Deconvolution of Targeted Protein–Protein Interaction Maps

Current proteomic techniques allow researchers to analyze chosen biological pathways or an ensemble of related protein complexes at a global level via the measure of physical protein–protein interactions by affinity purification mass spectrometry (AP-MS). Such experiments yield information-rich but complex interaction maps whose unbiased interpretation is challenging. Guided by current knowledge on the modular structure of protein complexes, we propose a novel statistical approach, named BI-MAP, complemented by software tools and a visual grammar to present the inferred modules. We show that the BI-MAP tools can be applied from small and very detailed maps to large, sparse, and much noisier data sets. The BI-MAP tool implementation and test data are made freely available

Deconvolution of Targeted Protein–Protein Interaction Maps

Current proteomic techniques allow researchers to analyze chosen biological pathways or an ensemble of related protein complexes at a global level via the measure of physical protein–protein interactions by affinity purification mass spectrometry (AP-MS). Such experiments yield information-rich but complex interaction maps whose unbiased interpretation is challenging. Guided by current knowledge on the modular structure of protein complexes, we propose a novel statistical approach, named BI-MAP, complemented by software tools and a visual grammar to present the inferred modules. We show that the BI-MAP tools can be applied from small and very detailed maps to large, sparse, and much noisier data sets. The BI-MAP tool implementation and test data are made freely available

Deconvolution of Targeted Protein–Protein Interaction Maps

Current proteomic techniques allow researchers to analyze chosen biological pathways or an ensemble of related protein complexes at a global level via the measure of physical protein–protein interactions by affinity purification mass spectrometry (AP-MS). Such experiments yield information-rich but complex interaction maps whose unbiased interpretation is challenging. Guided by current knowledge on the modular structure of protein complexes, we propose a novel statistical approach, named BI-MAP, complemented by software tools and a visual grammar to present the inferred modules. We show that the BI-MAP tools can be applied from small and very detailed maps to large, sparse, and much noisier data sets. The BI-MAP tool implementation and test data are made freely available

Detection of Chemical Engagement of Solute Carrier Proteins by a Cellular Thermal Shift Assay

Solute carriers (SLCs) are transmembrane proteins that transport various nutrients, metabolites, and drugs across cellular membranes. Despite the relevance of SLCs to cell homeostasis, metabolism, and disease states, for the majority of SLCs we lack experimental evidence regarding the nature of the cognate ligands, whether endobiotic or xenobiotic. Moreover, even for the roughly 20 SLCs for which inhibitors have been characterized, engagement assays in cells are limited to the accessibility of radiolabeled or fluorescent probes. The cellular thermal shift assay (CETSA) has been introduced as a powerful method to assess target engagement by monitoring ligand-induced changes in the thermal stability of cellular proteins. We addressed the question of whether CETSA could be modified to become routinely applicable to membrane transporters such as SLCs. We used SLC16A1 (MCT1) and SLC1A2 (EAAT2) as targets to establish robust conditions by which chemical engagement of SLCs can be detected. Using immunoblotting, we demonstrate that treatment with the SLC16A1 inhibitors AZD3965 and AR-C155858 stabilized endogenous SLC16A1 in HEK293 cell lysates as well as intact cells. In addition, the high-affinity ligand of SLC16A1, l-lactate, and the low-affinity ligand, formate, resulted in strong and weak stabilization of SLC16A1, respectively. Moreover, we observed stabilization of SLC1A2 upon treatment with the selective inhibitor WAY-213613. We propose that the experimental approach presented here should be generally and easily applicable for monitoring the engagement of chemical ligands by SLCs in cellular settings and thus assisting in their deorphanization

List of c-Abl point mutants investigated in this study with summary of the effect of mutations.

<p>Mutants were tested for c-Abl activity via immunoblotting of HEK293 lysates or immunoprecipitates (IP) and via kinase activity assay. The numbering of residues is in agreement with the sequence of the isoform Ib. Activity scoring (effect of the mutation):, nt, not tested, − inactive (mutation disruptive), + weakly active (mutation mildly disruptive), ++ activity similar to wild-type (mutation neutral), +++ hyperactive (mutation activating) (See also Supplemental Table S1).</p><p>List of c-Abl point mutants investigated in this study with summary of the effect of mutations.</p

Effect of point mutations on the kinase activity of c-Abl.

<p>Abl proteins were immunoprecipitated and assayed for phosphorylation of an optimal Abl substrate peptide. The kinase activity was normalized to the amount of protein and to the activity of the wild-type CD or SH2-CD construct. <b>A</b> M297L was found to decrease kinase activity, whereas M297G had an activating effect in the absence of the SH2 domain. The kinase-dead mutant D382N presented no activity, and the known inactivating (I164E) and activating (T231R) mutations also show, accordingly, a decreased and increased activity. <b>B</b> The M297G mutant is significantly more active in the context of the isolated kinase domain, but not in the presence of the SH2 domain. The error bars are standard deviations from biological quadruplicates (n = 4, **P<0.01, Student <i>t</i> test). <b>C</b> Mutations E294P and E294P V299P have an activating effect. The reactions were performed at 37°C. <b>D</b> The activity of wild-type and E294P V299P Abl proteins was measured at increasing substrate concentrations and 25 µM ATP. <b>E</b> Y339G substitution is neutral, whereas Y339P diminishes Abl activity. The effect is seen both at 24°C and at an elevated temperature. <b>F, G</b> The ratio of the kinase activity at the elevated and room temperatures. Except for Y339P, the SH2-CD proteins retain their activity at the elevated temperature, whereas the activity of the CD constructs is reduced at least 2-fold. The error bars are standard deviations from technical triplicates except for (B). (See also Figures S4 and S5).</p

Domain organization and crystal structures of Abl kinase.

<p><b>A</b> The c-Abl isoform Ib is characterized by myristoylation (Myr) on Gly-2 of the N-terminal capping region (cap). The tyrosine kinase domain is preceded by the SH3 and SH2 domains and a connecting linker. The last exon region contains nuclear localization signals and a C-terminal actin binding domain (ABD). <b>B</b> In the down-regulated state (PDB entry 2FO0), the SH2 domain binds the C-lobe of the kinase domain, the myristate is bound in its cognate pocket and the SH3 domain binds the SH2-CD linker. <b>C</b> In the active “top-hat” conformation (PDB entry 1OPL), the SH2 domain moves to interact with the N-lobe of the kinase domain. The αC helix and the activation loop are highlighted in red and pink, respectively. <b>D</b> Positions of the most important point mutations at the SH2-CD interface and in the β3-αC loop.</p

The free energy of conformational changes of the A-loop.

<p>The free energy surfaces of the A-loop transition from open (active-like) to closed (inactive-like) conformation in case of the ABL catalytic domain alone (left) and in presence of the SH2 regulatory domain in the “top-hat” conformation as a function of the contact map distances to the respective reference structures. For the deepest minima a representative structure is also shown below with the CD colored in blue, the SH2 in green, the A-loop in yellow and the aC-helix in red.</p

Allosteric coupling and flexibility of c-Abl.

<p><b>A</b> Allosteric couplings of residues in the CD to the SH2 domain. High values (yellow and red) indicate strong allosteric interactions (See also Supplemental <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003863#pcbi.1003863.s001" target="_blank">Figure S1</a> A–C). <b>B</b> Free CD colored by RMSF from MD simulations. <b>C</b> SH2-CD construct colored by RMSF. (See also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003863#pcbi.1003863.s002" target="_blank">Figure S2</a>).</p

Evaluating the Promiscuous Nature of Tyrosine Kinase Inhibitors Assessed in A431 Epidermoid Carcinoma Cells by Both Chemical- and Phosphoproteomics

Deregulation of protein tyrosine kinase signaling has been linked to many diseases, most notably cancer. As a consequence, small molecule inhibitors of protein tyrosine kinases may provide powerful strategies for treatment. Following the successful introduction of imatinib in the treatment of chronic myelogenous leukemia, such drugs are also now evaluated for other types of cancer. However, many developed kinase inhibitors are not very target-specific and therefore may induce side effects. The importance of such side effects is certainly cell-proteome dependent. Understanding the all-inclusive action of a tyrosine kinase inhibitor on each individual cell-type entails the identification of potential targets, combined with monitoring the downstream effects revealing the signaling networks involved. Here, we explored a multilevel quantitative mass spectrometry–based proteomic strategy to identify the direct targets and downstream signaling effect of four tyrosine kinase inhibitors (imatinib, dasatinib, bosutinib, and nilotinib) in epidermoid carcinoma cells, as a model system for skin-cancer. More than 25 tyrosine kinases showed affinity to the drugs, with imatinib and nilotinib displaying a high specificity, especially when compared to dasatinib and bosutinib. Consequently, the latter two drugs showed a larger effect on downstream phosphotyrosine signaling. Many of the proteins affected are key regulators in cell adhesion and invasion. Our data represents a multiplexed view on the promiscuous action of certain tyrosine kinase inhibitors that needs to be taking into consideration prior to the application of these drugs in the treatment of different forms of cancer