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1.
  • 2019
  • Tidskriftsartikel (refereegranskat)
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2.
  • Fossati, Andrea, et al. (författare)
  • PCprophet : a framework for protein complex prediction and differential analysis using proteomic data
  • 2021
  • Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18:5, s. 520-527
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. Approaches based on biochemical fractionation of intact, native complexes and correlation of protein profiles have shown promise. However, most approaches for interpreting cofractionation datasets to yield complex composition and rearrangements between samples depend considerably on protein–protein interaction inference. We introduce PCprophet, a toolkit built on size exclusion chromatography–sequential window acquisition of all theoretical mass spectrometry (SEC-SWATH-MS) data to predict protein complexes and characterize their changes across experimental conditions. We demonstrate improved performance of PCprophet over state-of-the-art approaches and introduce a Bayesian approach to analyze altered protein–protein interactions across conditions. We provide both command-line and graphical interfaces to support the application of PCprophet to any cofractionation MS dataset, independent of separation or quantitative liquid chromatography–MS workflow, for the detection and quantitative tracking of protein complexes and their physiological dynamics.
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3.
  • Greening, Chris, et al. (författare)
  • Minimal and hybrid hydrogenases are active from archaea
  • Ingår i: Cell. - 1097-4172. ; 187
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbial hydrogen (H 2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H 2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H 2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H 2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H 2-metabolizing enzymes.
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  • Resultat 1-3 av 3

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