Fine mapping of protein interaction surfaces with a PCR-based mutagenesis screen in yeast.
Explore the source record for details and available documents.
Animals↗
SEARCH · PubMed Health
Results for “Protein Interaction Mapping”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Mapping protein-protein interactions in solution by NMR spectroscopy.
NMR is very well suited to the study of especially weak protein-protein interactions, as no crystallization is required. The available NMR methods to this end are reviewed and illustrated with applications from the recent biochemical literature: intermolecular NOEs, cross-saturation, chemical shift perturbation, dynamics and exchange perturbation, paramagnetic methods, and dipolar orientation. Most of these methods are now routinely applied for complexes with total molecular mass of 60 kDa and can likely be applied to systems up to 1000 kDa. A substantial fraction of complexes studied show distinct effects of induced fit affecting structural and dynamical properties beyond the contact interface.
Binding Sites↗
CGI-55 interacts with nuclear proteins and co-localizes to p80-coilin positive-coiled bodies in the nucleus.
The human protein CGI-55 has been described as a chromo-helicase-DNA-binding domain protein (CHD)-3 interacting protein and was also found to interact with the 3'-region of the plasminogen activator inhibitor (PAI)-1 mRNA. Here, we used CGI-55 as a "bait" in a yeast two-hybrid screen and identified eight interacting proteins: Daxx, Topoisomerase I binding RS (Topors), HPC2, UBA2, TDG, and protein inhibitor of activated STAT (signal transducer and activator of transcription) (PIAS)-1, -3, and -y. These proteins are either structurally or functionally associated with promyelocytic leukemia nuclear bodies (PML-NBs), protein sumoylation, or the regulation of transcription. The interactions of CGI-55 with Daxx, Topors, PIASy, and UBA2 were confirmed by in vivo colocalization experiments in HeLa cells, by using green (GFP) and red fluorescence fusion proteins. A mapping study of the CGI-55 binding site for these proteins revealed three distinct patterns of interaction. The fact that CGI-55-GFP has been localized in cytoplasm and nucleus in a dotted manner, and its interaction with proteins associated with PML-NBs, suggested that CGI-55 might be associated with nuclear bodies. Although Daxx and Topors co-localized with promyelocytic leukemia protein (PML), CGI-55 itself as well as PIASy and UBA2 showed only little co-localization with PML. However, we observed that CGI-55 localizes to the nucleolus and co-localizes with p80-coilin positive nuclear-coiled bodies.
Cell Nucleolus↗
Role of the cytoskeleton in signaling networks.
Intracellular signal transduction occurs through cascades of reactions involving dozens of proteins that transmit signals from the cell surface, through a crowded cellular environment filled with organelles and a filamentous cytoskeleton, to specific targets. Numerous signaling molecules are immobilized or transiently bound to the cytoskeleton, yet most models for signaling pathways have no specific role for this mesh, which is often presumed to function primarily as a scaffold that determines cell mechanics but not information flow. We combined analytical tools with several recently established large-scale protein-protein interaction maps for Saccharomyces cerevisiae to quantitatively address the role of the cytoskeleton in intracellular signaling. The results demonstrate that the network of signaling proteins is intimately linked to the cytoskeleton, suggesting that this interconnected filamentous structure plays a crucial and distinct functional role in signal transduction.
Cytoskeleton↗
Learning protein secondary structure from sequential and relational data.
We propose a method for sequential supervised learning that exploits explicit knowledge of short- and long-range dependencies. The architecture consists of a recursive and bi-directional neural network that takes as input a sequence along with an associated interaction graph. The interaction graph models (partial) knowledge about long-range dependency relations. We tested the method on the prediction of protein secondary structure, a task in which relations due to beta-strand pairings and other spatial proximities are known to have a significant effect on the prediction accuracy. In this particular task, interactions can be derived from knowledge of protein contact maps at the residue level. Our results show that prediction accuracy can be significantly boosted by the integration of interaction graphs.
Animals↗
Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability.
The four-member SPA protein family of Arabidopsis acts in concert with the E3 ubiquitin ligase COP1 to suppress photomorphogenesis in dark-grown seedlings. Here, we demonstrate that SPA proteins are, moreover, essential for photoperiodic flowering. Mutations in SPA1 cause phyA-independent early flowering under short day (SD) but not long day (LD) conditions, and this phenotype is enhanced by additional loss of SPA3 and SPA4 function. These spa1 spa3 spa4 triple mutants flower at the same time in LD and SD, indicating that the SPA gene family is essential for the inhibition of flowering under non-inductive SD. Among the four SPA genes, SPA1 is necessary and sufficient for normal photoperiodic flowering. Early flowering of SD-grown spa mutant correlates with strongly increased FT transcript levels, whereas CO transcript levels are not altered. Epistasis analysis demonstrates that both early flowering and FT induction in spa1 mutants is fully dependent on CO. Consistent with this finding, SPA proteins interact physically with CO in vitro and in vivo, suggesting that SPA proteins regulate CO protein function. Domain mapping shows that the SPA1-CO interaction requires the CCT-domain of CO, but is independent of the B-box type Zn fingers of CO. We further show that spa1 spa3 spa4 mutants exhibit strongly increased CO protein levels, which are not caused by a change in CO gene expression. Taken together, our results suggest, that SPA proteins regulate photoperiodic flowering by controlling the stability of the floral inducer CO.
Arabidopsis↗
Systems biology of bacterial chemotaxis.
Motile bacteria regulate chemotaxis through a highly conserved chemosensory signal-transduction system. System-wide analyses and mathematical modeling are facilitated by extensive experimental observations regarding bacterial chemotaxis proteins, including biochemical parameters, protein structures and protein-protein interaction maps. Thousands of signaling and regulatory chemotaxis proteins within a bacteria cell form a highly interconnected network through distinct protein-protein interactions. A bacterial cell is able to respond to multiple stimuli through a collection of chemoreceptors with different sensory modalities, which interact to affect the cooperativity and sensitivity of the chemotaxis response. The robustness or insensitivity of the chemotaxis system to perturbations in biochemical parameters is a product of the system's hierarchical network architecture.
Adaptation, Physiological↗
Automated modelling of signal transduction networks.
BACKGROUND: Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molecular description of the networks involved. RESULTS: We have developed a computational approach for generating static models of signal transduction networks which utilizes protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays. Networks are determined entirely by integrating protein-protein interaction data with microarray expression data, without prior knowledge of any pathway intermediates. In effect, this is equivalent to extracting subnetworks of the protein interaction dataset whose members have the most correlated expression profiles. CONCLUSION: We show that our technique accurately reconstructs MAP Kinase signaling networks in Saccharomyces cerevisiae. This approach should enhance our ability to model signaling networks and to discover new components of known networks. More generally, it provides a method for synthesizing molecular data, either individual transcript abundance measurements or pairwise protein interactions, into higher level structures, such as pathways and networks.
Computational Biology↗
Mapping tertiary interactions in protein folding reactions: a novel mass spectrometry- and chemical synthesis-based approach.
A novel mass spectrometry- and chemical synthesis-based approach for studying protein folding reactions is described, and its initial application to study the folding/unfolding reaction of a homo-hexameric enzyme 4-oxalocrotonate (4OT) is reported. This new approach involves the application of total chemical synthesis to prepare protein analogues that contain a photoreactive amino acid site-specifically incorporated into their primary amino acid sequence. To this end, a photoreactive amino acid-containing analogue of 4OT in which Pro-1 was replaced with p-benzoyl-l-phenylalanine (Bpa) was prepared. This analogue can be used to map structurally specific protein-protein interactions in 4OT's native folded state. These photocrosslinking studies and peptide mapping results with (PlBpa)4OT indicate that this construct is potentially useful for probing the structural properties of equilibrium and kinetic intermediates in 4OT's folding reaction.
Chromatography, Gel↗
[Screening and identification of proteins interacting with p38 MAP kinase via T7 phage-display screening system].
OBJECTIVE: To screen and identify proteins that interact with p38 mitogen-activated protein (MAP) kinases by means of T7 phage-display screening system. METHOD: His-tagged fusion protein of p38 MAP kinase was used to coat a 96-well ELISA plate and Ni-NTA resin, which served as the media for screening human lung and liver T7 phage cDNA libraries. RESULTS: After 4 rounds of biopanning, 86 independent plaques were selected and processed by EDTA. The inserted gene fragments from these plaques were amplified by PCR, the products purified by a gel recovery method. The sequences of the insertions were identified and analyzed with BLAST program in GenBank. Forty-six clones were found to encode proteins. CONCLUSION: T7 phage-display screening system is convenient, rapid and effective for screening the P38 MAP kinase-binding proteins.
Bacteriophage T7↗
Isolation of ATMEKK1 (a MAP kinase kinase kinase)-interacting proteins and analysis of a MAP kinase cascade in Arabidopsis.
In plants, a number of MAP kinase (MAPK), MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK) homologues have been reported. However, there have been no reports of protein-protein interactions between these kinases or molecular analysis of MAPK cascades in higher plants. To analyze a possible MAPK cascade in Arabidopsis thaliana, we took two molecular approaches. One is the two-hybrid screening of ATMEKK1 (a MAPKKK)-interacting proteins; the other is an analysis of physical and functional interactions among isolated MAPK, MAPKK, and MAPKKK homologues from Arabidopsis. In two-hybrid screening using ATMEKK1 as bait, we isolated a novel MAPKK homologue, ATMKK2, a MAPK homologue, ATMPK4, and an unknown protein. ATMKK2 has high sequence similarity with MEK1 (a MAPKK) in Arabidopsis. Based on yeast two-hybrid analysis, we detected protein-protein interactions between ATMEKK1 and ATMKK2/MEK1 (MAPKKs), between ATMKK2/MEK1 and ATMPK4 (a MAPK), and between ATMPK4 and ATMEKK1. ATMPK4 and ATMKK2/MEK1 interacted with two distinct regions of ATMEKK1, the N-terminal regulatory domain and the C-terminal kinase domain, respectively. Coexpression of ATMEKK1 increased the ability of two closely related MAPKKs, ATMKK2 and MEK1, to complement a growth defect of the yeast pbs2 mutant. Coexpression of ATMPK4 and MEK1 complemented a growth defect of the yeast mpk1 and bck1 mutants. By contrast, other combinations of MAPKs and MAPKKs did not suppress these yeast mutations. These results suggest that ATMEKK1, ATMKK2/MEK1, and ATMPK4 may constitute a MAP kinase cascade.
Alanine↗
Multiple interactions among proteins encoded by the mite-transmitted wheat streak mosaic tritimovirus.
The genome organization of the mite-transmitted wheat streak mosaic virus (WSMV) appears to parallel that of members of the Potyviridae with monopartite genomes, but there are substantial amino acid dissimilarities with other potyviral polyproteins. To initiate studies on the functions of WSMV-encoded proteins, a protein interaction map was generated using a yeast two-hybrid system. Because the pathway of proteolytic maturation of the WSMV polyprotein has not been experimentally determined, random libraries of WSMV cDNA were made both in DNA-binding domain and activation domain plasmid vectors and introduced into yeast. Sequence analysis of multiple interacting pairs revealed that interactions largely occurred between domains within two groups of proteins. The first involved interactions among nuclear inclusion protein a, nuclear inclusion protein b, and coat protein (CP), and the second involved helper component-proteinase (HC-Pro) and cylindrical inclusion protein (CI). Further immunoblot and deletion mapping analyses of the interactions suggest that subdomains of CI, HC-Pro, and P1 interact with one another. The two-hybrid assay was then performed using full-length genes of CI, HC-Pro, P1, P3, and CP, but no heterologous interactions were detected. In vitro binding assay using glutathione-S-transferase fusion proteins and in vitro translation products, however, revealed mutual interactions among CI, HC-Pro, P1, and P3. The failure to detect interactions between full-length proteins by the two-hybrid assay might be due to adverse effects of expression of viral proteins in yeast cells. The capacity to participate in multiple homomeric and heteromeric molecular interactions is consistent with the pleiotropic nature of many potyviral gene mutants and suggests mechanisms for regulation of various viral processes via a network of viral protein complexes.
Animals↗
Direct interaction of C/EBPdelta and Sp1 at the GC-enriched promoter region synergizes the IL-10 gene transcription in mouse macrophage.
We previously reported that LPS activates the transcription of the IL-10 gene through the Sp1 and C/EBP binding sites and indicated that Sp1, C/EBPbeta and C/EBPdelta can coactivate the IL-10 gene expression in mouse macrophage cells [Liu Y.-W., Tseng H.-P., Chen L.-C., Chen B.-K., Chang W.-C. J. Immunol. 171: 821-828, 2003]. In the present report, we demonstrated the direct physical interaction between C/EBPdelta and Sp1, and also mapped the interaction domains of these two proteins. C/EBPdelta binds to Sp1 via its basic region leucine zipper domain. The C-terminus of Sp1 was also the major region interacting with C/EBPdelta. However, both glutamine- and serine/threonine-rich homologus regions of Sp1 also interacted with C/EBPdelta. The binding of Sp1 and C/EBPdelta as a complex to the Sp1 binding site on the promoter of IL-10 was further confirmed by using the DNA affinity precipitation assay. By using Sp1-deficient SL2 cells, we also found that the overexpressions of C/EBPdelta and Sp1 synergically activate the transcriptional activity of IL-10 gene. Taken together, our present results revealed a novel mechanism of a superactivation of Sp1 by C/EBPdelta via a direct interaction between these two transcription factors leading to the activation of the IL-10 gene in mouse macrophage cells.
Animals↗
Proteomics strategies for protein identification.
The information from genome sequencing provides new approaches for systems-wide understanding of protein networks and cellular function. DNA microarray technologies have advanced to the point where nearly complete monitoring of gene expression is feasible in several organisms. An equally important goal is to comprehensive survey cellular proteomes and profile protein changes under different cellular states. This presents a complex analytical problem, due to the chemical variability between proteins and peptides. Here, we discuss strategies to improve accuracy and sensitivity of peptide identification, distinguish represented protein isoforms, and quantify relative changes in protein abundance.
Computational Biology↗
The ATCG of drug discovery.
The publication of human and microbial genomic sequences has resulted in the availability of large amounts of data that are directly relevant to the discovery of novel and useful drug targets. The elucidation of the function of new genes is not a simple matter and human genetic studies have been among the most useful in identifying genes implicated in disease, although homologs, or orthologs, of human genes in mouse, worm, fly and yeast genomes have also been useful in deciphering gene function. The advent of genomics has led into the study of protein structure and function under the rubric of proteomics. Proteins function in a cell mostly by interacting with other proteins, and protein interaction maps of cellular circuits are now available. Screening strategies to address protein-protein interactions are being developed, and many drug targets in the future are expected to be directed towards these interactions. In addition to using genetic and analytical approaches for finding new drug targets, chemical libraries can be used to inhibit the activity of new proteins, and thus reveal function. The combination of high-throughput screening with testing compounds for ADME (absorption, distribution, metabolism and excretion) and toxicity will help in the early clarification of clinical utility of both new drug targets, as well as drug candidates.
Animals↗
Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations.
A map of protein-protein interactions provides valuable insight into the cellular function and machinery of a proteome. By measuring the similarity between two Gene Ontology (GO) terms with a relative specificity semantic relation, here, we proposed a new method of reconstructing a yeast protein-protein interaction map that is solely based on the GO annotations. The method was validated using high-quality interaction datasets for its effectiveness. Based on a Z-score analysis, a positive dataset and a negative dataset for protein-protein interactions were derived. Moreover, a gold standard positive (GSP) dataset with the highest level of confidence that covered 78% of the high-quality interaction dataset and a gold standard negative (GSN) dataset with the lowest level of confidence were derived. In addition, we assessed four high-throughput experimental interaction datasets using the positives and the negatives as well as GSPs and GSNs. Our predicted network reconstructed from GSPs consists of 40,753 interactions among 2259 proteins, and forms 16 connected components. We mapped all of the MIPS complexes except for homodimers onto the predicted network. As a result, approximately 35% of complexes were identified interconnected. For seven complexes, we also identified some nonmember proteins that may be functionally related to the complexes concerned. This analysis is expected to provide a new approach for predicting the protein-protein interaction maps from other completely sequenced genomes with high-quality GO-based annotations.
Databases, Genetic↗
A type IV-secretion-like system is required for conjugative DNA transport of broad-host-range plasmid pIP501 in gram-positive bacteria.
Plasmid pIP501 has a very broad host range for conjugative transfer among a wide variety of gram-positive bacteria and gram-negative Escherichia coli. Functionality of the pIP501 transfer (tra) genes in E. coli was proven by pIP501 retrotransfer to Enterococcus faecalis (B. Kurenbach, C. Bohn, J. Prabhu, M. Abudukerim, U. Szewzyk, and E. Grohmann, Plasmid 50:86-93, 2003). The 15 pIP501 tra genes are organized in a single operon (B. Kurenbach, J. Kopeć, M. Mägdefrau, K. Andreas, W. Keller, C. Bohn, M. Y. Abajy, and E. Grohmann, Microbiology 152:637-645, 2006). The pIP501 tra operon is negatively autoregulated at the transcriptional level by the conjugative DNA relaxase TraA. Three of the 15 pIP501-encoded Tra proteins show significant sequence similarity to the Agrobacterium type IV secretion system proteins VirB1, VirB4, and VirD4. Here we report a comprehensive protein-protein interaction map of all of the pIP501-encoded Tra proteins determined by the yeast two-hybrid assay. Most of the interactions were verified in vitro by isolation of the protein complexes with pull-down assays. In conjunction with known or postulated functions of the pIP501-encoded Tra proteins and computer-assisted prediction of their cellular location, we propose a model for the first type IV-secretion-like system encoded by a conjugative plasmid from gram-positive bacteria.
Bacterial Proteins↗
Pathway studio--the analysis and navigation of molecular networks.
SUMMARY: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules. AVAILABILITY: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/.
Database Management Systems↗