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Protein Interaction Mapping (3):
Recent article
Protein Interaction Mapping
Abstract
We screened a set of proteins from the G-protein complex using two-hybrid complementation in yeast. After deep and exhaustive interrogation, we detected 544 interactions between 434 proteins, of which 68 highly interconnected proteins form the core G-protein interactome. Within this core, over half...
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PMID: 21952135
PDF is available here.
PDF is available here.
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Proteomics (11)18 2011
Abstract
This review covers progress in proteome research on Mycoplasma pneumoniae made over the last 5 years. This bacterium is one of the smallest known self-replicating bacteria. With fewer than 700 proposed proteins, it is well suited to a comprehensive proteome analysis. While all of the...
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PMID: 21751371
PDF is available here.
PDF is available here.
Abstract
We investigated the function and calcium regulation of the COOH-terminal end segment of TnI. A TnI model molecule was labeled with Alexa fluor 532 at a Cys engineered at the COOH-terminal end and used to reconstitute tertiary troponin complex. A Ca(2+) -regulated conformational change in the COOH te...
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PMID: 21777381
PDF is available here.
PDF is available here.
Abstract
About 1000 gene symbols each could be assigned to the pathophysiological description of DN and to the clinical context. Direct feature comparison showed minor overlap, whereas on the level of molecular pathways, the complement and coagulation cascade, PPAR signaling, and the renin-angiotensin system...
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PMID: 21491608
PDF is available here.
PDF is available here.
Proteomics (11)12 2011
Abstract
We concurrently profiled the proteome of dorsal-lateral (DLP) and ventral (VP) prostate lobes of both TRAMP and littermate WT C57BL/6 mice of 18 wk by 2-D LC-MALDI-TOF/TOF with iTRAQ labeling. A total of 483 and 748 proteins were identified at critical false discovery rates of 1 and 5%. In WT mice...
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PMID: 21598396
PDF is available here.
PDF is available here.
Proteomics (11)12 2011
Abstract
We identified 46 proteins that were altered at protein expression levels. The protein changes detected by 2-DE/MS were verified by functional protein assays. These identified proteins include some key proteins involved in cellular stress response, metabolism, adhesion, cytoskeletal dynamics, cell gr...
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PMID: 21595037
PDF is available here.
PDF is available here.
Abstract
Abstract
A comparative study of proteome maps from control and Cd-exposed rat liver was performed using a new technology of two-dimensional liquid chromatography separation method (PF-2D system, Beckman Coulter). Rats were fed for one month 0 or 100 μg Cd g(-1). The between-replicate and bet...
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PMID: 21093054
PDF is available here.
PDF is available here.
Xenobiotica (41)5 2011
Abstract
We present a basic method for the purification of the endogenous Par-6/aPKC protein complex, which plays a central role in orchestrating asymmetric cell divisions in the developing nervous system of Drosophila. The procedure can be subdivided into the following steps: acquisition of sufficient start...
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PMID: 18641959
PDF is available here.
PDF is available here.
Abstract
The ability to study proteins and protein interactions inside cells and tissues is important for elucidating how cells function in health and disease. The in situ proximity ligation assay (in situ PLA) presented here can be used to visualize proteins, protein-protein interactions, and post-translatio...
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PMID: 21455970
PDF is available here.
PDF is available here.
Nucleic Acids Research (39)5 2011
Abstract
ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein-protein interfaces with regard to its suitability for small molecule drug design. To this end, ANCHOR exploits the so-called anchor residues, i.e. amino acid side-chains deeply buried at protein-protein interfaces, to indi...
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PMID: 20525787
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of hRPC62. This subunit folds as a four-tandem extended winged helix (eWH) protein that is structurally related to the transcription factor TFIIEα N terminus. Through biochemical analyses, we mapped the protein-protein interactions of hRPC62, hRPC32 and hRPC39. In ad...
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PMID: 21358628
PDF is available here.
PDF is available here.
Abstract
We provide a proof of principle for such an approach. Using a set of protein complexes representing known interactors in their unbound form, we show that a standard docking program can distinguish the true interactors from a background of 922 non-redundant potential interactors. We additionally show...
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PMID: 21326236
PDF is available here.
PDF is available here.
Abstract
We focused our strategy on the allosteric inhibitors capable of targeting the NS2B-NS3pro interface rather than the NS3pro active site. Using virtual ligand screening of the diverse, ∼275,000-compound library and the catalytic domain of the two-component West Nile virus (WNV) NS2B-NS3pro as a rece...
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PMID: 21050032
PDF is available here.
PDF is available here.
Abstract
Understanding the role of G protein-coupled receptor (GPCR; also known as a 7 transmembrane receptor) heteromerization in the physiology and pathophysiology of cellular function has now become a major research focus. However, there is currently a lack of cell-based assays capable of...
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PMID: 21133678
PDF is available here.
PDF is available here.
Cell Cycle (10)3 2011
Abstract
We show that CtIP, which is recruited to DSB-containing chromatin, interacts with both TopBP1 and Nbs1 in a damage-dependent manner. An N-terminal region containing the first two BRCT repeats of TopBP1 is essential for the interaction with CtIP. Furthermore, two distinct regions in the N-terminus of...
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PMID: 21263215
PDF is available here.
PDF is available here.
Abstract
The analysis of protein-protein interactions has the growing importance in modern proteomics. It is caused by necessity of in-depth functional study of proteins which, as a rule, operate in living systems due to each other interaction in the stable or dynamic protein complexes. In this review, the br...
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PMID: 21460877
PDF is available here.
PDF is available here.
Abstract
We elucidate the molecular mechanism of autoinhibition and activation of LapD based on structure-function analyses and crystal structures of the entire periplasmic domain and the intracellular signaling unit in two different states. In the absence of c-di-GMP, the intracellular module assumes an ina...
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PMID: 21304926
PDF is available here.
PDF is available here.
Abstract
We developed a computational framework to build molecular connectivity maps by integrating mutated and differentially expressed genes of neurological and psychiatric diseases to determine its relationship with aging....
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PMID: 21226925
PDF is available here.
PDF is available here.
Abstract
With the huge amount of uncharacterized protein sequences generated in the post-genomic age, it is highly desirable to develop effective computational methods for quickly and accurately predicting their functions. The information thus obtained would be very useful for both basic research and drug dev...
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PMID: 21283518
PDF is available here.
PDF is available here.
Abstract
We analyzed the effect of the absence of AQP4 on the morphology and protein composition of sarcolemma as well as on the whole skeletal muscle proteome. Immunofluorescence analysis showed that the absence of AQP4 did not perturb the expression and cellular localization of the dystrophin-glycoprotein...
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PMID: 21552523
PDF is available here.
PDF is available here.
Abstract
We describe the application of experimental data and modeling of intracellular endocytic trafficking mechanisms with a focus on the process of clathrin-mediated endocytosis. A detailed parts-list for the protein-protein interactions in clathrin-mediated endocytosis has been available for some time....
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PMID: 21792431
PDF is available here.
PDF is available here.
Abstract
ABSTRACT Nucleotide-binding domain, leucine-rich repeat containing proteins (NLRs) activate caspase-1 in response to a variety of bacterium-derived signals in macrophages. NLR-mediated activation of caspase-1 by Legionella pneumophila occurs through both an NLRC4/NAIP5-dependent path...
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PMID: 21771913
PDF is available here.
PDF is available here.
Abstract
We analyse for the first time the statistical link between the properties of G-protein-coupled receptors and GPCR ligands. The technique of mutual information (MI) is able to reveal statistical inter-dependence between variations in amino acid residues on the one hand and variations in ligand molecu...
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PMID: 21326864
PDF is available here.
PDF is available here.
Abstract
Our findings show that there is a "central core of cervical cancer" protein expression pattern, and suggest that 14-3-3zeta is key to determine if the cell proliferates or dies. In addition, our bioinformatics analysis suggests that the neoplastic phenotype is governed by a non-canonical regulatory...
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PMID: 21696634
PDF is available here.
PDF is available here.
médecine/sciences (27)6-7 2011
Abstract
Abstract
We analyzed how mutations in LCA5 affect the connectivity of the encoded protein lebercilin at the interactome level. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Using a generally applicable affinity proteomics approach, we showed that...
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PMID: 21606596
PDF is available here.
PDF is available here.
Abstract
High-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines...
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PMID: 21595981
PDF is available here.
PDF is available here.
Abstract
Hypersensitive cell death, a form of avirulent pathogen-induced programmed cell death (PCD), is one of the most efficient plant innate immunity. However, its regulatory mechanism is poorly understood. AtLSD1 is an important negative regulator of PCD and only two proteins, AtbZIP10 and AtMC1, have bee...
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PMID: 21526181
PDF is available here.
PDF is available here.
Abstract
We experimentally assay-binding affinities for a variety of mutants and determine their relative free energy of binding, ΔΔG, to rank the importance of interface residues to binding. We then compare how accurately, precisely and reliably computational methods for calculating ΔΔG can replicate th...
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PMID: 20656696
PDF is available here.
PDF is available here.
Abstract
Bioinformatics can be used to predict protein function, leading to an understanding of cellular activities, and equally-weighted protein-protein interactions (PPI) are normally used to predict such protein functions. The present study provides a weighting strategy for PPI to improve...
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PMID: 21524280
PDF is available here.
PDF is available here.
Virology Journal (8)1 2011
Abstract
We analyse the effect of these differences upon the binding of Influenza A virus NS1 protein to a range of cellular proteins involved in polarity and signal transduction....
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PMID: 21247458
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)53 2010
Abstract
We show a novel interaction between the transcription elongation factor Bur1-Bur2 and replication protein A (RPA), the eukaryotic single-stranded DNA-binding protein with functions in DNA repair, recombination, and replication. Bur1 interacted via its C-terminal domain with RPA, and bur1-ΔC mutants...
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PMID: 21075850
PDF is available here.
PDF is available here.
Neuroreport (21)18 2010
Abstract
We observed retrovirus-induced RXRα–Nurr1 heterodimer interactions with, and transactivation of, the TH promoter region in cultured rat embryonic neural precursor cells. Interestingly, forced expression of RXRα with Nurr1 remarkably reduced Nurr1 activity in TH+ dopaminergic neuron generation an...
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PMID: 22066143
PDF is available here.
PDF is available here.
Abstract
Abstract
Abstract
Experimental Cell Research (316)19 2010
Abstract
We characterize here ORP11, a member of the oxysterol-binding protein family. ORP11 is present at highest levels in human ovary, testis, kidney, liver, stomach, brain, and adipose tissue. Immunohistochemistry demonstrates abundant ORP11 in the epithelial cells of kidney tubules, testicular tubules,...
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PMID: 20599956
PDF is available here.
PDF is available here.
Thrombosis and Haemostasis (104)5 2010
Abstract
We review here published information on these topics and touch upon ongoing studies aimed at finding definitive answers to outstanding questions relevant for a better understanding of thrombosis and haemostasis....
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PMID: 20941453
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of the core of a lethal toxin complex to 3.1-Å resolution; the structure contains a PA octamer bound to four LF PA-binding domains (LF(N)). The first α-helix and β-strand of each LF(N) unfold and dock into a deep amphipathic cleft on the surface of the PA octamer,...
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PMID: 21037566
PDF is available here.
PDF is available here.
ACS Chemical Biology (5)10 2010
GSK4112, a small molecule chemical probe for the cell biology of the nuclear heme receptor Rev-erbα.
Abstract
We describe the development of a biochemical assay measuring the interaction between Rev-erbα and a peptide from the nuclear receptor corepressor-1 (NCoR). The assay was utilized to identify a small molecule ligand for Rev-erbα, GSK4112 (1), that was competitive with heme. In cells, 1 profiled as...
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PMID: 20677822
PDF is available here.
PDF is available here.
ACS Chemical Biology (5)10 2010
GSK4112, a small molecule chemical probe for the cell biology of the nuclear heme receptor Rev-erbα.
Abstract
We describe the development of a biochemical assay measuring the interaction between Rev-erbα and a peptide from the nuclear receptor corepressor-1 (NCoR). The assay was utilized to identify a small molecule ligand for Rev-erbα, GSK4112 (1), that was competitive with heme. In cells, 1 profiled as...
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PMID: 20677822
PDF is available here.
PDF is available here.
Abstract
Our data highlight a potential role of α-synuclein in regulating the microtubule dynamics in neurons. The association of α-synuclein with tubulin may further provide insight into the biological and pathophysiological function of synuclein....
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PMID: 19826908
PDF is available here.
PDF is available here.
Abstract
Interactions between proteins are central to any cellular process, and mapping these into a protein network is informative both for the function of individual proteins and the functional organization of the cell as a whole. Many strategies have been developed that are up to this task, and the last 1...
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PMID: 20973641
PDF is available here.
PDF is available here.
Abstract
We show that a statistical model built using sequence- and annotation-based features of bait proteins is able to identify bait features that are significant determinants of the outcome of interaction proteomics experiments. We show that bait features are able to explain in part the disparities obser...
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PMID: 20731387
PDF is available here.
PDF is available here.
Journal of Proteomics (73)10 2010
Abstract
We discuss identity-based studies employing tandem mass spectrometry that analyzed clinical material as well as model systems. Through meta-analysis we provide a list of CRC-associated tissue proteins discovered in multiple studies, with the greater majority being 2D gel-based discoveries coupled to...
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PMID: 20601272
PDF is available here.
PDF is available here.
Abstract
Biomarkers for colorectal cancer (CRC) early diagnosis are currently lacking. The purpose of this study was to interpret molecular events in the early stage of CRC that may bring about new biomarkers for early diagnosis. Methylation isotope labeling assistant gel-enhanced liquid chromatography-mass...
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PMID: 20666480
PDF is available here.
PDF is available here.
Abstract
We fractionated the cytoplasm of HCT116 colon cancer cells and used a proteomic approach to analyze cytoplasmic HMGB1-binding proteins. Pull-down experiments using recombinant HMGB1 protein as bait, followed by mass spectrometry analysis identified 162 interacting proteins. Among them were 74 protei...
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PMID: 20812762
PDF is available here.
PDF is available here.
Molecular Cell (39)4 2010
Abstract
We found a XPD protein complex containing MMS19 that was assumed to be a regulator of TFIIH. However, the MMS19-XPD complex did not contain any other subunits of TFIIH. Instead, it included FAM96B (now designated MIP18), Ciao1, and ANT2. MMS19, MIP18, and XPD localized to the mitotic spindle during...
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PMID: 20797633
PDF is available here.
PDF is available here.
Molecular Cell (39)4 2010
Abstract
We show that the Pol I-specific subunits A49 and A34.5 form a subcomplex that binds DNA and is related to TFIIF and TFIIE. The N-terminal regions of A49 and A34.5 form a dimerization module that stimulates polymerase-intrinsic RNA cleavage and has a fold that resembles the TFIIF core. The C-terminal...
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PMID: 20797630
PDF is available here.
PDF is available here.
Systems Biology, IET (4)5 2010
Abstract
The problem of reverse engineering in the topology of functional interaction networks from time-course experimental data has received considerable attention in literature, due to the potential applications in the most diverse fields, comprising engineering, biology, economics and soc...
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PMID: 20831343
PDF is available here.
PDF is available here.
Biophysical Journal (99)4 2010
Abstract
We implement sensitized emission Förster resonance energy transfer (FRET) stoichiometry under total internal reflection fluorescence (TIRF) microscopy. We demonstrate through quantitative analysis and modeling that evanescent fields must be precisely matched between FRET excitation wavelengths to i...
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PMID: 20713017
PDF is available here.
PDF is available here.
Abstract
Biological networks are often modeled by random graphs. A better modeling vehicle is a multigraph where each pair of nodes is connected by a Poisson number of edges. In the current model, the mean number of edges equals the product of two propensities, one for each node. In this context it is possibl...
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PMID: 20554690
PDF is available here.
PDF is available here.
Infection and Immunity (78)8 2010
Abstract
The YopM protein of Yersinia sp. is a type III secreted effector that is required for virulence in murine models of infection. YopM has previously been shown to contain leucine-rich repeats (LRRs) and to interact with two host kinases, RSK1 and PRK2, although the consequence of these interactions is...
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PMID: 20515922
PDF is available here.
PDF is available here.
Abstract
Our data reveal that HE induces modest inhibition of IL-12p70 responses to lipopolysaccharide (LPS) whereas Hz significantly impairs IL-12p70 responses to IFNgamma/LPS through down-regulation of IL-12p35 and p40 gene expression. Although reactive oxygen species (ROS) are generated after short-term e...
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PMID: 20211185
PDF is available here.
PDF is available here.
Journal of General Virology (91)Pt 8 2010
Abstract
Bunyamwera virus NSs protein is involved in the inhibition of cellular transcription and the interferon (IFN) response, and it interacts with the Med8 component of Mediator. A spontaneous mutant of a recombinant NSs-deleted Bunyamwera virus (rBUNdelNSs2) was identified and characterized. This mutant...
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PMID: 20427562
PDF is available here.
PDF is available here.
Journal of General Virology (91)Pt 8 2010
Abstract
We observed that UL114 was much less abundant than UL44. Interaction of UL114 with UL54, independent of the UL54 carboxyl terminus, but not with UL44 was detected in vitro. Our data are consistent with a direct UL114-UL54 interaction, and suggest that UL114 and UL54 act in concert during base excisi...
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PMID: 20410316
PDF is available here.
PDF is available here.
Journal of General Virology (91)Pt 8 2010
Abstract
We conducted a yeast two-hybrid screening. As a result, we identified a cellular protein termed bovine NIK- and IKKbeta-binding protein (NIBP), which is involved in protein trafficking and nuclear factor kappa B (NF-kappaB) signalling in cells. The interaction of NS5A with NIBP was confirmed both in...
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PMID: 20444997
PDF is available here.
PDF is available here.
Journal of Virology (84)16 2010
Abstract
We showed that SUMO binding by IE2 is necessary for its efficient transactivation function and for viral growth. IE2 bound physically to SUMO-1 through a SUMO-interacting motif (SIM). Mutations in SIM (mSIM) or in both SUMOylation sites and SIM (KR/mSIM), significantly reduced IE2 transactivation ef...
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PMID: 20519406
PDF is available here.
PDF is available here.
Journal of Virology (84)16 2010
Abstract
We show here that another Nedd4-like ubiquitin ligase, Nedd4-1, corrected release defects resulting from the disruption of PTAP (PTAP(-)), suggesting that HIV-1 Gag also recruits Nedd4-1 to facilitate virus release. Notably, Nedd4-1 remediation of HIV-1 PTAP(-) budding defects is independent of cell...
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PMID: 20519395
PDF is available here.
PDF is available here.