A multifaceted platform for exploring nucleotide-based post-translational modifications
Nucleotide-based post-translational modifications (nbPTMs) play key roles in health and disease, from bacterial pathogenesis to cancer. However, technical challenges of these versatile, but chemically complex protein modifications have constrained our fundamental understanding of even the most intensely studied nbPTMs for decades. The overarching aim of this proposal is to establish, apply and disseminate a methodology to unveil novel types of nbPTMs and allow site-specific proteomic analyses. The conceptual innovation lies in a strategy for turning the complex chemical structures of nbPTMs from a challenge to an advantage. First, shared chemical moieties will be exploited to develop pan-specific enrichment of multiple nbPTMs. For this purpose, we will generate the first nbPTMs-specific antibodies by converting specific signalling proteins into biotechnology tools for chemoenzymatic synthesis of challenging peptide antigens (aim 1). Second, we will take advantage of the chemical lability of nbPTMs to analyse modified peptides using a nucleobase-targeted mass spectrometry approach (aim 2). The unbiased scope of our methodology will make possible the discovery of as yet unknown forms of nbPTMs (aim 3) and nbPTM site mapping throughout eukaryotic proteomes (aim 4). These new materials, methods, discoveries and datasets will be made publicly available to allow future investigations of nbPTMs by the scientific community. The new substrates, sites and nbPTMs will provide starting points for biological characterization (aim 5). Poised at the interface of biology and technology, this interdisciplinary research project has the potential to explore new territories within established biomedical fields and to contribute to the knowledge base for improved treatment of diseases.