Identification of protein complexes from co-immunoprecipitation data

Motivation: Advanced technologies are producing large-scale protein–protein interaction data at an ever increasing pace. A fundamental challenge in analyzing these data is the inference of protein machineries. Previous methods for detecting protein complexes have been mainly based on analyzing binary protein–protein interaction data, ignoring the more involved co-complex relations obtained from co-immunoprecipitation experiments

Fyn-Mediated Regulation of Protein Kinase A

Protein kinases are enzymes important for signal transduction in the regulation of cellular processes. The cAMP-dependent protein kinase A (PKA) has been previously reported to regulate the activity of the Src family kinase Fyn, an event important for cellular migration. This study aimed to characterize the reciprocal interaction, in which Fyn regulates PKA. In addition to our preliminary, unpublished findings that Fyn phosphorylates the PKA catalytic subunit at Y69 to increase its catalytic activity, we have shown through co-immunoprecipitation that Fyn physically associates with PKA in HEK293 cells. Quantitative mass spectrometry and subsequent biochemical validation shows that PKACα undergoes enhanced binding to a complex of centrosomal and Golgi-localized A-kinase anchoring proteins when Fyn is overexpressed, independent of Fyn kinase activity. Fyn was found in this complex, as well, implicating its involvement as an adaptor protein. Co-immunoprecipitation experiments with various Fyn alleles demonstrated the dispensability of the Fyn SH3 domain and the functioning SH2 domain in binding to PKACα. GST-fusion proteins containing either of these domains were also unable to enrich PKACα from HEK293 lysates. Fyn was found to bind PKACα independent of its association with the regulatory subunit, and preliminary data suggests that this interaction is direct through purified protein pulldown experiments. We hypothesize that this regulatory interaction activates PKA at the centrosome and Golgi apparatus, facilitating the potential phosphorylation of proximal substrates involved in cytoskeletal organization and mitotic processes

Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions.

Life and death fate decisions allow cells to avoid massive apoptotic death in response to genotoxic stress. Although the regulatory mechanisms and signalling pathways controlling DNA repair and apoptosis are well characterized, the precise molecular strategies that determine the ultimate choice of DNA repair and survival or apoptotic cell death remain incompletely understood. Here we report that a protein tyrosine phosphatase, EYA, is involved in promoting efficient DNA repair rather than apoptosis in response to genotoxic stress in mammalian embryonic kidney cells by executing a damage-signal-dependent dephosphorylation of an H2AX carboxy-terminal tyrosine phosphate (Y142). This post-translational modification determines the relative recruitment of either DNA repair or pro-apoptotic factors to the tail of serine phosphorylated histone H2AX (gamma-H2AX) and allows it to function as an active determinant of repair/survival versus apoptotic responses to DNA damage, revealing an additional phosphorylation-dependent mechanism that modulates survival/apoptotic decisions during mammalian organogenesis

The E5 protein of BPV-4 interacts with the heavy chain of MHC class I and irreversibly retains the MHC complex in the Golgi apparatus

BPV-4 E5 inhibits transcription of the bovine MHC class I heavy chain (HC) gene, increases degradation of HC and downregulates surface expression of MHC class I by retaining the complex in the Golgi apparatus (GA). Here we report that transcription inhibition can be alleviated by interferon treatment and the degradation of HC can be reversed by treatment with inhibitors of proteasomes and lysosomes. However, the inhibition of transport of MHC class I to the cell surface is irreversible. We show that E5 is capable of physically interacting with HC. Together with the inhibition of the vacuolar ATPase (due to the interaction between E5 and 16k subunit c), the interaction between E5 and HC is likely to be responsible for retention of MHC class I in the GA. C-terminus deletion mutants of E5 are incapable of either downregulating surface MHC class I or interacting with HC, establishing that the C-terminus domain of E5 is important in the inhibition of MHC class I

E5 protein of human papillomavirus 16 downregulates HLA class I and interacts with the heavy chain via its first hydrophobic domai

Human papillomavirus type 16 E5 protein (HPV-16 E5) is expressed early in papillomavirus infection and is localised primarily in the cell Golgi apparatus (GA) and endoplasmic reticulum. E5 prevents transport of the major histocompatibility class I (MHC I; HLA class I in humans) to the cell surface and retains the complex in the GA. We report that these effects are due, at least in part, to the interaction between E5 and HLA I heavy chain (HC). We also demonstrate that the down-regulation of surface HLA I and interaction with HC are mediated by the first hydrophobic domain of E5. Although E5 downregulates classical HLA selectively as it does not downregulate non-classical HLA, the interaction with the HC of classical HLA I is not specific for a particular haplotype of HLA I. This suggests that E5 can interfere with antigen presentation by most, if not all, classical HLA I haplotypes, with potentially serious consequences as the ability of infected cells to present antigenic peptides to effector T cells would be compromised