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  • Journal article

  • Sulfotyrosine, an interaction specificity determinant for extracellular protein-protein interactions

    • Authors : Stewart, Valley (2023)

  • Tyrosine sulfation, a post-translational modification, can enhance and often determine protein-protein interaction specificity. Sulfotyrosyl residues (sTyr) are formed by tyrosylprotein sulfotransferase during maturation in the golgi apparatus, and most often occur singly or as a cluster of two or three sTyr within a six-residue span. With both negative charge and aromatic character, sTyr enables numerous atomic contacts as visualized in binding interfac...
  • Journal article

  • System-wide profiling by proteome integral solubility alteration assay of drug residence times for target characterization

    • Authors : Sabatier, Pierre (2023)

  • Most drugs used in the clinic and drug candidates target multiple proteins, and thus detailed characterization of their efficacy targets is required. While current methods rely on quantitative measurements at thermodynamic equilibrium, kinetic parameters such as the residence time of a drug on its target provide a better proxy for efficacy in vivo. Here, we present Residence Time Proteome Integral Solubility Alteration (ResT-PISA) assay which provides monitor...
  • Journal article

  • The amino acid composition of a protein influences its expression

    • Authors : Thompson, Reece (2023)

  • The quantity of each protein in a cell only is only partially correlated with its gene transcription rate. Independent influences on protein synthesis levels include mRNA sequence motifs, amino acyl-tRNA synthesis levels, elongation factor action, and protein susceptibility to degradation. Here we report two novel forms of interaction between the amino acid composition of a protein and its expression level. In animals, the differing origin...
  • Journal article

  • Computational design of Matrix Metalloprotenaise-9 (MMP-9) resistant to auto-cleavage

    • Authors :  Bonadio, Alessandro (2023)

  • Matrix metalloproteinase-9 (MMP-9) is an endopeptidase that remodels the extracellular matrix and has been implicated as a major driver in cancer metastasis. Hence, there is a high demand for MMP-9 inhibitors for therapeutic purposes. For such drug design efforts, large amounts of MMP-9 are required. Yet, the catalytic domain of MMP-9 (MMP-9Cat) is an intrinsically unstable enzyme that tends to auto-cleave within minutes, making it di...
  • 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

  • The most probable ancestral sequence reconstruction yields proteins without systematic bias in thermal stability or activity

    • Authors : Sennett, Michael A. (2023)

  • Ancestral sequence resurrection (ASR) is the inference of extinct biological sequences from extant sequences, the most popular of which are based on probabilistic models of evolution. ASR is becoming a popular method for studying the evolution of enzyme characteristics. The properties of ancestral enzymes are biochemically and biophysically characterized to gain some knowledge regarding the origin of some enzyme property. Current methodology relies on resurrection ...
  • 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...
  • Journal article

  • Filter paper disks as a matrix for manipulation of recombinant proteins

    • Authors : Ball, Eric H. (2023)

  • AbstractF ilter paper provides an excellent matrix for retention of proteins containing a cellulose binding domain. To use this capability for manipulating recombinant fusion proteins, binding and elution parameters were explored and procedures developed for small scale purification, modification and assay. Proteins were tagged with the cellulose binding domain from the C thermocellum CipB gene via a cleavable linker. Filter paper disks of 6mm&...
  • Journal article

  • Three-dimensional envelope and subunit interactions of the plastid-encoded RNA polymerase from Sinapis alba

    • Authors : Ruedas, Rémi (2023)

  • RNA polymerases (RNAPs) involved in gene transcription are found in all living organisms with degrees of complexity ranging from single polypeptide chains to multimeric enzymes. In the chloroplasts, the nuclear-encoded RNA polymerase and the plastid-encoded RNA polymerase (PEP) are both involved in the selective transcription of the plastid genome. The PEP is a prokaryotic-type multimeric RNAP found in different states depending on light stimuli ...