, breast, lung, ovary, uterus, prostate and kidney. A monoclonal antibody crossreacting with the yeast Candida albicans and Nup88 was used to investigate the expression of cross-reactive antigens in chick embryos, in an attempt to identify an experimental model for studying the role played by Nup88 during cell development and differentiation. All cells in the trilaminar embryo were labeled with the antibody, but as development advanced and organogenesis was completed, expression of the corresponding antigen became more restricted. Thus, some structures continued to be intensely labeled (skin epithelium, oropharyngeal endothelium, perichondral mesenchymal tissue), whereas others ( muscular tissue, vascular endothelium, respiratory endothelium, digestive tract mucosa, peripheral nerves, medullary white matter and the retinal axons) were more moderately stained. No immunoreactivity was observed in the medullary grey matter or cartilage. A specific band of 53 kDa observed by Western blotting of chick embryo extracts suggested that the chicken antigen recognized by the monoclonal antibody is the homologue of human Nup88, which is associated with the high proliferation and low differentiation of tumor cells. The present results indicate that the role of Nup88 in cell differentiation and organ development could be fruitfully investigated using the developing chick embryo as an experimental model.

Animals↗
PubMed1998

Chemical transformation of mouse liver cells results in altered cyclin D-CDK protein complexes.

Dysregulated cell proliferation is one phenotypic change associated with neoplasia. Key protein complexes involved in regulating cell division are composed of cyclins, cyclin-dependent kinases (CDK) and CDK inhibitors (CDI). Many virally transformed cells in culture exhibit disrupted cyclin-CDK-CDI complexes, suggesting that such changes may play a mechanistic role in viral transformation. To determine whether similar alterations may be involved in chemical carcinogenesis we characterized cyclin D1-CDK-CDI protein complexes in a non-tumorigenic mouse liver cell line and investigated whether complexes were altered after transformation with the genotoxic carcinogens N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) or 3-methylcholanthrene (MC). In non-tumorigenic mouse liver cells cyclin D1 associated with CDK6, CDK4 or CDK2 to form binary (cyclin D1-CDK), tertiary (cyclin D1-CDK-p27KIP1) or quaternary (cyclin D1-CDK-p21WAF1-PCNA) complexes. After chemical transformation of mouse liver cells with either MC or MNNG, select cyclin D1-CDK-CDI protein complexes were altered. In MC-transformed cells formation of various binary, tertiary and quaternary cyclin D1-CDK-(CDI) protein complexes was reduced, resulting in decreased CDK4 kinase activity. Interestingly, CDK6 kinase activity was dramatically elevated due to high levels of cyclin D3 in association with CDK6. In MNNG-transformed cells select cyclin D1-CDK6-CDI and cyclin D1-CDK2-CDI protein complexes were altered but CDK6 and CDK4 kinase activity remained unaffected. Distinct changes in cyclin D1-CDK-CDI complexes found between the two chemically transformed mouse liver cell lines suggest that each cell line harbored unique mutations or alterations that differentially contributed to stabilization of cyclin D1-CDK-CDI holoenzymes. p53 gene mutations were not detected in the MC- or MNNG-transformed mouse liver cell lines and thus were not involved in disrupting cyclin D1-CDK-CDI protein complexes. In summary, this study presents evidence that D-type CDK protein complexes can be altered physically and functionally after chemical transformation with genotoxic carcinogens, suggesting that components of the cell cycle machinery can be targeted during chemical carcinogenesis.

Animals↗
PubMed1983

Isolation of PS II reaction centre and its relationship to the minor chlorophyll-protein complexes.

Evidence is presented for the identification of the chlorophyll- protein complex CPa-1 (CP 47) as the reaction centre of photosystem II (PS II). We have developed a simple, rapid method using octyl glucoside solubilization to obtain preparations from spinach and barley that are highly enriched in PS II reaction centre activity (measured as the light-driven reduction of diphenylcarbazide by 2,6-dichlorophenolindophenol). These preparations contain only the two minor chlorophyll-protein complexes CPa-1 and CPa-2. During centrifugation on a sucrose density gradient, there is a partial separation of the two CPa complexes from each other, and a complete separation from other chlorophyll-protein complexes. The PS II activity comigrates with CPa-1 but not CPa-2, strongly suggesting that the former is the reaction centre complex of PS II. Reaction centre preparations are sensitive to the herbicide 3(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), but only at much higher concentrations than those required to inhibit intact thylakoid membranes. A model of PS II incorporating our current knowledge of the chlorophyll-protein complexes is presented. It is proposed that CPa-2 and the chlorophyll a + b complex CP 29 may function as internal antenna complexes surrounding the reaction centre, with the addition of variable amounts of the major chlorophyll a + b light-harvesting complex.

Chlorophyll↗
PubMed1985

Hybridization selection of nucleic acid-protein complexes. 1. Detection of proteins cross-linked to specific mRNAs and DNA sequences by irradiation of intact Escherichia coli cells with ultraviolet light.

A method is presented for the detection in crude lysates of subnanogram amounts of proteins covalently bound to a specific nucleic acid sequence. The sensitivity of this method enabled us to study proteins cross-linked to specific DNA and mRNA sequences by irradiation of intact Escherichia coli cells with ultraviolet light. Among the proteins cross-linked to pBR322 DNA, the single strand binding protein, the HU-proteins, and the RNA polymerase beta and sigma subunits were present. Some, but not all proteins were cross-linked to 5-bromodeoxyuridine-substituted DNA more efficiently than to normal DNA. Ribosomal protein S1 is by far the most prominent protein cross-linked to mRNAs. Among the proteins cross-linked in smaller amounts to mRNAs are translation initiation factor IF 1, and at least six proteins of the 30 S ribosomal subunit, among which is S21. No 50 S proteins, nor IF-2, IF-3 or any of the elongation factors could be detected. Some UV-induced nucleic acid-protein cross-links were found to be heat-labile. It is concluded that the method employed may be used to compare the proteins interacting with different mRNAs, as well as single-copy DNA sequences from bacteria and eucaryotes with low complexity genomes.

Bacterial Proteins↗