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  • Journal article

  • Screening of candidate host cell membrane proteins involved in SARS-CoV-2 entry

    • Authors : Kotani, Norihiro (2023)

  • Coronavirus disease (COVID-19) represents a real threat to the global population, and understanding the biological features of the causative virus, i.e., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is imperative for mitigating this threat. Analyses of proteins such as primary receptors and co-receptors (co-factors), which are involved in the entry of SARSCoV- 2 into host cells, will provide important clues to help control the virus. Here,&#...
  • Journal article

  • Protein-Peptide Turnover Profiling reveals wiring of phosphorylation during protein maturation

    • Authors : Hammarén, Henrik M. (2023)

  • Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods that rely on pulsed metabolic labeling are very popular to quantify turnover rates on a proteome-wide scale. Such data have often been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture&...
  • Journal article

  • AMPylation is a specific lysosomal protein posttranslational modification in neuronal maturation

    • Authors :  Becker, Tobias (2021)

  • Protein AMPylation is a pervasive posttranslational modification with an emerging role in neurodevelopment. In metazoans the two highly conserved protein AMP-transferases together with a diverse group of AMPylated proteins have been identified using chemical proteomics and biochemical techniques. However, the function of this modification remains largely unknown. Particularly problematic is the localization of thus far identified AMPylated proteins and putative&#x...
  • Journal article

  • HaloTag9: an engineered protein tag to improve fluorophore performance

    • Authors : Frei, Michelle S. (2021)

  • HaloTag9 is an engineered variant of HaloTag7 with up to 40% higher brightness and increased fluorescence lifetime when labeled with fluorogenic rhodamines. Moreover, combining HaloTag9 with HaloTag7 and other fluorescent probes enabled live-cell multiplexing using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. The increased brightness of HaloTag9 and its use in fluorescence lifetime multiplexing makes it a...
  • Journal article

  • Comparative host interactomes of the SARS-CoV-2 nonstructural protein 3 and human coronavirus homologs

    • Authors : Almasy, Katherine M. (2021)

  • Human coronaviruses have become an increasing threat to global health; three highly pathogenic strains have emerged since the early 2000s, including most recently SARS-CoV-2, the cause of COVID-19. A better understanding of the molecular mechanisms of coronavirus pathogenesis is needed, including how these highly virulent strains differ from those that cause milder, common-cold like disease. While significant progress has been made in understanding how SARS-CoV-2 ...
  • Journal article

  • CheSPI: Chemical shift Secondary structure Population Inference

    • Authors : Nielsen, Jakob Toudahl (2021)

  • NMR chemical shifts (CSs) are delicate reporters of local protein structure, and recent advances in random coil CS (RCCS) prediction and interpretation now offer the compelling prospect of inferring small populations of structure from small deviations from RCCSs. Here, we present CheSPI, a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder. It is demonstrated that CheSPI can p...