Altered central carbon metabolism is a hallmark of many diseases including diabetes, obesity, heart disease and cancer. Identifying metabolic changes will open opportunities for better understanding aetiological processes and identifying new diagnostic, prognostic, and therapeutic targets. Comprehensive and robust analysis of primary metabolic pathways in cells, tissues and bio-fluids, remains technically challenging. We report on the development and validation of a highly reproducible and robust untargeted method using anion-exchange tandem mass spectrometry (IC-MS) that enables analysis of 431 metabolites, providing detailed coverage of central carbon metabolism. We apply the method in an untargeted, discovery-driven workflow to investigate the metabolic effects of isocitrate dehydrogenase 1 (IDH1) mutations in glioblastoma cells. IC-MS provides comprehensive coverage of central metabolic pathways revealing significant elevation of 2-hydroxyglutarate and depletion of 2-oxoglutarate. Further analysis of the data reveals depletion in additional metabolites including previously unrecognised changes in lysine and tryptophan metabolism.
Poly(ADP-ribosyl)ation (PAR) is a versatile and complex posttranslational modification composed of repeating units of ADP-ribose arranged into linear or branched polymers. This scaffold is linked to the regulation of many of cellular processes including the DNA damage response, alteration of chromatin structure and Wnt signalling. Despite decades of research, the principles and mechanisms underlying all steps of PAR removal remain actively studied. In this work, we synthesise well-defined PAR branch point molecules and demonstrate that PARG, but not ARH3, can resolve this distinct PAR architecture. Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages. We find that ARH3-dependent hydrolysis requires both rearrangement of a catalytic glutamate and induction of an unusual, square-pyramidal magnesium coordination geometry.
has made ap rovisionalp atent application based on the discoveries demonstrated in this manuscript.Keywords: antiviral agents · nucleotide analogues · radical-SAM enzyme · tyrosyl radicals · viperin Figure 6. The proposed mechanism of catalysis by TtRSAD2. The 5'-dAdo radicalabstractst he Ha tom (red) at the C4' position of ribose to generate a C4'-centred radical intermediate. As ar esult of hyperconjugation between a po rbitalonC 4' and the s C3'ÀO3' orbital, assisted by ap rotein amino acid residue( AH), the 3'-OHg roupo ft he riboseforms awater molecule. The proton to generate the water molecule is provided by tyrosine either indirectly through ap roton hoppingp athway(1) or directly (2). Spontaneously, an electron from tyrosine reduces the substrate-radical intermediate. As a result, the nucleotide analogue product and ap rotein tyrosylradical are formed. The [4 FeÀ4S] 2 + clusteri sre-reduced and then,t he tyrosyl radicali s reducedbya ne lectron from the [4 FeÀ4S] + cluster.
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