scholarly journals Prediction of Protein Interactions by the Domain and Sub-cellular Localization Information

2005 ◽  
pp. 1024-1027
Author(s):  
Jinsun Hong ◽  
Kyungsook Han
Keyword(s):  
Protein Interactions ◽  
Cellular Localization ◽  
Localization Information

scholarly journals Integrating Protein Localization with Automated Signaling Pathway Reconstruction

2019 ◽  
Author(s):  
Ibrahim Youssef ◽  
Jeffrey Law ◽  
Anna Ritz
Keyword(s):  
Signal Transduction ◽  
Signaling Pathways ◽  
Protein Interactions ◽  
Cellular Localization ◽  
Protein Localization ◽  
Dynamic Program ◽  
Reconstruction Algorithms ◽  
Ppi Networks ◽  
Cellular Compartments ◽  
Localization Information

AbstractUnderstanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists generate testable hypotheses about signaling. However, automatic reconstruction of signaling pathways suffers from many interactions with the same confidence score leading to many equally good candidates. Further, some reconstructions are biologically misleading due to ignoring protein localization information. We proposeLocPL, a method to improve the automatic reconstruction of signaling pathways from PPIs by incorporating information about protein localization in the reconstructions. The method relies on a dynamic program to ensure that the proteins in a reconstruction are localized in cellular compartments that are consistent with signal transduction from the membrane to the nucleus.LocPLand existing reconstruction algorithms are applied to two PPI networks and assessed using both global and local definitions of accuracy.LocPLproduces more accurate and biologically meaningful reconstructions on a versatile set of signaling pathways.LocPLis a powerful tool to automatically reconstruct signaling pathways from PPIs that leverages cellular localization information about proteins. The underlying dynamic program and signaling model are flexible enough to study cellular signaling under different settings of signaling flow across the cellular compartments.

scholarly journals Integrating protein localization with automated signaling pathway reconstruction

2019 ◽  
Vol 20 (S16) ◽  
Author(s):  
Ibrahim Youssef ◽  
Jeffrey Law ◽  
Anna Ritz
Keyword(s):  
Signal Transduction ◽  
Signaling Pathways ◽  
Protein Interactions ◽  
Cellular Localization ◽  
Protein Localization ◽  
Dynamic Program ◽  
Reconstruction Algorithms ◽  
Ppi Networks ◽  
Cellular Compartments ◽  
Localization Information

Abstract Background Understanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists generate testable hypotheses about signaling. However, automatic reconstruction of signaling pathways suffers from many interactions with the same confidence score leading to many equally good candidates. Further, some reconstructions are biologically misleading due to ignoring protein localization information. Results We propose LocPL, a method to improve the automatic reconstruction of signaling pathways from PPIs by incorporating information about protein localization in the reconstructions. The method relies on a dynamic program to ensure that the proteins in a reconstruction are localized in cellular compartments that are consistent with signal transduction from the membrane to the nucleus. LocPL and existing reconstruction algorithms are applied to two PPI networks and assessed using both global and local definitions of accuracy. LocPL produces more accurate and biologically meaningful reconstructions on a versatile set of signaling pathways. Conclusion LocPL is a powerful tool to automatically reconstruct signaling pathways from PPIs that leverages cellular localization information about proteins. The underlying dynamic program and signaling model are flexible enough to study cellular signaling under different settings of signaling flow across the cellular compartments.

Na+-dependent phosphate transporters in the murine osteoclast: cellular distribution and protein interactions

2003 ◽  
Vol 284 (6) ◽  
pp. C1633-C1644 ◽  
Author(s):  
Mohammed A. Khadeer ◽  
Zhihui Tang ◽  
Harriet S. Tenenhouse ◽  
Maribeth V. Eiden ◽  
Heini Murer ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Bone Resorption ◽  
Protein Interactions ◽  
Cellular Localization ◽  
Fluorescent Protein ◽  
Basolateral Membrane ◽  
Atp Synthesis ◽  
Cellular Distribution ◽  
Green Fluorescent ◽  
Carboxy Terminal

We previously demonstrated that inhibition of Na-dependent phosphate (Pi) transport in osteoclasts led to reduced ATP levels and diminished bone resorption. These findings suggested that Na/Picotransporters in the osteoclast plasma membrane provide Pifor ATP synthesis and that the osteoclast may utilize part of the Pireleased from bone resorption for this purpose. The present study was undertaken to define the cellular localization of Na/Picotransporters in the mouse osteoclast and to identify the proteins with which they interact. Using glutathione S-transferase (GST) fusion constructs, we demonstrate that the type IIa Na/Picotransporter (Npt2a) in osteoclast lysates interacts with the Na/H exchanger regulatory factor, NHERF-1, a PDZ protein that is essential for the regulation of various membrane transporters. In addition, NHERF-1 in osteoclast lysates interacts with Npt2a in spite of deletion of a putative PDZ-binding domain within the carboxy terminus of Npt2a. In contrast, deletion of the carboxy-terminal TRL amino acid motif of Npt2a significantly reduced its interaction with NHERF-1 in kidney lysates. Studies in osteoclasts transfected with green fluorescent protein-Npt2a constructs indicated that Npt2a colocalizes with NHERF-1 and actin at or near the plasma membrane of the osteoclast and associates with ezrin, a linker protein associated with the actin cytoskeleton, likely via NHERF-1. Furthermore, we demonstrate by RT/PCR of osteoclast RNA and in situ hybridization that the type III Na/Picotransporter, PiT-1, is also expressed in mouse osteoclasts. To examine the cellular distribution of PiT-1, we infected mouse osteoclasts with a retroviral vector encoding PiT-1 fused to an epitope tag. PiT-1 colocalizes with actin and is present on the basolateral membrane of the polarized osteoclast, similar to that previously reported for Npt2a. Taken together, our data suggest that association of Npt2a with NHERF-1, ezrin, and actin, and of PiT-1 with actin, may be responsible for membrane sorting and regulation of these Na/Picotransporters in the osteoclast.

scholarly journals Analysis of IFITM-IFITM Interactions by a Flow Cytometry-Based FRET Assay

2019 ◽  
Vol 20 (16) ◽  
pp. 3859 ◽  
Author(s):  
Michael Winkler ◽  
Florian Wrensch ◽  
Pascale Bosch ◽  
Maike Knoth ◽  
Michael Schindler ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Protein Interactions ◽  
Viral Entry ◽  
Cellular Localization ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Yellow Fluorescent Protein ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Protein Protein Interactions

The interferon-induced transmembrane proteins 1–3 (IFITM1–3) inhibit host cell entry of several viruses. However, it is incompletely understood how IFITM1–3 exert antiviral activity. Two phenylalanine residues, F75 and F78, within the intramembrane domain 1 (IM1) were previously shown to be required for IFITM3/IFITM3 interactions and for inhibition of viral entry, suggesting that IFITM/IFITM interactions might be pivotal to antiviral activity. Here, we employed a fluorescence resonance energy transfer (FRET) assay to analyze IFITM/IFITM interactions. For assay calibration, we equipped two cytosolic, non-interacting proteins, super yellow fluorescent protein (SYFP) and super cyan fluorescent protein (SCFP), with signals that target proteins to membrane rafts and also analyzed a SCFP-SYFP fusion protein. This strategy allowed us to discriminate background signals resulting from colocalization of proteins at membrane subdomains from signals elicited by protein–protein interactions. Coexpression of IFITM1–3 and IFITM5 fused to fluorescent proteins elicited strong FRET signals, and mutation of F75 and F78 in IFITM3 (mutant IFITM3-FF) abrogated antiviral activity, as expected, but did not alter cellular localization and FRET signals. Moreover, IFITM3-FF co-immunoprecipitated efficiently with wild type (wt) IFITM3, lending further support to the finding that lack of antiviral activity of IFITM3-FF was not due to altered membrane targeting or abrogated IFITM3-IFITM3 interactions. Collectively, we report an assay that allows quantifying IFITM/IFITM interactions. Moreover, we confirm residues F75 and F78 as critical for antiviral activity but also show that these residues are dispensable for IFITM3 membrane localization and IFITM3/IFITM3 interactions.

High-Throughput Analysis of Antigen Recognition by the B Cell Receptors of Malignant Lymphomas with High-Density Protein Microarrays.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2945-2945
Author(s):  
Mareike Frick ◽  
Alla Bulashevska ◽  
Marcus Duehren-von Minden ◽  
Kristina Heining-Mikesch ◽  
Dietmar Pfeifer ◽  
...  
Keyword(s):  
B Cell ◽  
Protein Interactions ◽  
Cellular Localization ◽  
Pathogenic Bacteria ◽  
Protein Microarrays ◽  
Genetic Alterations ◽  
High Density ◽  
Antigen Recognition ◽  
Z Score ◽  
B Cell Lymphomas

Abstract Abstract 2945 Poster Board II-921 The etiology of indolent B cell lymphomas (iNHL) is largely unknown. However, systemic autoimmune diseases are associated with certain iNHL. Organ-restricted chronic inflammation, i.e. H. pylori-associated gastritis, Sjogren's syndrome, and others, plays an etiological role in extranodal marginal zone lymphoma (MZL). Finally, shared structural features of the B cell receptor (BCR) suggest antigen recognition in iNHL etiology, particularly in CLL. Indeed, recognition of common autoantigens has been shown for CLL BCR. However, there has been no unbiased comparative assessment of antigen binding by iNHL BCR. We measured binding of lymphoma BCR simultaneously to 8000 human proteins displayed on high-density microarrays. BCR from 45 lymphomas, including 13 mantle cell lymphomas (MCL), 10 CLL, 5 nodal MZL, 5 diffuse large B-cell lymphomas (DLBCL), 4 follicular lymphomas (FL), 3 myelomas, 2 splenic MZL, and 2 LPL, were expressed as recombinant Fab fragments in E. coli. The most abundant among the 19 represented different VH segments were VH 4-34 (n=10), 1-69 (6), 3-30 (4), 3-21 (3), and 1-8 (3). Bound Fab was detected by 647AlexaFluor-goat-anti-human IgG. Z-scores and Z-factors (Zhang et al., 1999) were calculated for each Fab-protein interaction. Fab binding was defined as either Z-score >1.65 and Z-factor >0, or Z-score >1 and Z-factor >0.5. 108 robust Fab-Protein interactions were identified that involved 48 different proteins. 21 NHL BCR, derived from all lymphoma types, did not bind any protein. 12 BCR recognized one protein only. 9 BCR were highly polyreactive as defined by binding to ≥5 proteins (3 VH4-34-utilizing Fabs, 3 VH1-69 Fabs, 1 VH1-8 Fab, 1 VH3-21 Fab, and the only VH2-26 Fab). All Fab-protein interactions were analyzed by biclustering after adaptation of the Bimax algorithm used in gene expression studies to the protein microarray platform. 28 biclusters involving 11 Fabs and 21 proteins were identifed. 11 of the bicluster proteins have a nuclear localization; the cellular localization of 6 proteins is unknown. Subsequent hierarchical clustering of the biclusters distinguished three separate clusters. The DILIMOT algorithm identifed GxAxSxA as a potential consensus protein motif among 8 proteins clustering together (Scons=5.29×10-23, p=3.83×10-8). Although the arrays used here carried the most comprehensive assembly of proteins available, they represent only a small fraction of the human proteome. Therefore, homologues to recognized proteins were identified by BLAST search and included, among others, the paraneoplastic neuronal autoantigen Ma1 as being potentially recognized by 4 lymphomas, including a primary CNS DLBCL, and 2 cell wall proteins of pathogenic bacteria. There was no preponderance of any particular NHL entity within the biclusters, except a group of 3 MZL Fabs. Each of these MZL BCR utilized VH1-69 and Vk3-20, and all 3 were classified as polyreactive with very similar protein recognition patterns, including calcium binding and coiled domain 1 and the autoantigens cardiolipin and Ro-60/SS-A. This study of a broad selection of lymphoma types and BCR structures establishes protein microarrays as a novel and valuable platform to study antigen recognition by lymphoma cells in an unbiased and quantitative fashion, and thereby to deduct a comprehensive view of antigen stimulation in iNHL development. The currently available array generations permit unbiased identification of directly recognized candidate autoantigens and potentially bound homologues in appr. 60% of cases. The remaining cases may recognize carbohydrate and/or microbial antigens not represented on the array. In addition, the development of appropriate bioinformatic tools within this study permitted to define recurrent oligo- and polyreactivity patterns of antigen recognition by lymphoma BCR. With the possible exception of MZL, these patterns appear to operate across various lymphoma entities, generally suggesting two different components in lymphoma development: A requirement for BCR-mediated stimulation in the majority of cases which may occur during various scenarios and may be specific or follow definable patterns of cross-reactivity, and full malignant transformation of the stimulated cell by genetic alterations. The latter step would be expected to define the lymphoma type through the nature of the oncogenic event and the maturation stage of the cell of origin. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Combining Unique Multiplex Gateway Cloning and Bimolecular Fluorescence Complementation (BiFC) for High-Throughput Screening of Protein–Protein Interactions

2016 ◽  
Vol 21 (10) ◽  
pp. 1100-1111 ◽  
Author(s):  
Adriana Lepur ◽  
Lucija Kovačević ◽  
Robert Belužić ◽  
Oliver Vugrek
Keyword(s):  
High Throughput ◽  
Protein Interaction ◽  
Protein Interactions ◽  
High Throughput Screening ◽  
Cellular Localization ◽  
Interaction Analysis ◽  
Bimolecular Fluorescence Complementation ◽  
Galectin 3 ◽  
Fluorescence Complementation ◽  
Bimolecular Fluorescence

Protein interaction networks are the basis for human metabolic and signaling systems. Interaction studies often use bimolecular fluorescence complementation (BiFC) to reveal the formation and cellular localization of protein complexes. However, large-scale studies were either far from native conditions in human cells or limited by laborious restriction/ligation cloning techniques. Here, we describe a new tool for protein interaction screening based on Gateway-compatible BiFC vectors. We made a set of four new vectors that permit fusion of candidate proteins to the N or C fragment of Venus in all fusion positions. We have validated the vectors and confirmed self-association of AHCY, AHCYL1, and galectin-3. In a high-throughput BiFC screen, we identified new AHCY interaction partners: galectin-3 and PUS7L. We also describe additional steps in protein interaction analysis, applied for AHCY–galectin-3 interaction. First, we classified the interaction in intracellular vesicles using CellCognition, machine learning free software. Then we identified the vesicles as endosomal pathway compartments, in line with known galectin-3 trafficking route. This offers a platform to rapidly identify and localize new protein interactions inside living cells, a prerequisite to validate in silico interactome data, and ultimately decode complex protein networks.

scholarly journals Malignant Peritoneal Mesothelioma Interactome with 417 Novel Protein-Protein Interactions

2021 ◽  
Author(s):  
Kalyani B. Karunakaran ◽  
Madhavi K. Ganapathiraju
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Protein Interactions ◽  
Cellular Localization ◽  
Expression Profiles ◽  
Abdominal Cavity ◽  
Peritoneal Mesothelioma ◽  
Pleural Mesothelioma ◽  
Malignant Peritoneal Mesothelioma ◽  
Protein Protein Interactions

Abstract Malignant peritoneal mesothelioma (MPeM) is an aggressive cancer affecting the peritoneal lining of the abdominal cavity and intra-abdominal organs, with a median survival of ~2.5 years. We constructed an ‘MPeM interactome’ with over 400 computationally predicted protein-protein interactions (PPIs) and over 4,700 known PPIs of 59 literature-curated genes whose activity affects MPeM. Known PPIs of the 59 MPeM-associated genes were derived from BioGRID and HPRD databases. Novel PPIs were predicted by applying the HiPPIP algorithm, which computes features of protein pairs such as cellular localization, molecular function, biological process membership, genomic location of the gene, and gene expression in microarray experiments, and classifies the pairwise features as interacting or non-interacting based on a random forest model. 75.6% of the interactome and 65% of the novel interactors in it were supported by transcriptomic evidence in rodent and human peritoneal mesothelioma/mesothelial cell lines and tumor specimens. 152 drugs targeted 427 proteins in the MPeM interactome. Comparative transcriptome analysis of peritoneal mesothelioma-associated versus drug-induced gene expression profiles revealed 39 repurposable drugs, out of which 29 were effective against peritoneal/pleural mesothelioma and/or peritoneal metastasis/primary peritoneal cancer in clinical trials, animal models or cell lines. Functional modules of chromosomal segregation, transcriptional deregulation, positive regulation of IL-6 production and hematopoiesis were identified from the interactome. Genes with tissue-specific expression in 2 sites of extramedullary hematopoiesis (spleen and thymus) and those correlated with unfavorable prognosis in liver, renal, pancreatic and lung cancers were noted. MPeM interactome showed extensive overlap with the malignant pleural mesothelioma (MPM) interactome and MPM cell line expression profiles. Our findings demonstrate the utility of the MPeM interactome in discovering systems-level functional links among MPeM genes and generating clinically translatable results such as repurposed drugs.

Cellular regulation of endothelial nitric oxide synthase

2001 ◽  
Vol 280 (2) ◽  
pp. F193-F206 ◽  
Author(s):  
Roland Govers ◽  
Ton J. Rabelink
Keyword(s):  
Nitric Oxide ◽  
Protein Interactions ◽  
Cellular Localization ◽  
Fluid Shear Stress ◽  
Transcriptional Level ◽  
Protein Protein Interactions ◽  
Cellular Regulation ◽  
Complex Regulation ◽  
Oxide Synthase ◽  
Endothelial Nitric Oxide

Renal function is highly dependent on endothelium-derived nitric oxide (NO). Several renal disorders have been linked to impaired NO bioavailability. The enzyme that is responsible for the synthesis of NO within the renal endothelium is endothelial NO synthase (eNOS). eNOS-mediated NO generation is a highly regulated cellular event, which is induced by calcium-mobilizing agonists and fluid shear stress. eNOS activity is regulated at the transcriptional level but also by a variety of modifications, such as acylation and phosphorylation, by its cellular localization, and by protein-protein interactions. The present review focuses on the complex regulation of eNOS within the endothelial cell.

scholarly journals Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome

2018 ◽  
Author(s):  
Lixin Cheng ◽  
Kwong-Sak Leung
Keyword(s):  
Protein Interactions ◽  
Cellular Localization ◽  
A Priori ◽  
Specific Sequence ◽  
Nuclear Compartment ◽  
Protein Interactome ◽  
Moonlighting Proteins ◽  
Non Coding Rnas ◽  
Identification And Characterization

AbstractMoonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a methodology, MoonFinder, for the identification of moonlighting lncRNAs. MoonFinder is a statistical algorithm identifying moonlighting lncRNAs without a priori knowledge through the integration of protein interactome, RNA-protein interactions, and functional annotation of proteins. We identify 155 moonlighting lncRNA candidates and uncover that they are a distinct class of lncRNAs characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncRNAs tend to have shorter but more exons and the moonlighting lncRNAs have a localization tendency of residing in the cytoplasmic compartment in comparison with the nuclear compartment. Moreover, moonlighting lncRNAs and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases.

scholarly journals The Fusion of CLEC12A and MIR223HG Arises from a trans-Splicing Event in Normal and Transformed Human Cells

2021 ◽  
Vol 22 (22) ◽  
pp. 12178
Author(s):  
Bijay P. Dhungel ◽  
Geoffray Monteuuis ◽  
Caroline Giardina ◽  
Mehdi S. Tabar ◽  
Yue Feng ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Transcriptional Activation ◽  
Cellular Localization ◽  
Chromosomal Rearrangements ◽  
Chimeric Protein ◽  
Cell Surface Receptor ◽  
Lectin Domain ◽  
Normal Tissues ◽  
Chimeric Rnas ◽  
Trans Splicing

Chimeric RNAs are often associated with chromosomal rearrangements in cancer. In addition, they are also widely detected in normal tissues, contributing to transcriptomic complexity. Despite their prevalence, little is known about the characteristics and functions of chimeric RNAs. Here, we examine the genetic structure and biological roles of CLEC12A-MIR223HG, a novel chimeric transcript produced by the fusion of the cell surface receptor CLEC12A and the miRNA-223 host gene (MIR223HG), first identified in chronic myeloid leukemia (CML) patients. Surprisingly, we observed that CLEC12A-MIR223HG is not just expressed in CML, but also in a variety of normal tissues and cell lines. CLEC12A-MIR223HG expression is elevated in pro-monocytic cells resistant to chemotherapy and during monocyte-to-macrophage differentiation. We observed that CLEC12A-MIR223HG is a product of trans-splicing rather than a chromosomal rearrangement and that transcriptional activation of CLEC12A with the CRISPR/Cas9 Synergistic Activation Mediator (SAM) system increases CLEC12A-MIR223HG expression. CLEC12A-MIR223HG translates into a chimeric protein, which largely resembles CLEC12A but harbours an altered C-type lectin domain altering key disulphide bonds. These alterations result in differences in post-translational modifications, cellular localization, and protein–protein interactions. Taken together, our observations support a possible involvement of CLEC12A-MIR223HG in the regulation of CLEC12A function. Our workflow also serves as a template to study other uncharacterized chimeric RNAs.

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