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PubMed2006

FAMS complex: a fully automated homology modeling system for protein complex structures.

The formation of a protein-protein complex is responsible for many biological functions; therefore, three-dimensional structures of protein complexes are essential for deeper understandings of protein functions and the mechanisms of diseases at the atomic level. However, compared with individual proteins, complex structures are difficult to solve experimentally because of technical limitations. Thus a method that can predict protein complex structures would be invaluable. In this study, we developed new software, FAMS Complex; a fully automated homology modeling system for protein complex structures consisting of two or more molecules. FAMS Complex requires only sequences and alignments of the target protein as input and constructs all molecules simultaneously and automatically. FAMS Complex is likely to become an essential tool for structure-based drug design, such as in silico screening to accelerate drug discovery before an experimental structure is solved. Moreover, in this post-genomic era when huge amounts of protein sequence information are available, a major goal is the determination of protein-protein interaction networks on a genomic scale. FAMS Complex will contribute to this goal, because its procedure is fully automated and so is suited for large-scale genome wide modeling.

Automation↗
PubMedDate not supplied

Retinoblastoma protein complexes with C/EBP proteins and activates C/EBP-mediated transcription.

The retinoblastoma protein (RB) recruits histone deacetylase (HDAC) to repress E2F-mediated transactivation that plays a critical role in cell cycle regulation. RB is also involved in activation of expression of a number of tissue specific- and differentiation-related genes. In this study, we examined the mechanism by which RB stimulated the expression of a differentiation-related gene, the surfactant protein D (SP-D), which plays important roles in innate host defense and the regulation of surfactant homeostasis. We demonstrated that RB specifically stimulated the activity of human SP-D gene promoter. The RB family member, p107 but not p130, also increased SP-D promoter activity. Activation by RB was mediated through a NF-IL6 (C/EBP beta) binding motif in the human SP-D promoter, and this sequence specifically bound to C/EBP alpha, C/EBP beta, and C/EBP delta. RB formed stable complexes with all three C/EBP family members. RB small pocket (amino acid residues 379-792), but not the C-pocket (amino acid residues 792-928), was necessary and sufficient for its interaction with C/EBP proteins. Furthermore, we demonstrated that the complexes containing RB and C/EBP proteins directly interacted with C-EBP binding site on DNA. These findings indicate that RB plays a positive, selective, and direct role in the C/EBP-dependent transcriptional regulation of human SP-D expression.

Amino Acid Motifs↗
PubMed2004

A novel method for scoring of docked protein complexes using predicted protein-protein binding sites.

Docking algorithms produce many possible structures of a protein-protein complex. In most cases some of them resemble the correct structure within an r.m.s.d. of <3 A. A major challenge in the field of docking is to extract the correct structure out of this pool, the so-called 'scoring'. Here, we introduce a new scoring function, which discriminates between the many wrong and few true conformations. The scoring function is based on measuring the tightness of fit of the two docked proteins at a predicted binding interface. The location of the binding interface is identified using the recently developed computer algorithm ProMate. The new scoring function does not rely on energy considerations. It is therefore tolerant to low-resolution descriptions of the interface. A linear relation between the score and the r.m.s.d. relative to the 'true structure' is found in most of the cases evaluated. The function was tested on the docking results of 21 complexes in their unbound form. It was found to be successful in 77% of the examined cases, defining success as scoring a 'true' result with a p value of better than 0.1.

Algorithms↗
PubMed2006

Identifying protein complexes in high-throughput protein interaction screens using an infinite latent feature model.

We propose a Bayesian approach to identify protein complexes and their constituents from high-throughput protein-protein interaction screens. An infinite latent feature model that allows for multi-complex membership by individual proteins is coupled with a graph diffusion kernel that evaluates the likelihood of two proteins belonging to the same complex. Gibbs sampling is then used to infer a catalog of protein complexes from the interaction screen data. An advantage of this model is that it places no prior constraints on the number of complexes and automatically infers the number of significant complexes from the data. Validation results using affinity purification/mass spectrometry experimental data from yeast RNA-processing complexes indicate that our method is capable of partitioning the data in a biologically meaningful way. A supplementary web site containing larger versions of the figures is available at http://public.kgi.edu/wild/PSBO6/index.html.

Algorithms↗
PubMed1975

Enhancement of encephalitogenic activity by the formation of myelin basic protein-brain acidic protein complex.

Encephalitogenic protein fraction (BEC) was isolated from bovine brain tissue by extraction with salt-ethanol mixture at neutral pH, instead of employing dilute mineral acid. The fraction BEC was separated into two fractions. An acid-soluble protein was encephalitogenic and the major component was very alike to the basic protein of myelin (Al). The other was acid-insoluble acidic protein that was not encephalitogenic even at a dose of 100 mug. The acidic protein formed an insoluble complex with Al rotein which was purified by Eylar's method. Encephalitogenic activity of the complex was higher than Al protein in young guinea pigs when injected with complete Freund's adjuvant.However, this enhancement of encephalitogenic activity was not observed in aged guinea pigs. The complex showed higher blastogenic activity than Al protein alone with peripheral blood lymphocytes from guinea pigs immunized with Al protein and complete Freund's adjuvant. These results show that an adjuvant-like acidic protein is present in brain tissue and the complex with Al protein enhances the induction of experimental allergic encephalomyelitis (EAE).

Age Factors↗
PubMed1998

Identification of an evolutionarily conserved heterotrimeric protein complex involved in protein targeting.

In Caenorhabditis elegans, lin-2, lin-7, and lin-10 genetically interact to control the trafficking of the Let-23 growth factor receptor to the basolateral surface of body epithelia. The human homologue of the lin-10 gene has recently been identified as a member of the X11 gene family. The X11 proteins contain one phosphotyrosine binding (PTB) and two PSD-95.Dlg.ZO-1 (PDZ) domains as well as an extended amino terminus. We have previously shown that the PTB domain of X11alpha (also known as Mint1) can bind to the amyloid precursor protein (APP) in a phosphotyrosine-independent fashion and can markedly inhibit the processing of APP to the amyloid beta (Abeta) peptide. Here, we report that X11alpha directly binds to the mammalian homologue of Lin-2 (mLin-2), also known as CASK. This binding is mediated by direct interaction between the Calmodulin Kinase II (CKII)-like domain of mLin-2 and the amino terminus of X11alpha. Furthermore, we can detect direct interactions between mLin-2 and mammalian Lin-7 (mLin-7). In mouse brain, we have identified a heterotrimeric complex that contains mLin-2, mLin-7, and X11alpha and that is likely important for the localization of proteins in polarized cells. This complex may play an important role in the trafficking and processing of APP in neurons.

Adaptor Proteins, Signal Transducing↗
PubMed1984

Monoclonal antibodies to heterogeneous nuclear RNA-protein complexes. The core proteins comprise a conserved group of related polypeptides.

Hybridomas secreting monoclonal antibodies that react with heterogeneous nuclear ribonucleoprotein (hnRNP) core proteins have been isolated by immunizing BALB/c mice with RNP particles isolated from chicken and screening the fusion products with mouse RNP complexes. The antibodies show varying affinities for the hnRNP core proteins that have been blotted onto nitrocellulose. The majority of the immunoglobulins react with all the core group proteins although several recognize subsets of the hnRNP polypeptides. The clones are specific for different antigenic determinants as shown by their inability to compete with one another for binding sites. A mild proteolytic digestion of hnRNP proteins generates fragments that have uniformly lost 12 kDa and contain the antigenic determinants recognized by several of the monoclonal antibodies. Thus, it appears the core proteins comprise a family of related polypeptides possessing underlying structural similarities. Polypeptides similar in number and molecular weights that have antigenic determinants cross-reactive with those of mouse RNP have been found in a number of organisms, thereby emphasizing their possible common structure and function in higher eukaryotes. No difference in the distribution within the cell of individual or groups of core proteins has so far been detected by indirect immunofluorescence.

Animals↗
PubMed2006

3D complex: a structural classification of protein complexes.

Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Amino Acid Sequence↗
PubMed2005

Distribution of tight DNA-protein complexes along the barley chromosome 1H, as revealed by microsatellite marker analysis.

The distribution of DNA complexes with proteins resistant to routine deproteinisation procedures (tightly bound proteins, TBP) was studied on the barley chromosome 1H by means of microsatellite analysis. The polypeptide spectrum of the barley shoot TBP was similar to that formerly described for other organisms. In order to reveal developmental changes in the distribution of the TBP, DNA was extracted from dry grains, coleoptiles, root tips, and young and old leaves. In the seeds, all the studied DNA sites were evenly distributed between free DNA and DNA containing the tight DNA-protein complexes. Germination made the interaction between TBP and chromosomal loci specific. In coleoptile DNA, sites containing microsatellites located in the distal part of the long arm of the chromosome were not bound to the TBP anymore, however, the centromeric markers were found exclusively in the tight DNA-protein complexes. A similar but not identical distribution of markers was observed in the root tips and young leaves. Leaf senescence was accompanied by a loss in interaction specificity between chromosomal loci and tightly bound proteins. These results are considered to reflect changes in chromatin domain interaction with the nuclear matrix during plant development.

Chromosomes, Plant↗
PubMed1994

Modifications of low density lipoprotein induced by the interaction with human plasma glycosaminoglycan-protein complexes.

Glycosaminoglycan (GAG)-protein complexes from human plasma were separated into low charge (LC-GP) and high charge (HC-GP) components. LC-GP and HC-GP differed with respect to GAG and protein composition and to molecular size. The in vitro interaction of both GAG-protein complexes with human LDL was investigated. LC-GP did not precipitate LDL. On the contrary, HC-GP formed insoluble complexes with LDL, following a biphasic behaviour on increasing HC-GP concentration. In the presence of a HC-GP/LDL ratio higher than 0.02 the interaction stoichiometry was shifted towards the formation of soluble complexes. Papain treatment of HC-GP completely prevented LDL precipitation. Moreover, the extent of HC-GP-induced precipitation of LDL was markedly reduced by the simultaneous addition of LC-GP. Data obtained with standard GAGs showed that heparin (HE) and chondroitin-6-sulphate (C6S) were the most effective ligands in precipitating LDL. However, the shape of precipitation curves was markedly different. C6S behaved similarly to HC-GP, suggesting that GAG chains could play an important role in insoluble complex formation with LDL. Steady-state fluorescence anisotropy investigation indicated that HC-GP induced a significant decrease in the microviscosity of LDL hydrophobic region. This effect was no longer detectable after either addition of LC-GP or papain treatment of HC-GP. Differential scanning calorimetry (DSC) demonstrated that both lipid and protein components of LDL were affected by the interaction with HC-GP. The temperature of irreversible thermal unfolding of apo B100 was shifted to a lower value and a second peak appeared in the region of the reversible melting of cholesterol esters. Both the fluorescence anisotropy and the DSC data obtained with standard HE and C6S indicated that GAG chains were directly involved in affecting physico-chemical properties of complexed LDL. These results suggest that the interaction with plasma HC-GP could modify LDL structural properties. However, LC-GP is likely to act as a modulator, probably preventing the interaction between HC-GP and circulating LDL.

Blood Proteins↗
PubMed1980

Purification of a membrane-associated protein complex required for protein translocation across the endoplasmic reticulum.

The capacity of microsomal membranes to translocate nascent presecretory proteins across their lipid bilayer can be largely abolished by extracting them with high ionic strength buffers. It can be reconstituted by adding the salt extract back to the depleted membranes [Warren, G. & Doberstein, B. (1978) Nature (London) 273, 569-571]. Utilizing hydrophobic chromatography, we purified to homogeneity a protein component of the salt extract that reconstitutes the translocation activity of the extracted membranes. This component behaves as a homogeneous species upon gel filtration, ion-exchange chromatography, adsorption chromatography, and sucrose-gradient centrifugation. When examined by polyacrylamide gel electrophoresis in NaDodSO4, six polypeptides with apparent Mr of 72,000, 68,000, 54,000, 19,000, 14,000, and 9000 are observed in about equal and constant stoichiometry, suggesting that they are subunits of a complex. The sedimentation coefficient of 11S is in good agreement with the sum of the Mr of the subunits. The Mr 68,000 and 9000 subunits label intensely with N-[3H]ethylmaleimide. Thus, the reported sulfhydryl group requirement of the translocation activity in the unfractionated extract [Jackson, R. C., Walter, P. & Blobel, G. (1980) Nature (London), 286, 174-176] may be localized to either or both the Mr 68,000 and 9000 subunits of the purified complex.

Animals↗
PubMed2007

The plant heterotrimeric G-protein complex.

Heterotrimeric G-protein complexes couple extracellular signals via cell surface receptors to downstream enzymes called effectors. Heterotrimeric G-protein complexes, together with their cognate receptors and effectors, operate at the apex of signal transduction. In plants, the number of G-protein complex components is dramatically less than in other multicellular eukaryotes. An understanding of how multiple signals propagate transduction through the G-protein node can be found in the unique structural and kinetic properties of the plant heterotrimeric G-protein complex. This review addresses these unique features and speculates on why the repertoire of G-protein signaling elements is dramatically simpler than that in all other multicellular eukaryotes.

Amino Acid Sequence↗
PubMed1997

Potentiation of etoposide-induced apoptosis by staurosporine in human tumor cells is associated with events downstream of DNA-protein complex formation.

UNLABELLED: Protein kinase inhibitors have demonstrated potential for use in the therapy of human cancers, in particular leukemia. Staurosporine, a protein kinase inhibitor with broad specificity, enhances the cytotoxic effects of various antitumor agents with different modes of action. The topoisomerase II inhibitor, etoposide, has shown clinical activity against a wide range of tumor types. PURPOSE: The purpose of this study was to assess the effects of staurosporine on etoposide-induced cell death processes in a human tumor of epithelial origin. METHODS: Modulation of etoposide-induced apoptosis by staurosporine in HeLa cells was assessed by cell morphology, extraction of low molecular weight DNA, quantitation of DNA-protein complexes, and measurements of rates of DNA synthesis. The effects on cellular genes implicated in apoptosis were determined by Northern and Western blotting, along with assays of cyclin-dependent kinase activities. RESULTS: Staurosporine exhibited a two- to three-fold potentiation of apoptosis caused by etoposide in HeLa cells when applied concurrently, or immediately following etoposide removal, but did not alter the quantity of DNA-protein complexes produced by etoposide. Etoposide-induced apoptosis, and its potentiation by staurosporine, were associated with reduced c-myc expression, and a moderate increase in p21WAF1/CIP1 mRNA and protein levels. Inhibitors of cyclic AMP-dependent protein kinase and protein kinase C, which exhibit greater specificity than staurosporine, were without effect on apoptosis caused by etoposide, whereas use of the tyrosine phosphatase inhibitor, vanadate, resulted in its abrogation. The potentiation of etoposide-induced apoptosis by staurosprine was associated with a significant increase in cyclin A-dependent kinase activity. In addition, etoposide caused substantial inhibition of DNA synthesis. CONCLUSION: These results indicate that staurosporine potentiates apoptosis through events which occur downstream of DNA damage, and implicate unscheduled activation of cyclin A-dependent kinase during inhibition of DNA synthesis as a possible cause.

Apoptosis↗
PubMed1999

Presenilin mutations associated with Alzheimer disease cause defective intracellular trafficking of beta-catenin, a component of the presenilin protein complex.

The presenilin proteins are components of high-molecular-weight protein complexes in the endoplasmic reticulum and Golgi apparatus that also contain beta-catenin. We report here that presenilin mutations associated with familial Alzheimer disease (but not the non-pathogenic Glu318Gly polymorphism) alter the intracellular trafficking of beta-catenin after activation of the Wnt/beta-catenin signal transduction pathway. As with their effect on betaAPP processing, the effect of PS1 mutations on trafficking of beta-catenin arises from a dominant 'gain of aberrant function' activity. These results indicate that mistrafficking of selected presenilin ligands is a candidate mechanism for the genesis of Alzheimer disease associated with presenilin mutations, and that dysfunction in the presenilin-beta-catenin protein complexes is central to this process.

Alzheimer Disease↗
PubMed2001

Protein quantification from complex protein mixtures using a proteomics methodology with single-cell resolution.

We have developed an extremely sensitive technique, termed immuno-detection amplified by T7 RNA polymerase (IDAT) that is capable of monitoring proteins, lipids, and metabolites and their modifications at the single-cell level. A double-stranded oligonucleotide containing the T7 promoter is conjugated to an antibody (Ab), and then T7 RNA polymerase is used to amplify RNA from the double-stranded oligonucleotides coupled to the Ab in the Ab-antigen complex. By using this technique, we are able to detect the p185(her2/neu) receptor from the crude lysate of T6-17 cells at 10(-13) dilution, which is 10(9)-fold more sensitive than the conventional ELISA method. Single-chain Fv fragments or complementarity determining region peptides of the Ab also can be substituted for the Ab in IDAT. In a modified protocol, the oligonucleotide has been coupled to an Ab against a common epitope to create a universal detector species. With the linear amplification ability of T7 RNA polymerase, IDAT represents a significant improvement over immuno-PCR in terms of sensitivity and has the potential to provide a robotic platform for proteomics.

3T3 Cells↗