Development of Dimethylsulfonium Probes for Broad Profiling of Methyllysine Reader Proteins

Development of oligoglycine‐based dimethylsulfonium probes for unbiased crosslinking to methyllysine readers. The general probe facilitates profiling of site‐specific methyllysine readers, evaluation of selectivity and activity of reader inhibitors, and global profiling of methyllysine readers. This strategy provides a versatile tool for the investigation of methyllysine readers. Abstract Lysine methylation is a crucial post‐translational modification regulating various cellular processes. Reader proteins recognize specific methylated proteins as key mediators for the biological function of lysine methylation. Due to a correlation between reader activity and cell signaling of disorders, readers serve as attractive therapeutic targets. Despite proteomic advances identifying thousands of methylation sites, far fewer methyllysine readers have been characterized. Current research relies exclusively on site‐specific probes, which are restricted to individual sites but incapable of global profiling. Here, an oligoglycine‐based dimethylsulfonium peptide is reported as a general probe that is capable of binding and crosslinking to readers without bias toward particular sites or domains. The general reactivity to methyllysine readers in vitro is first demonstrated. The probe to cell nuclei is next applied, and the general probe enables identification of site‐specific readers by methyllysine peptide competition. In addition, the probe shows the potential for assessment of reader inhibitor activity and selectivity. Furthermore, bioinformatic analysis is performed to predict potential readers in the human genome, and global profiling of the potential readers in the nuclear proteome was achieved using the general probe. Thus, such a sulfonium probe provides a novel tool for global reader profiling, complementing the site‐specific probes. Development of oligoglycine-based dimethylsulfonium probes for unbiased crosslinking to methyllysine readers. The general probe facilitates profiling of site-specific methyllysine readers, evaluation of selectivity and activity of reader inhibitors, and global profiling of methyllysine readers. This strategy provides a versatile tool for the investigation of methyllysine readers. Abstract Lysine methylation is a crucial post-translational modification regulating various cellular processes. Reader proteins recognize specific methylated proteins as key mediators for the biological function of lysine methylation. Due to a correlation between reader activity and cell signaling of disorders, readers serve as attractive therapeutic targets. Despite proteomic advances identifying thousands of methylation sites, far fewer methyllysine readers have been characterized. Current research relies exclusively on site-specific probes, which are restricted to individual sites but incapable of global profiling. Here, an oligoglycine-based dimethylsulfonium peptide is reported as a general probe that is capable of binding and crosslinking to readers without bias toward particular sites or domains. The general reactivity to methyllysine readers in vitro is first demonstrated. The probe to cell nuclei is next applied, and the general probe enables identification of site-specific readers by methyllysine peptide competition. In addition, the probe shows the potential for assessment of reader inhibitor activity and selectivity. Furthermore, bioinformatic analysis is performed to predict potential readers in the human genome, and global profiling of the potential readers in the nuclear proteome was achieved using the general probe. Thus, such a sulfonium probe provides a novel tool for global reader profiling, complementing the site-specific probes. Advanced Science, EarlyView.