4. Conclusions
With the introduction of high throughput technologies in structural and molecular biology a large number of recombinant systems are now available, allowing for parallel testing of protein:protein and protein:peptide interactions. At the same time advances in materials and chemical synthesis have allowed for parallel synthesis of peptides on a small foot-print on solid support. These advances have had a particular impact in chromatin biology, where readers of epigenetic post-translational modifications are now readily available in recombinant form, offering an opportunity to rapidly identify potential interacting linear motifs employing peptide array technologies. The use of enzymes that control the deposition of PTMs on proteins is technologically challenging and as such the reconstitution of nuclesomes in cells, decorated with specific modifications in order to study interactions is a difficult, if not impossible, task. Peptide arrays have paved the way by allowing massive parallel synthesis of peptides carrying PTMs which, in the case of histones, can be recognized by effector reader modules. Lysine acetylation has long being suggested as a potential regulatory modification [2] however the specific linear motifs carrying acetylated lysines that are recognized by reader domains of the bromodomain class have remained elusive, although many known motifs have been disclosed over the years [30]. The use of peptide array technologies has facilitated the identification of various motifs that carry acetylation and are recognized by the bromodomain class of readers as well as the effect of adjacent post translational modifications in the recognition process. Coupled with orthogonal biophysical methods, such as in-solution binding studies and structural biology, peptide arrays offer a powerful tool that can be used to rapidly cover protein space in order to establish acetylation-dependent networks of interactions shedding light into the biological significance of post translational modifications. Further advances in this technology will soon allow for proteome-wide coverage, allowing generating hypothesis for understanding larger networks of interactions governing signaling. The protocols and technology are affordable and mature enough as exemplified by the many reports employing these tools to better understand protein:protein interactions.