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  • 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...
  • 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

  • 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

  • DTX3L and USP28 fine-tune DNA double strand repair through mutual regulation of their protein levels

    • Authors : Ashok, Yashwanth (2023)

  • The DNA damage response involves a complex protein network with members mediating different post-translational modifications such as ubiquitination and deubiquitination. Thereby the E3 ubiquitin ligase DTX3L as well as the deubiquitinase USP28 are recruited especially to DNA double strand breaks (DSBs) suggesting mutual functional interactions. Here we present evidence for the existence of such crosstalk. Mechanistically we show that DTX3L interacts with USP28 and ubiq...
  • Journal article

  • Tannic Acid Inhibits α-Synuclein Amyloid Fibril Formation via Binding to the Monomer N-terminal Domain

    • Authors : Stoeber, Jonathan (2021)

  • α-Synuclein (αS) is an intrinsically disordered protein (IDP) that aggregates into amyloid fibrils during the progression of Parkinson’s Disease and other synucleinopathies. The N-terminal domain (residues 1-60) is now understood to play a critical role in the initial nucleation of aggregation, as well as a pivotal role in the monomer-fibril interaction underlying amyloid seeding. Here we report on the interaction between αS and&#x...
  • Journal article

  • Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity

    • Authors : Park, Sang Ho (2021)

  • SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects ...