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  • 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. ...
  • 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...
  • Journal article

  • Identification and characterization of novel plasma proteins in drug resistant HIV/AIDS patients by SWATH-MS

    • Authors : Barik, Sushanta Kumar (2021)

  • Acquired immunodeficiency syndrome is one of the most important diseases caused by human immunodeficiency virus. Understanding its molecular pathogenesis is essential to manage the disease at the population level. In this study, a quantitative analysis of plasma proteins was carried out in drug resistant and drug respondent patients using the SWATH-MS. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) is a prime technique to seek...
  • 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

  • Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

    • Authors : Sahil, Mohammad (2023)

  • Bacterial transcription initiation mainly occurs via two diverse RNA polymerases, namely 70 and 54. While 70 polymerase transcribes housekeeping genes and does not require any external activation to form transcriptionally competent open complex, the alternate polymerase 54 require regulatory proteins, typically AAA+ ATPases, that aid in converting the closed RNA polymerase complex to an active open state.1,2 External stimuli and enviro...
  • Journal Article

  • Exploring the Theoretical Propensity for Liquid-Liquid Phase Separation in the Organization of Golgi Matrix Proteins

    • Authors : Mendes, Luis Felipe S.; Costa-Filho, Antonio J. (2023)

  • Eukaryotic cells evolved to possess efficient secretory machinery capable of transporting a significant fraction of their proteome. The number of proteins predicted to enter the secretory pathway can reach up to 36% of the total proteome in humans (1). Proteins entering the secretory pathway are efficiently sorted to a specific destination: the extracellular space, the plasma membrane, or the interior of the endomembrane system. The machinery also has&#x...
  • Journal Article

  • Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase

    • Authors : Cordoba, John J (2023)

  • In eukaryotes, DNA polymerase α-primase (pol-prim) initiates DNA synthesis during replication, generating the first ~30 nucleotides of nascent strands.1–5 Pol-prim is unique among replicative polymerases in its ability to perform de novo synthesis from a single-stranded DNA template; the primers it creates are required for further synthesis by the processive polymerases ε and δ that perform the bulk of nascent strand synthesis6,7. Pol-prim plays a particularly...