In this regard, DNA-based surface patterning seems to favor the formation of clathrin hotspots to a lesser extent

In this regard, DNA-based surface patterning seems to favor the formation of clathrin hotspots to a lesser extent. protein-protein interactions, describe controls and strategies to prevent the misinterpretation of data, and show that the use of DNA-based linker systems can lead to the improvement of the technical platform. 0.0001) with respect to the number of pattern-positive cells. This finding shows that the specific accumulation of EGFR in micropatterns and the Grb2 interaction occurs on nonfunctionalized patterns, but both were less pronounced (mean fluorescence contrast 0.08 0.01) than they were in the presence of the specific capture protein (mean fluorescence contrast 0.24 0.03, 0.001) (Figure 5D). Open in a separate window Figure 5 Specificity of prey protein copatterning. (A) Schematic illustrations of variations in the substrate-cell interface. (B) HeLa cells stably expressing Grb2-YFP were grown for at least 3C4 h on unmodified 1-m BSA grids (left) or on completely functionalized anti-EGFR antibody-coated surfaces (right). Ten minutes after EGF stimulation (170 nM), large-area surface scans were captured to deliver a representative snapshot of the Grb2-YFP distribution. Insets show enlarged areas of the overall scans. (C) Quantitation of the number of pattern-positive cells. (D) Quantitation of fluorescence contrast. Error bars are based on the mean SE of more than 300 cells. *** 0.05 and **** 0.001 for comparison of different levels of substrate functionalization. Graphical illustrations are not drawn to scale. These results indicate that comprehensive controls are necessary for the accurate quantitative analysis of the specific EGFR-Grb2 interaction. Furthermore, the presence of other receptors should be taken into consideration, particularly those reported to interact with Grb2 and are internalized via CME, such as the ephrin type-A1 receptor (EphA1) [35,36], c-Met receptor [37,38], platelet-derived growth factor receptor (PDGFR) [39,40], fibroblast Bephenium hydroxynaphthoate growth factor receptor 2 (FGFR2) [41,42], and 2-adrenergic receptors (2Ars) [43,44]. These receptors might potentially contribute to copatterning and, thus, impair the quantitative analysis of the bait-prey interaction of interest. 3.4. Towards more Reliable Live Cell Micropatterning Experiments The above-described effects are not limited to the arrangement of membrane-anchored bait and cytosolic prey molecules. In cases where both interaction partners (bait as well as prey) are membrane-bound, the likelihood of misinterpretation and detection of false-positive copatterning may be even higher since both interaction partners can be directly affected by CME. This potential problem might be of particular concern in studies of cellular signaling based on receptor heterodimerization and oligomerization and receptor transactivation studies. Due to these circumstances, a detailed control and critical analysis of the putative bait-prey interactions studied on microstructure substrates are essential. To prevent the misinterpretation and quantitation of false-positive copatterning events, the following experimental controls and suggestions should be considered. 1) From a general point of view, each bait/prey interaction pair under investigation requires independent validation with respect to the reported effects. For example, prior to experiments, preferred desensitization routes of the receptors under investigation should be elaborated and the likelihood of unspecific bait/prey co-recruitment on patterned surfaces with different substrate functionalization should be determined (e.g., as shown in Bephenium hydroxynaphthoate Figure 4). 2) The formation of internalization hotspots within the micropatterned areas should be tested. This strategy might not be limited to CME since other pathways of desensitization, such as caveolin-dependent or clathrin/caveolin-independent endocytosis, may as well have an effect on the PPIs [45]. While it could be shown that non-CME endocytic proteins, such Bephenium hydroxynaphthoate as caveolin1, are not enriched on patterned substrates [32], careful analysis through the use of control markers (e.g., fluorescent cavin fusion proteins [46], Ywhaz bulk phase markers such as Lucifer yellow [47], or specific monovalent fluorescent ligand conjugates [48]) is mandatory. 3) In the case of solely membrane-bound interaction partners, the bait and prey surface proteins should be accordingly exchanged to prove co-patterning under different bait/prey conditions. As an example of such a control experiment, we describe a thought experiment based on the putative interaction between the EGFR and MHC (major histocompatibility complex) class I molecules [49]. In the first set of experiments, the EGFR serves as bait, and the MHC class I molecule is used as the prey protein, Bephenium hydroxynaphthoate while copatterning is analyzed. Subsequently, the MHC class I molecule is used as the bait, and the EGFR serves as the prey. Again, copatterning can be analyzed, and putative differences are evaluated with respect.