Analysis of proteins copurifying with the cd4/lck complex using one-dimensional polyacrylamide gel electrophoresis and mass spectrometry: comparison with affinity-tag based protein detection and evaluation of different solubilization methods

Bernhard, Oliver K.; Cunningham, Anthony L.; Sheil, Margaret M.

doi:10.1016/j.jasms.2003.12.006

Cited by 9 publications

(3 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most of these interactions are associated with reasonable confidence levels. 58,59 Enhancement of EGFR signalling by HCV NS3/4A and NS5A proteins is important for viral replication and persistence. 60,61 Interestingly, EGFR is upregulated in lymph node metastasis in HCC, while SLC25A5 levels are downregulated, 20 suggesting that the Core interaction with SLC25A5 may be involved in regulating EGFR activity and host energy metabolism and consequently HCV replication and propagation.…”

Section: Host Energy Metabolism and Cell Adhesionmentioning

confidence: 99%

Network based analysis of hepatitis C virus Core and NS4B protein interactions

et al. 2010

View full text Add to dashboard Cite

Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. Here we attempt to further our understanding of the biological context of protein interactions in HCV pathogenesis, by investigating interactions between HCV proteins Core and NS4B and human host proteins. Using the yeast two-hybrid (Y2H) membrane protein system, eleven human host proteins interacting with Core and 45 interacting with NS4B were identified, most of which are novel. These interactions were used to infer overall protein interaction maps linking the viral proteins with components of the host cellular networks. Core and NS4B proteins contribute to highly compact interaction networks that may enable the virus to respond rapidly to host physiological responses to HCV infection. Analysis of the interaction networks highlighted enriched biological pathways likely influenced in HCV infection. Inspection of individual interactions offered further insights into the possible mechanisms that permit HCV to evade the host immune response and appropriate host metabolic machinery. Follow-up cellular assays with cell lines infected with HCV genotype 1b and 2a strains validated Core interacting proteins ENO1 and SLC25A5 and host protein PXN as novel regulators of HCV replication and viral production. ENO1 siRNA knockdown was found to inhibit HCV replication in both the HCV genotypes and viral RNA release in genotype 2a. PXN siRNA inhibition was observed to inhibit replication specifically in genotype 1b but not in genotype 2a, while SLC25A5 siRNA facilitated a minor increase in the viral RNA release in genotype 2a. Thus, our analysis can provide potential targets for more effective anti-HCV therapeutic intervention.

show abstract

Section: Host Energy Metabolism and Cell Adhesionmentioning

confidence: 99%

Network based analysis of hepatitis C virus Core and NS4B protein interactions

et al. 2010

View full text Add to dashboard Cite

show abstract

“…An association of CD4 and components of the cytoskeleton has been reported [26,27]. CD4 and TUBB were also found co‐purified in a study of CD4/lck interaction partners using sodium dodecyl sulphate–polyacrylamide gel electrophoresis and mass spectrometry [28]. Polymorphisms in the promoter region of the human CD4 gene and their association to T1D have been analysed in a Danish family material [29,30].…”

Section: Resultsmentioning

confidence: 96%

Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

Brorsson

Hansen

Lage

et al. 2009

Diabetes Obesity Metabolism

View full text Add to dashboard Cite

Aim-To develop novel methods for identifying new genes that contribute to the risk of developing type 1 diabetes within the Major Histocompatibility Complex (MHC) region on chromosome 6, independently of the known linkage disequilibrium (LD) between human leucocyte antigen (HLA)-DRB1, -DQA1, -DQB1 genes.Methods-We have developed a novel method that combines single nucleotide polymorphism (SNP) genotyping data with protein-protein interaction (ppi) networks to identify disease-associated network modules enriched for proteins encoded from the MHC region. Approximately 2500 SNPs located in the 4 Mb MHC region were analysed in 1000 affected offspring trios generated by the Type 1 Diabetes Genetics Consortium (T1DGC). The most associated SNP in each gene was chosen and genes were mapped to ppi networks for identification of interaction partners. The association testing and resulting interacting protein modules were statistically evaluated using permutation.Results-A total of 151 genes could be mapped to nodes within the protein interaction network and their interaction partners were identified. Five protein interaction modules reached statistical significance using this approach. The identified proteins are well known in the pathogenesis of T1D, but the modules also contain additional candidates that have been implicated in β-cell development and diabetic complications.Conclusions-The extensive LD within the MHC region makes it important to develop new methods for analysing genotyping data for identification of additional risk genes for T1D. Combining genetic data with knowledge about functional pathways provides new insight into mechanisms underlying T1D.

show abstract

“…Most reports to date have analysed CD4 interaction complexes in lymphoid cell lines, revealing some of the well-known associating proteins, such as LCK, CD45, transferrin receptor (CD71), CD98, myosins, vimentin, tubulins, actins, annexin II and lymphocyte phosphatase associated phosphoprotein (LPAP) [29], [30], [31], [32]. However, little is known about how CD4 antigen is arranged at the surface of Mφ, which notably lack LCK expression.…”

Section: Introductionmentioning

confidence: 99%

Proteomic-Based Identification of CD4-Interacting Proteins in Human Primary Macrophages

et al. 2011

View full text Add to dashboard Cite

BackgroundHuman macrophages (Mφ) express low levels of CD4 glycoprotein, which is constitutively recycled, and 40–50% of its localization is intracellular at steady-state. Although CD4-interacting proteins in lymphoid cells are well characterised, little is known about the CD4 protein interaction-network in human Mφ, which notably lack LCK, a Src family protein tyrosine kinase believed to stabilise CD4 at the surface of T cells. As CD4 is the main cellular receptor used by HIV-1, knowledge of its molecular interactions is important for the understanding of viral infection strategies.Methodology/Principal FindingsWe performed large-scale anti-CD4 immunoprecipitations in human primary Mφ followed by high-resolution mass spectrometry analysis to elucidate the protein interaction-network involved in induced CD4 internalization and degradation. Proteomic analysis of CD4 co-immunoisolates in resting Mφ showed CD4 association with a range of proteins found in the cellular cortex, membrane rafts and components of clathrin-adaptor proteins, whereas in induced internalization and degradation CD4 is associated with components of specific signal transduction, transport and the proteasome.Conclusions/SignificanceThis is the first time that the anti-CD4 co-immunoprecipitation sub-proteome has been analysed in human primary Mφ. Our data have identified important Mφ cell surface CD4-interacting proteins, as well as regulatory proteins involved in internalization and degradation. The data give valuable insights into the molecular pathways involved in the regulation of CD4 expression in Mφ and provide candidates/targets for further biochemical studies.

show abstract

Analysis of proteins copurifying with the cd4/lck complex using one-dimensional polyacrylamide gel electrophoresis and mass spectrometry: comparison with affinity-tag based protein detection and evaluation of different solubilization methods

Cited by 9 publications

References 24 publications

Network based analysis of hepatitis C virus Core and NS4B protein interactions

Network based analysis of hepatitis C virus Core and NS4B protein interactions

Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

Proteomic-Based Identification of CD4-Interacting Proteins in Human Primary Macrophages

Contact Info

Product

Resources

About