Integrated mass spectrometry strategies to decipher metabolite-protein cross regulation

About This Grant

Integrated mass spectrometry strategies to decipher protein-metabolite cross regulation Cellular metabolism relies on protein enzymes to convert substrates to products, working in interconnected networks to generate important biological precursors, remove toxic waste, balance redox and defend energy potential. However, the study of metabolic regulation in both healthy and disease states has proven challenging in part due to the intricate cross-regulation between metabolites and proteins. Current strategies to characterize metabolic regulation have generally focused on characterizing metabolites or protein enzymes, but not both. Consequently, how metabolites and proteins interact in the cellular context remains an open question in the field of metabolism and cellular biology. To bridge this gap, the Skinner lab is focused on characterizing the interactions between metabolites and proteins in the cellular context by using mass spectrometry to integrate existing multi-tiered methods in addition to developing new techniques to enhance the characterization and scope of both protein and metabolite measurements. Our primary research focus is on the regulation of proteins and metabolism by redox cofactors through signaling of sulfur-containing metabolites (Area 1) and the effect of vitamin B6 on metabolic and redox regulation as it is converted to protein cofactor pyridoxal-5-phosphate (PLP) (Area 2). These two areas each represent critical intersections of metabolome and proteome that play a key role across a variety of disease states. To better understand these two ranges of metabolite and protein cross-regulation, we will apply top-down proteomics and native mass spectrometry analyses of intact protein complexes coupled with full-scan and stable isotope labeling metabolomics to simultaneously probe metabolites and proteins. In Area 1, we will characterize how the abundance and redox state of specific thiol metabolites and cellular nicotinamide adenine dinucleotide phosphate (NADP+) redox state can modulate glycolysis and other core metabolic pathways Protein thiols have been demonstrated to be covalently modified at high stoichiometry with a variety of different groups, making this a likely axis for metabolic regulation. In Area 2, we will examine another key intersection between metabolite and protein regulation; the metabolism of vitamin B6 to its active form PLP prior to acting as a cofactor for 53 human enzymes. Specifically, we will characterize how some PLP-containing enzymes seem more resistant to extended B6 deficiency than others and how changes in subcellular nicotinamide adenine dinucleotide (NAD+) redox state can affect PLP levels and vice versa. This project integrates metabolomics with native mass spectrometry and proteomics and applies it to two pressing questions in the field of systems biology and regulation that lie at the intersection of metabolome and proteome.