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Interaction Network (interaction + network)
Kinds of Interaction Network Selected AbstractsInteraction networks: Lessons from large-scale studies in yeastPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 20 2009Gerard Cagney Abstract Saccharomyces cerevisiae is the simplest eukaryotic model organism and has made countless contributions to cell biology. The ease with which it can be genetically manipulated has made it a favourite organism among technologists for developing methods for large-scale analysis based on reverse genetics. Consequently, more genomewide datasets describing aspects of gene and protein biology are available for yeast than for any other organism. This has led to the pioneering of many computational analysis techniques using yeast data. Here, we make a brief survey of yeast physical and genetic interaction networks, highlighting major experimental and computational achievements first described in this organism. [source] Networks and dominance hierarchies: does interspecific aggression explain flower partitioning among stingless bees?ECOLOGICAL ENTOMOLOGY, Issue 2 2010KAI DWORSCHAK 1. The distribution of consumers among resources (trophic interaction network) may be shaped by asymmetric competition. Dominance hierarchy models predict that asymmetric interference competition leads to a domination of high quality resources by hierarchically superior species. 2. In order to determine the competitive dominance hierarchy and its effect on flower partitioning in a local stingless bee community in Borneo, interspecific aggressions were tested among eight species in arena experiments. 3. All species tested were strongly mutually aggressive in the arena, and the observed interactions were often lethal for one or both opponents. Aggression significantly increased with body size differences between fighting pairs and was asymmetric: larger aggressors were superior over smaller species. Additional aggression tests involved dummies with surface extracts, and results suggest that species- and colony-specific surface profiles are important in triggering the aggressive behaviour. 4. Sixteen stingless bee species were observed foraging on 41 species of flowering plants. The resulting bee,flower interaction network showed a high degree of generalisation (network-level specialisation H2' = 0.11), corresponding to a random, opportunistic distribution of bee species among available flower species. 5. Aggressions on flowers were rare and only occurred at a low level. The dominance hierarchy obtained in the arena experiments did not correlate significantly with plant quality, estimated as the number of flowers per plant or as total bee visitation rate. 6. Our findings suggest that asymmetries in interference competition do not necessarily translate into actual resource partitioning in the context of complex interacting communities. [source] Secondary structure of lipidated Ras bound to a lipid bilayerFEBS JOURNAL, Issue 23 2008Jörn Güldenhaupt Ras proteins are small guanine nucleotide binding proteins that regulate many cellular processes, including growth control. They undergo distinct post-translational lipid modifications that are required for appropriate targeting to membranes. This, in turn, is critical for Ras biological function. However, most in vitro studies have been conducted on nonlipidated truncated forms of Ras proteins. Here, for the first time, attenuated total reflectance-FTIR studies of lipid-modified membrane-bound N-Ras are performed, and compared with nonlipidated truncated Ras in solution. For these studies, lipidated N-Ras was prepared by linking a farnesylated and hexadecylated N-Ras lipopeptide to a truncated N-Ras protein (residues 1,181). It was then bound to a 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine bilayer tethered on an attenuated total reflectance crystal. The structurally sensitive amide I absorbance band in the IR was detected and analysed to determine the secondary structure of the protein. The NMR three-dimensional structure of truncated Ras was used to calibrate the contributions of the different secondary structural elements to the amide I absorbance band of truncated Ras. Using this novel approach, the correct decomposition was selected from several possible solutions. The same parameter set was then used for the membrane-bound lipidated Ras, and provided a reliable decomposition for the membrane-bound form in comparison with truncated Ras. This comparison indicates that the secondary structure of membrane-bound Ras is similar to that determined for the nonlipidated truncated Ras protein for the highly conserved G-domain. This result validates the multitude of investigations of truncated Ras without anchor in vitro. The novel attenuated total reflectance approach opens the way for detailed studies of the interaction network of the membrane-bound Ras protein. [source] Some highlights of research on aging with invertebrates, 2009AGING CELL, Issue 5 2009Linda Partridge Summary This annual review focuses on invertebrate model organisms, which shed light on new mechanisms in aging and provide excellent systems for both genome-wide and in-depth analysis. This year, protein interaction networks have been used in a new bioinformatic approach to identify novel genes that extend replicative lifespan in yeast. In an extended approach, using a new, human protein interaction network, information from the invertebrates was used to identify new, candidate genes for lifespan extension and their orthologues were validated in the nematode Caenorhabditis elegans. Chemosensation of diffusible substances from bacteria has been shown to limit lifespan in C. elegans, while a systematic study of the different methods used to implement dietary restriction in the worm has shown that they involve mechanisms that are partially distinct and partially overlapping, providing important clarification for addressing whether or not they are conserved in other organisms. A new theoretical model for the evolution of rejuvenating cell division has shown that asymmetrical division for either cell size or for damaged cell constituents results in increased fitness for most realistic levels of cellular protein damage. Work on aging-related disease has both refined our understanding of the mechanisms underlying one route to the development of Parkinson's disease and has revealed that in worms, as in mice, dietary restriction is protective against cellular proteotoxicity. Two systematic studies genetically manipulating the superoxide dismutases of C. elegans support the idea that damage from superoxide plays little or no role in aging in this organism, and have prompted discussion of other kinds of damage and other kinds of mechanisms for producing aging-related decline in function. [source] Chemical synthesis and biotinylation of the thrombospondin domain TSR2PROTEIN SCIENCE, Issue 5 2009Theresa K. Tiefenbrunn Abstract The type 1 repeat domain from thrombospondin has potent antiangiogenic activity and a structurally interesting fold, making it an attractive target for protein engineering. Chemical synthesis is an attractive approach for studying protein domains because it enables the use of unnatural amino acids for site-specific labeling and detailed structure-function analysis. Here, we demonstrate the first total chemical synthesis of the thrombospondin type 1 repeat domain by native chemical ligation. In addition to the natural domain, five sites for side chain modification were evaluated and two were found to be compatible with oxidative folding. Several challenges were encountered during peptide synthesis due to the functional complexity of the domain. These challenges were overcome by the use of new solid supports, scavengers, and the testing of multiple ligation sites. We also describe an unusual sequence-specific protecting group migration observed during cleavage resulting in +90 Da and +194 Da adducts. Synthetic access to this domain enables the synthesis of a number of variants that can be used to further our understanding of the biochemical interaction network of thrombospondin and provide insight into the structure and function of this important antitumorogenic protein domain. [source] A domain level interaction network of amyloid precursor protein and A, of Alzheimer's diseasePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 12 2010Victoria M. Perreau Abstract The primary constituent of the amyloid plaque, ,-amyloid (A,), is thought to be the causal "toxic moiety" of Alzheimer's disease. However, despite much work focused on both A, and its parent protein, amyloid precursor protein (APP), the functional roles of APP and its cleavage products remain to be fully elucidated. Protein,protein interaction networks can provide insight into protein function, however, high-throughput data often report false positives and are in frequent disagreement with low-throughput experiments. Moreover, the complexity of the CNS is likely to be under represented in such databases. Therefore, we curated the published work characterizing both APP and A, to create a protein interaction network of APP and its proteolytic cleavage products, with annotation, where possible, to the level of APP binding domain and isoform. This is the first time that an interactome has been refined to domain level, essential for the interpretation of APP due to the presence of multiple isoforms and processed fragments. Gene ontology and network analysis were used to identify potentially novel functional relationships among interacting proteins. [source] The impact of miR-34a on protein output in hepatocellular carcinoma HepG2 cellsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2010Jun Cheng Abstract MicroRNAs are small non-coding RNA molecules that play essential roles in biological processes ranging from cell cycle to cell migration and invasion. Accumulating evidence suggests that miR-34a, as a key mediator of p53 tumor suppression, is aberrantly expressed in human cancers. In the present study, we aimed to explore the precise biological role of miR-34a and the global protein changes in HCC cell line HepG2 cells transiently transfected with miR-34a. Transfection of miR-34a into HepG2 cells caused suppression of cell proliferation, inhibition of cell migration and invasion. It also induced an accumulation of HepG2 cells in G1 phase. Among 116 protein spots with differential expression separated by 2-DE method, 34 proteins were successfully identified by MALDI-TOF/TOF analysis. Of these, 15 downregulated proteins may be downstream targets of miR-34a. Bioinformatics analysis produced a protein,protein interaction network, which revealed that the p53 signaling pathway and cell cycle pathway were two major hubs containing most of the proteins regulated by miR-34a. Cytoskeletal proteins such as LMNA, GFAP, MACF1, ALDH2, and LOC100129335 are potential targets of miR-34a. In conclusion, abrogation of miR-34a function could cause downstream molecules to switch on or off, leading to HCC development. [source] The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3-D cellPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2009Yose Y. Widjaja Abstract Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40,000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net. [source] Quantitative assessment of the structural bias in protein,protein interaction assaysPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2008Åsa K. Björklund Abstract With recent publications of several large-scale protein,protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of experimental biases on some of the protein properties suggested to be enriched in highly connected proteins. Finally, we use support vector machines (SVM) to assess the contribution of these properties to protein interactivity. We find that protein abundance is the most important factor for detecting interactions in tandem affinity purifications (TAP), while it is of less importance for Yeast Two Hybrid (Y2H) screens. Consequently, sequence conservation and/or essentiality of hubs may be related to their high abundance. Further, proteins with disordered structure are over-represented in Y2H screens and in one, but not the other, large-scale TAP assay. Hence, disordered regions may be important both in transient interactions and interactions in complexes. Finally, a few domain families seem to be responsible for a large part of all interactions. Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset. [source] Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approachPROTEOMICS - CLINICAL APPLICATIONS, Issue 9 2008Gabriela Bomfim Ferreira Abstract Dendritic cells (DCs) are unique antigen presenting cells, which upon maturation change from a specialized antigen-capturing cell towards a professional antigen presenting cells. In this study, a 2-D DIGE analysis of immature and mature DCs was performed, to identify proteins changing in expression upon maturation. The protein expression profile of immature and mature DCs, derived from CD14+ peripheral blood monocytes was investigated using two pH ranges (pH,4,7 and 6,9) (n,=,4). Ninety one differentially expressed spots (p<0.01) were detected, from which we identified 74 spots (81.32%) corresponding to 41 different proteins. The proteins identified play a role in diverse processes, such as antigen processing/presentation, vesicle transport and cytoskeleton remodeling. In addition, a protein interaction network contained 29 (out of 41) proteins, suggesting that, although they functionally originate from distinct classes, these proteins are acting as a protein-interactome. In conclusion, the proteins shown here to be altered in expression upon maturation are in line with the morphological and functional changes observed during the maturation process, providing a better understanding of the processes involved. This will open new avenues for investigating treatment regimens for immune-associated disorders. [source] Proteomics cataloging analysis of human expressed prostatic secretions reveals rich source of biomarker candidatesPROTEOMICS - CLINICAL APPLICATIONS, Issue 4 2008Runsheng Li Abstract Expressed prostatic secretions (EPS) contain proteins of prostate origin that may reflect the health status of the prostate and be used as diagnostic markers for prostate diseases including prostatitis, benign prostatic hyperplasia, and prostate cancer. Despite their importance and potential applications, a complete catalog of EPS proteins is not yet available. We, therefore, undertook a comprehensive analysis of the EPS proteome using 2-D micro-LC combined with MS/MS. Using stringent filtering criteria, we identified a list of 114 proteins with at least two unique-peptide hits and an additional 75 proteins with only a single unique-peptide hit. The proteins identified include kallikrein 2 (KLK2), KLK3 (prostate-specific antigen), KLK11, and nine cluster of differentiation (CD) molecules including CD10, CD13, CD14, CD26, CD66a, CD66c, CD 143, CD177, and CD224. To our knowledge, this list represents the first comprehensive characterization of the EPS proteome, and it provides a candidate biomarker list for targeted quantitative proteomics analysis using a multiple reaction monitoring (MRM) approach. To help prioritize candidate biomarkers, we constructed a protein,protein interaction network of the EPS proteins using Cytoscape (www.cytoscape.org), and overlaid the expression level changes from the Oncomine database onto the network. [source] Network modules help the identification of key transport routes, signaling pathways in cellular and other networksANNALEN DER PHYSIK, Issue 12 2009R. Palotai Abstract Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks , for example the specialized signaling cascades of cellular networks filter noise and efficiently adapt the network structure to new stimuli. However, our general understanding of transport mechanisms and signaling pathways in complex systems is yet limited. Here we summarize the key network structures involved in transport, list the solutions available to overloaded systems for relaxing their load and outline a possible method for the computational determination of signaling pathways. We highlight that in addition to hubs, bridges and the network skeleton, the overlapping modular structure is also essential in network transport. Path-lenghts in the module-space of the yeast protein-protein interaction network indicated that module-based paths may cross fewer modular boundaries than shortest paths. Moreover, by locating network elements in the space of overlapping network modules and evaluating their distance in this ,module space', it may be possible to approximate signaling pathways computationally, which, in turn could serve the identification of signaling pathways of complex systems. Our model may be applicable in a wide range of fields including traffic control or drug design. [source] Granulin-epithelin precursor binds directly to ADAMTS-7 and ADAMTS-12 and inhibits their degradation of cartilage oligomeric matrix proteinARTHRITIS & RHEUMATISM, Issue 7 2010Fengjin Guo Objective To determine 1) whether a protein interaction network exists between granulin-epithelin precursor (GEP), ADAMTS-7/ADAMTS-12, and cartilage oligomeric matrix protein (COMP); 2) whether GEP interferes with the interactions between ADAMTS-7/ADAMTS-12 metalloproteinases and COMP substrate, including the cleavage of COMP; 3) whether GEP affects tumor necrosis factor , (TNF,),mediated induction of ADAMTS-7/ADAMTS-12 expression and COMP degradation; and 4) whether GEP levels are altered during the progression of arthritis. Methods Yeast two-hybrid, in vitro glutathione S-transferase pull-down, and coimmunoprecipitation assays were used to 1) examine the interactions between GEP, ADAMTS-7/ADAMTS-12, and COMP, and 2) map the binding sites required for the interactions between GEP and ADAMTS-7/ADAMTS-12. Immunofluorescence cell staining was performed to visualize the subcellular localization of GEP and ADAMTS-7/ADAMTS-12. An in vitro digestion assay was employed to determine whether GEP inhibits ADAMTS-7/ADAMTS-12,mediated digestion of COMP. The role of GEP in inhibiting TNF,-induced ADAMTS-7/ADAMTS-12 expression and COMP degradation in cartilage explants was also analyzed. Results GEP bound directly to ADAMTS-7 and ADAMTS-12 in vitro and in chondrocytes, and the 4 C-terminal thrombospondin motifs of ADAMTS-7/ADAMTS-12 and each granulin unit of GEP mediated their interactions. Additionally, GEP colocalized with ADAMTS-7 and ADAMTS-12 on the cell surface of chondrocytes. More importantly, GEP inhibited COMP degradation by ADAMTS-7/ADAMTS-12 in a dose-dependent manner through 1) competitive inhibition through direct protein,protein interactions with ADAMTS-7/ADAMTS-12 and COMP, and 2) inhibition of TNF,-induced ADAMTS-7/ADAMTS-12 expression. Furthermore, GEP levels were significantly elevated in patients with either osteoarthritis or rheumatoid arthritis. Conclusion Our observations demonstrate a novel protein,protein interaction network between GEP, ADAMTS-7/ADAMTS-12, and COMP. Furthermore, GEP is a novel specific inhibitor of ADAMTS-7/ADAMTS-12,mediated COMP degradation and may play a significant role in preventing the destruction of joint cartilage in arthritis. [source] Crystallization and preliminary X-ray crystallographic characterization of a public CMV-specific TCR in complex with its cognate antigenACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Jean-Baptiste Reiser The T-cell response to human cytomegalovirus is characterized by a dramatic reduction of clonal diversity in patients undergoing chronic inflammation or immunodepression. In order to check whether all the selected high-avidity T-cell clones recognize the immunodominant pp65 peptide antigen pp65495,503 (NLVPMVATV) presented by the major histocompatibility complex (MHC) molecule HLA-A2 in a similar manner, several public high-affinity T-cell receptors (TCRs) specific for the pp65495,503,HLA-A2 complex have been investigated. Expression, purification and crystallization were performed and preliminary crystallographic data were collected to 4.7,Å resolution for the RA15 TCR in complex with the pp65495,503,HLA-A2 complex. Comparison of the RA15,pp65495,503,HLA-A2 complex molecular-replacement solution with the structure of another high-affinity pp65495,503,HLA-A2-specific TCR, RA14, shows a shared docking mode, indicating that the clonal focusing could be accompanied by the selection of a most favoured peptide-readout mode. However, the position of the RA15 V, domain is significantly shifted, suggesting a different interatomic interaction network. [source] Nested distributions of bat flies (Diptera: Streblidae) on Neotropical bats: artifact and specificity in host-parasite studiesECOGRAPHY, Issue 3 2009Bruce D. Patterson We examined the structure of ectoparasitic bat fly infestations on 31 well-sampled bat species, representing 4 Neotropical families. Sample sizes varied from 22 to 1057 bats per species, and bat species were infested by 4 to 27 bat fly species. Individual bats supported smaller infracommunities (the set of parasites co-occurring on an individual host), ranging from 1 to 5 fly species in size, and no bat species had more than 6 bat fly species characteristically associated with it (its primary fly species). Nestedness analyses used system temperature (BINMATNEST algorithm) because it is particularly well-suited for analysis of interaction networks, where parasite records may be nested among hosts and host individuals simultaneously nested among parasites. Most species exhibited very low system temperatures (mean 3.14°; range 0.14,12.28°). Simulations showed that nested structure for all 31 species was significantly stronger than simulated values under 2 of the 3 null hypotheses, and about half the species were also nested under the more stringent conditions of the third null hypothesis. Yet this structure disappears when analyses are restricted to "primary" associations of fly species (flies on their customary host species), which exclude records thought to be atypical, transient, or potential contaminants. Despite comprising a small fraction of total parasite records, such anomalies represent a considerable part of the statistical state-space, offering the illusion of significant ecological structure. Only well understood and well documented systems can make distinctions between primary and other occurrence records. Generally, nestedness appears best developed in host-parasite systems where infestations are long-term and accumulate over time. Dynamic, short-term infestations by highly mobile parasites like bat flies may appear to be nested, but such structure is better understood in terms of host specificity and accidental occurrences than in terms of prevalence, persistence, or hierarchical niche relations of the flies. [source] Charting protein complexes, signaling pathways, and networks in the immune systemIMMUNOLOGICAL REVIEWS, Issue 1 2006Angela Bauch Summary:, Systematic deciphering of protein,protein interactions has the potential to generate comprehensive and instructive signaling networks and to fuel new therapeutic and diagnostic strategies. Here, we describe how recent advances in high-throughput proteomic technologies, involving biochemical purification methods and mass spectrometry analysis, can be applied systematically to the characterization of protein complexes and the computation of molecular networks. The networks obtained form the basis for further functional analyses, such as knockdown by RNA interference, ultimately leading to the identification of nodes that represent candidate targets for pharmacological exploitation. No individual experimental approach can accurately elucidate all critical modulatory components and biological aspects of a signaling network. Such functionally annotated protein,protein interaction networks, however, represent an ideal platform for the integration of additional datasets. By providing links between molecules, they also provide links to all previous observations associated with these molecules, be they of genetic, pharmacological, or other origin. As exemplified here by the analysis of the tumor necrosis factor (TNF)-,/nuclear factor-,B (NF-,B) signaling pathway, the approach is applicable to any mammalian cellular signaling pathway in the immune system. [source] Some highlights of research on aging with invertebrates, 2009AGING CELL, Issue 5 2009Linda Partridge Summary This annual review focuses on invertebrate model organisms, which shed light on new mechanisms in aging and provide excellent systems for both genome-wide and in-depth analysis. This year, protein interaction networks have been used in a new bioinformatic approach to identify novel genes that extend replicative lifespan in yeast. In an extended approach, using a new, human protein interaction network, information from the invertebrates was used to identify new, candidate genes for lifespan extension and their orthologues were validated in the nematode Caenorhabditis elegans. Chemosensation of diffusible substances from bacteria has been shown to limit lifespan in C. elegans, while a systematic study of the different methods used to implement dietary restriction in the worm has shown that they involve mechanisms that are partially distinct and partially overlapping, providing important clarification for addressing whether or not they are conserved in other organisms. A new theoretical model for the evolution of rejuvenating cell division has shown that asymmetrical division for either cell size or for damaged cell constituents results in increased fitness for most realistic levels of cellular protein damage. Work on aging-related disease has both refined our understanding of the mechanisms underlying one route to the development of Parkinson's disease and has revealed that in worms, as in mice, dietary restriction is protective against cellular proteotoxicity. Two systematic studies genetically manipulating the superoxide dismutases of C. elegans support the idea that damage from superoxide plays little or no role in aging in this organism, and have prompted discussion of other kinds of damage and other kinds of mechanisms for producing aging-related decline in function. [source] A combinatorial approach to studying protein complex composition by employing size-exclusion chromatography and proteome analysisJOURNAL OF SEPARATION SCIENCE, JSS, Issue 10 2007Shi-Sheng Li Abstract The genome sequences of numerous organisms are available now, but gene sequences alone do not provide sufficient information to accurately deduce protein functions. Protein function is largely dependent on the association of multiple polypeptide chains into large structures with interacting subunits that regulate and support each other. Therefore, the mapping of protein interaction networks in a physiological context is conducive to deciphering protein functions, including those of hypothetical proteins. Although several high-throughput methods to globally identify protein interactions have been reported in recent years, these approaches often have a high rate of nonspecific or artificial interactions detected. For instance, the fraction of false positives of the protein interactions identified by yeast two-hybrid assay has been predicted to be of the order of 50%. We have developed a strategy to globally map Bacillus subtilis protein,protein interactions in a physiological context by fractionating the cell lysates using size-exclusion chromatography (SEC), followed by proteome analysis. Components of both known and unknown protein complexes, multisubunits and multiproteins, have been identified using this strategy. In one case, the partners of the B. subtilis protein complex have been coexpressed in Escherichia coli, and the formation of the overexpressed protein complex has been further confirmed by a pull-down assay. [source] A domain level interaction network of amyloid precursor protein and A, of Alzheimer's diseasePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 12 2010Victoria M. Perreau Abstract The primary constituent of the amyloid plaque, ,-amyloid (A,), is thought to be the causal "toxic moiety" of Alzheimer's disease. However, despite much work focused on both A, and its parent protein, amyloid precursor protein (APP), the functional roles of APP and its cleavage products remain to be fully elucidated. Protein,protein interaction networks can provide insight into protein function, however, high-throughput data often report false positives and are in frequent disagreement with low-throughput experiments. Moreover, the complexity of the CNS is likely to be under represented in such databases. Therefore, we curated the published work characterizing both APP and A, to create a protein interaction network of APP and its proteolytic cleavage products, with annotation, where possible, to the level of APP binding domain and isoform. This is the first time that an interactome has been refined to domain level, essential for the interpretation of APP due to the presence of multiple isoforms and processed fragments. Gene ontology and network analysis were used to identify potentially novel functional relationships among interacting proteins. [source] Experimental and computational tools useful for (re)construction of dynamic kinase,substrate networksPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2009Chris Soon Heng Tan Abstract The explosion of site- and context-specific in vivo phosphorylation events presents a potentially rich source of biological knowledge and calls for novel data analysis and modeling paradigms. Perhaps the most immediate challenge is delineating detected phosphorylation sites to their effector kinases. This is important for (re)constructing transient kinase,substrate interaction networks that are essential for mechanistic understanding of cellular behaviors and therapeutic intervention, but has largely eluded high-throughput protein-interaction studies due to their transient nature and strong dependencies on cellular context. Here, we surveyed some of the computational approaches developed to dissect phosphorylation data detected in systematic proteomic experiments and reviewed some experimental and computational approaches used to map phosphorylation sites to their effector kinases in efforts aimed at reconstructing biological signaling networks. [source] The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3-D cellPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2009Yose Y. Widjaja Abstract Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40,000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net. [source] Interaction networks: Lessons from large-scale studies in yeastPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 20 2009Gerard Cagney Abstract Saccharomyces cerevisiae is the simplest eukaryotic model organism and has made countless contributions to cell biology. The ease with which it can be genetically manipulated has made it a favourite organism among technologists for developing methods for large-scale analysis based on reverse genetics. Consequently, more genomewide datasets describing aspects of gene and protein biology are available for yeast than for any other organism. This has led to the pioneering of many computational analysis techniques using yeast data. Here, we make a brief survey of yeast physical and genetic interaction networks, highlighting major experimental and computational achievements first described in this organism. [source] Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustnessPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 2 2006Dong Li Abstract High-throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale-free and high-degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small-world property with similar diameter at 4,5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of "systems biology". [source] Making the right connections: biological networks in the light of evolutionBIOESSAYS, Issue 10 2009Christopher G. Knight Abstract Our understanding of how evolution acts on biological networks remains patchy, as is our knowledge of how that action is best identified, modelled and understood. Starting with network structure and the evolution of protein,protein interaction networks, we briefly survey the ways in which network evolution is being addressed in the fields of systems biology, development and ecology. The approaches highlighted demonstrate a movement away from a focus on network topology towards a more integrated view, placing biological properties centre-stage. We argue that there remains great potential in a closer synergy between evolutionary biology and biological network analysis, although that may require the development of novel approaches and even different analogies for biological networks themselves. [source] Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures,BIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009Bhaskar Dutta Abstract The research that aims at furthering our understanding of plant primary metabolism has intensified during the last decade. The presented study validated a systems biology methodological framework for the analysis of stress-induced molecular interaction networks in the context of plant primary metabolism, as these are expressed during the first hours of the stress treatment. The framework involves the application of time-series integrated full-genome transcriptomic and polar metabolomic analyses on plant liquid cultures. The latter were selected as the model system for this type of analysis, because they provide a well-controlled growth environment, ensuring that the observed plant response is due only to the applied perturbation. An enhanced gas chromatography,mass spectrometry (GC,MS) metabolomic data correction strategy and a new algorithm for the significance analysis of time-series "omic" data are used to extract information about the plant's transcriptional and metabolic response to the applied stress from the acquired datasets; in this article, it is the first time that these are applied for the analysis of a large biological dataset from a complex eukaryotic system. The case-study involved Arabidopsis thaliana liquid cultures subjected for 30 h to elevated (1%) CO2 stress. The advantages and validity of the methodological framework are discussed in the context of the known A. thaliana or plant, in general, physiology under the particular stress. Of note, the ability of the methodology to capture dynamic aspects of the observed molecular response allowed for 9 and 24 h of treatment to be indicated as corresponding to shifts in both the transcriptional and metabolic activity; analysis of the pathways through which these activity changes are manifested provides insight to regulatory processes. Biotechnol. Bioeng. 2009;102: 264,279. © 2008 Wiley Periodicals, Inc. [source] Conserved features of type III secretionCELLULAR MICROBIOLOGY, Issue 9 2004A. P. Tampakaki Summary Type III secretion systems (TTSSs) are essential mediators of the interaction of many Gram-negative bacteria with human, animal or plant hosts. Extensive sequence and functional similarities exist between components of TTSS from bacteria as diverse as animal and plant pathogens. Recent crystal structure determinations of TTSS proteins reveal extensive structural homologies and novel structural motifs and provide a basis on which protein interaction networks start to be drawn within the TTSSs, that are consistent with and help rationalize genetic and biochemical data. Such studies, along with electron microscopy, also established common architectural design and function among the TTSSs of plant and mammalian pathogens, as well as between the TTSS injectisome and the flagellum. Recent comparative genomic analysis, bioinformatic genome mining and genome-wide functional screening have revealed an unsuspected number of newly discovered effectors, especially in plant pathogens and uncovered a wider distribution of TTSS in pathogenic, symbiotic and commensal bacteria. Functional proteomics and analysis further reveals common themes in TTSS effector functions across phylogenetic host and pathogen boundaries. Based on advances in TTSS biology, new diagnostics, crop protection and drug development applications, as well as new cell biology research tools are beginning to emerge. [source] Functional dissection of an intrinsically disordered protein: Understanding the roles of different domains of Knr4 protein in protein,protein interactionsPROTEIN SCIENCE, Issue 7 2010Adilia Dagkessamanskaia Abstract Knr4, recently characterized as an intrinsically disordered Saccharomyces cerevisiae protein, participates in cell wall formation and cell cycle regulation. It is constituted of a functional central globular core flanked by a poorly structured N-terminal and large natively unfolded C-terminal domains. Up to now, about 30 different proteins have been reported to physically interact with Knr4. Here, we used an in vivo two-hybrid system approach and an in vitro surface plasmon resonance (BIAcore) technique to compare the interaction level of different Knr4 deletion variants with given protein partners. We demonstrate the indispensability of the N-terminal domain of Knr4 for the interactions. On the other hand, presence of the unstructured C-terminal domain has a negative effect on the interaction strength. In protein interactions networks, the most highly connected proteins or "hubs" are significantly enriched in unstructured regions, and among them the transient hub proteins contain the largest and most highly flexible regions. The results presented here of our analysis of Knr4 protein suggest that these large disordered regions are not always involved in promoting the protein,protein interactions of hub proteins, but in some cases, might rather inhibit them. We propose that this type of regions could prevent unspecific protein interactions, or ensure the correct timing of occurrence of transient interactions, which may be of crucial importance for different signaling and regulation processes. [source] | ||||||||||||||||