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Targeted proteomics has been playing an increasingly important role in hypothesis-driven protein research and clinical biomarker discovery. We previously created a workflow, Tomahto, to enable real-time targeted pathway proteomics assays using two-dimensional multiplexing technology. Coupled with the TMT 11-plex reagent, hundreds of proteins of interest from up to 11 samples can be targeted and accurately quantified in a single-shot experiment with remarkable sensitivity. However, room remains to further improve the sensitivity, accuracy, and throughput, especially for targeted studies demanding a high peptide-level success rate. Here, bearing in mind the goal to improve peptide-level targeting, we introduce several new functionalities in Tomahto, featuring the integration of gas-phase fractionation using the FAIMS device, an accompanying software program (TomahtoPrimer) to customize fragmentation for each peptide target, and support for higher multiplexing capacity with the latest TMTpro reagent. We demonstrate that adding these features to the Tomahto platform significantly improves overall success rate from 89% to 98% in a single 60 min targeted assay of 290 peptides across human cell lines, while boosting quantitative accuracy via reducing TMT reporter ion interference. [ABSTRACT FROM AUTHOR]

Author(s): L. Robert Hollingsworth [sup.1] [sup.2] [sup.3] , Humayun Sharif [sup.1] [sup.2] , Andrew R. Griswold [sup.4] [sup.5] , Pietro Fontana [sup.1] [sup.2] , Julian Mintseris [sup.6] , Kevin B. [...], Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 1 (NLRP1) is an inflammasome sensor that mediates the activation of caspase-1 to induce cytokine maturation and pyroptosis.sup.1-4. Gain-of-function mutations of NLRP1 cause severe inflammatory diseases of the skin.sup.4-6. NLRP1 contains a function-to-find domain that auto-proteolyses into noncovalently associated subdomains.sup.7-9, and proteasomal degradation of the repressive N-terminal fragment of NLRP1 releases its inflammatory C-terminal fragment (NLRP1 CT).sup.10,11. Cytosolic dipeptidyl peptidases 8 and 9 (hereafter, DPP8/DPP9) both interact with NLRP1, and small-molecule inhibitors of DPP8/DPP9 activate NLRP1 by mechanisms that are currently unclear.sup.10,12-14. Here we report cryo-electron microscopy structures of the human NLRP1-DPP9 complex alone and with Val-boroPro (VbP), an inhibitor of DPP8/DPP9. The structures reveal a ternary complex that comprises DPP9, full-length NLRP1 and the NLRPT CT. The binding of the NLRP1 CT to DPP9 requires full-length NLRP1, which suggests that NLRP1 activation is regulated by the ratio of NLRP1 CT to full-length NLRP1. Activation of the inflammasome by ectopic expression of the NLRP1 CT is consistently rescued by co-expression of autoproteolysis-deficient full-length NLRP1. The N terminus of the NLRP1 CT inserts into the DPP9 active site, and VbP disrupts this interaction. Thus, VbP weakens the NLRP1-DPP9 interaction and accelerates degradation of the N-terminal fragment.sup.10 to induce inflammasome activation. Overall, these data demonstrate that DPP9 quenches low levels of NLRP1 CT and thus serves as a checkpoint for activation of the NLRP1 inflammasome. Structures of NLRP1-DPP9 alone and with a small-molecule inhibitor of DPP9 reveal the mechanisms through which NLRP1 is regulated, providing insights into the role of this complex in inflammasome regulation.

Brown and beige adipocytes are specialized cells that express uncoupling protein 1 (UCP1) and dissipate chemical energy as heat. These cells likely possess alternative UCP1-independent thermogenic mechanisms. Here, we identify a secreted enzyme, peptidase M20 domain containing 1 (PM20D1), that is enriched in UCP1(+) versus UCP1(-) adipocytes. We demonstrate that PM20D1 is a bidirectional enzyme in vitro, catalyzing both the condensation of fatty acids and amino acids to generate N-acyl amino acids and also the reverse hydrolytic reaction. N-acyl amino acids directly bind mitochondria and function as endogenous uncouplers of UCP1-independent respiration. Mice with increased circulating PM20D1 have augmented respiration and increased N-acyl amino acids in blood. Lastly, administration of N-acyl amino acids to mice improves glucose homeostasis and increases energy expenditure. These data identify an enzymatic node and a family of metabolites that regulate energy homeostasis. This pathway might be useful for treating obesity and associated disorders.

Different ligands stabilize specific conformations of the angiotensin II type 1 receptor (AT1R) that direct distinct signaling cascades mediated by heterotrimeric G proteins or β-arrestin. These different active conformations are thought to engage distinct intracellular transducers because of differential phosphorylation patterns in the receptor C-terminal tail (the "barcode" hypothesis). Here, we identified the AT1R barcodes for the endogenous agonist AngII, which stimulates both G protein activation and β-arrestin recruitment, and for a synthetic biased agonist that only stimulates β-arrestin recruitment. The endogenous and β-arrestin–biased agonists induced two different ensembles of phosphorylation sites along the C-terminal tail. The phosphorylation of eight serine and threonine residues in the proximal and middle portions of the tail was required for full β-arrestin functionality, whereas phosphorylation of the serine and threonine residues in the distal portion of the tail had little influence on β-arrestin function. Similarly, molecular dynamics simulations showed that the proximal and middle clusters of phosphorylated residues were critical for stable β-arrestin–receptor interactions. These findings demonstrate that ligands that stabilize different receptor conformations induce different phosphorylation clusters in the C-terminal tail as barcodes to evoke distinct receptor-transducer engagement, receptor trafficking, and signaling. Editor's summary: The specific patterns of phosphorylation in the intracellular tail of a G protein–coupled receptor (GPCR) are thought to act as a barcode that determines whether G proteins are stimulated or β-arrestins are recruited. Gareri et al. investigated the role of phosphorylation barcodes in signaling by the angiotensin II type 1 receptor (AT1R). AT1R elicits both G protein activation and β-arrestin recruitment in response to the endogenous agonist AngII but stimulates only β-arrestin recruitment in response to a synthetic biased agonist. The authors identified patterns of serine and threonine phosphorylation that stabilized specific conformations of β-arrestin and were necessary for β-arrestin function. These findings demonstrate the importance of phosphorylation barcodes in determining the consequences of AT1R activation. —Annalisa M. VanHook [ABSTRACT FROM AUTHOR]

Introduction Type 1 (T1D) and type 2 (T2D) diabetes together afflict 463 million people globally (1). While T1D results from autoimmune destruction of pancreatic insulin-producing [beta] cells, and T2D is [...], Resistance to regeneration of insulin-producing pancreatic [beta] cells is a fundamental challenge for type 1 and type 2 diabetes. Recently, small molecule inhibitors of the kinase DYRK1A have proven effective in inducing adult human [beta] cells to proliferate, but their detailed mechanism of action is incompletely understood. We interrogated our human insulinoma and [beta] cell transcriptomic databases seeking to understand why [beta] cells in insulinomas proliferate, while normal [beta] cells do not. This search reveals the DREAM complex as a central regulator of quiescence in human [beta] cells. The DREAM complex consists of a module of transcriptionally repressive proteins that assemble in response to DYRK1A kinase activity, thereby inducing and maintaining cellular quiescence. In the absence of DYRK1A, DREAM subunits reassemble into the pro-proliferative MMB complex. Here, we demonstrate that small molecule DYRK1A inhibitors induce human [beta] cells to replicate by converting the repressive DREAM complex to its pro-proliferative MMB conformation.