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Showing results 1 to 20 of 87
  • OER000002975.pdf.jpg
  • Journal article

  • A biosensor to gauge protein homeostasis resilience differences in the nucleus compared to cytosol of mammalian cells

    • Authors : Raeburn, Candice B. (2021)

  • An extensive network of chaperones and other proteins maintain protein homeostasis and guard against inappropriate protein aggregation that is a hallmark of neurodegenerative diseases. Using a fluorescence resonance energy-based biosensor that simultaneously reports on intact cellular chaperone holdase activity and detrimental aggregation propensity, we investigated the buffering capacity of the systems managing protein homeostasis in the nucleus of the human cell l...
  • OER000002618.pdf.jpg
  • Journal article

  • A conformational-dependent interdomain redox relay at the core of Protein Disulfide Isomerase activity

    • Authors : Melo, Eduardo P. (2023)

  • Protein disulfide isomerases (PDIs) are a family of molecular chaperones resident in the endoplasmic reticulum (ER) emerging as important factors in disease. In addition to an holdase function, some members catalyse disulfide bond formation and isomerization, a crucial step for native folding and prevention of aggregation of misfolded proteins. PDIs are characterized by a modular arrangement of thioredoxin-like domains, with the canonical, first identified PDIA1, ...
  • OER000002680.pdf.jpg
  • Journal article

  • A database of accurate electrophoretic migration patterns for human proteins in cell lines

    • Authors : Mylonas, Roman (2023)

  • Native molecular weight (MW) is one of the defining features of proteins. Denaturing gel electrophoresis (SDS-PAGE) is a very popular technique for separating proteins and determining their MW. Coupled with antibody-based detection, SDS-PAGE is widely applied for protein identification and quantitation. Yet, electrophoresis is poorly reproducible and the MWs obtained are often inaccurate. This hampers antibody validation and negatively impacts the reliability of western...
  • OER000002319.pdf.jpg
  • Journal Article

  • A global, integrated view of the ubiquitylation site occupancy and dynamics

    • Authors : Prus, Gabriela (2023)

  • Ubiquitylation regulates virtually all proteins and biological processes in a cell. However, the global site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have never been quantified. Here, we present the first integrated picture of ubiquitylation site occupancy and half-life. Ubiquitylation occupancy spans four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of 20...
  • OER000000280.pdf.jpg
  • Periodicals (Báo – Tạp chí)

  • A survey of pairwise epistasis supports an outside-in hierarchy of clade-specifying and function-defining residues in PSD95 PDZ3

    • Authors : Nedrud, David; Maestas, Willow Coyote; Schmidt, Daniel (2020)

  • Deep mutational scanning enables data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering as an economical and programmable deep mutational scanning technique. We validate this approach with an existing single mutant dataset in the PSD95 PDZ3 domain, and further characterize most pairwise double mutants to study how a mutation’s phenotype depends on mutations at other sites, a phenomenon called epistasis. ...
  • OER000002390.pdf.jpg
  • Journal Article

  • A widespread proteinaceous sulfur storage compartment in bacteria

    • Authors : Benisch, Robert (2023)

  • Intracellular compartmentalization is essential for all cells and enables the regulation and optimization of metabolism1. One of the main functions of subcellular compartments is the storage of nutrients2-4. As bacteria do generally not possess membrane-bound organelles, they often have to rely on functionally analogous protein-based compartments2,5-7. Encapsulin nanocompartments are one of the most prevalent protein-based compartmentalization strategies found in prokaryotes5,8. Here ...
  • OER000002609.pdf.jpg
  • Journal article

  • Ambient temperature crystal structure of Escherichia coli CyaY protein displays alternate conformation

    • Authors : Shafiei, Alaleh (2023)

  • Frataxin is a 23 KDa mitochondrial iron-binding protein that is involved in biogenesis of iron sulfur clusters. A deficiency in frataxin leads to Friedreich's ataxia, a progressive neurodegenerative disorder. The bacterial ortholog of eukaryotic mitochondrial frataxin, CyaY, is thought to play a role in iron sulfur cluster assembly as an iron supplier, making it an important target for study. Here, we present the first ambient tem...
  • OER000002591.pdf.jpg
  • Journal article

  • Ambient temperature crystal structure of Escherichia coli CyaY protein displays alternate conformation

    • Authors : Shafiei, Alaleh (2023)

  • Frataxin is a 23 KDa mitochondrial iron-binding protein that is involved in biogenesis of iron sulfur clusters. A deficiency in frataxin leads to Friedreich's ataxia, a progressive neurodegenerative disorder. The bacterial ortholog of eukaryotic mitochondrial frataxin, CyaY, is thought to play a role in iron sulfur cluster assembly as an iron supplier, making it an important target for study. Here, we present the first ambient tem...
  • OER000003037.pdf.jpg
  • 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...
  • OER000002549.pdf.jpg
  • Industry article

  • Anti-CRISPR protein mediated degradation of Cas9 in human cells

    • Authors : Tacca, Luisa Arake de (2023)

  • Bacteriophages encode anti-CRISPR (Acr) proteins that inactivate CRISPR-Cas bacterial8 immune systems, allowing successful invasion, replication, and prophage integration. Acr9 proteins inhibit CRISPR-Cas systems using a wide variety of mechanisms. AcrIIA1 is encoded by10 numerous phages and plasmids, binds specifically to the Cas9 HNH domain, and was the first11 Acr discovered to inhibit SpyCas9. Here we report the observation of AcrIIA1-induced degradation12 ...
  • OER000002542.pdf.jpg
  • Industry article

  • Bi-functional particles for real-time acidification and proteolysis multiplex assay in macrophages

    • Authors : Alejandre, Alba Méndez (2023)

  • Phagosome acidification and proteolysis are essential processes in the immune response to contain and eliminate pathogens. In recent years, there has been an increased desire for a rapid and accurate method of assessing these processes in real-time. Here, we outline the development of a multiplexed assay that allows simultaneous monitoring of phagosome acidification and proteolysis in the same sample using silica beads conjugated to pHrodo...
  • OER000002953.pdf.jpg
  • Journal article

  • Binding mechanism underlying FIH-1 suppression caused by the N-terminal disordered region of Mint3

    • Authors : Ten, Tensho (2021)

  • Mint3 is known to enhance aerobic ATP production, known as the Warburg effect, by binding to FIH-1. Since this effect is considered to be beneficial for cancer cells, the interaction is a promising target for cancer therapy. However, previous research has suggested that the interacting region of Mint3 with FIH-1 is intrinsically disordered, which makes investigation of this interaction challenging. Therefore, we adopted a physicochemical approach that co...
  • OER000002396.pdf.jpg
  • Journal Article

  • Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research

    • Authors : Reddy, Panga Jaipal. (2023)

  • Lyme disease , caused by an infection with the spirochete Borrelia burgdorferi, is the most common 36 vector-borne disease in North America. B. burgdorferi strains harbor extensive genomic and 37 proteomic variability and further comparison is key to understanding the spirochetes infectivity and 38 biological impacts of identified sequence variants. To achieve this goal, both transcript and mass 39 spectrometry (MS)-based proteomics was applied to assemble pe...
  • OER000002663.pdf.jpg
  • Journal article

  • Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha-Tubulins in Human Cells

    • Authors : Makarov, Dmytro  (2023)

  • Tubulin detyrosination-tyrosination cycle regulates the stability of microtubules. Thus far described on α-tubulins, the tyrosination level is maintained by a single tubulin-tyrosine ligase (TTL). However, the precise dynamics and tubulin isoforms which undergo (de)tyrosination in neurons are unknown. Here, we exploit the substrate promiscuity of the TTL to introduce an O-propargyl-L-tyrosine in neuroblastoma cells and neurons. Mass spectrometry-based chemical proteomics in neuroblas...