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  • Periodicals (Báo – Tạp chí)

  • PyXlinkViewer: a flexible tool for visualisation of protein chemical crosslinking data within the PyMOL molecular graphics system

    • Authors : Schiffrin, Bob; Radford, Sheena. E; Brockwell, David. J (2020)

  • Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yields inter-residue restraints that can be compared with high-resolution structural data. Distances greater than the crosslinker spacer-arm can reveal lowly-populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of&#...
  • Journal article

  • Lipopolysaccharide stimulation of RAW264.7 cells is a model for identifying novel clients of Hsc70

    • Authors : Rakus, John F; Ashley, Alex J; Kegley, Nicholas R (2020)

  • Heat shock cognate protein 71 kDa (Hsc70, Hspa8, Hspa10, Hsp73) is a member of the heat shock protein 70 kDa family of molecular chaperones. These chaperones function to aid the correct folding of client proteins using an ATP-dependent mechanism. Though Hsc70 is accepted to be a constitutively expressed protein, it has a well-documented function in modulating the induction of the pro-inflammatory cytokine TNFα by the LPS/TLR4 pathway. In this&#...
  • Journal article

  • In silico approach toward the identification of unique peptides from viral protein infection: Application to COVID-19

    • Authors : Orsburn, Benjamin C; Jenkins, Conor; Miller, Sierra M (2020)

  • We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity ...
  • Journal article

  • Quality control of HLA-DR molecules by the lysosomal aspartyl protease, cathepsin D

    • Authors : Shah, Nakul; McDonald, Sarah; Parker, Charles T.A (2020)

  • Major histocompatibility complex class II (MHCII) molecules display peptides on antigen-presenting cells (APCs) for inspection by CD4+ T cells. MHCII surface levels and life span are regulated post-translationally by peptide loading and ubiquitin-dependent lysosomal targeting, but proteases responsible for MHCII protein degradation remain unidentified. Here, we examined the role of aspartyl proteases in MHCII protein degradation and characterised the form of MHCII that is&#...
  • Journal article

  • S-Trap eliminates cell culture media polymeric surfactants for effective proteomic analysis of mammalian cell bioreactor supernatants

    • Authors : Zacchi, Lucia F; Recinos, Dinora Roche; Otte, Ellen (2020)

  • Proteomic analysis of bioreactor supernatants can inform on cellular metabolic status, viability, and productivity, as well as product quality, which can in turn help optimize bioreactor operation. Incubating mammalian cells in bioreactors requires the addition of polymeric surfactants such as Pluronic F68, which reduce the sheer stress caused by agitation. However, these surfactants are incompatible with mass spectrometry proteomics and must be eliminated during sampl...
  • Journal article

  • Seeking candidate molecules as prognostic healing markers in chronic venous ulcers

    • Authors : Cavassan, Nayara Rodrigues Vieira; Mariani, Noemia Aparecida Partelli; Camargo, Caio Cavassan (2020)

  • Seeking and identifying biomarker molecules in inflammatory exudate of chronic venous ulcers (CVUs) can aid health professionals in the healing prognosis. The therapeutic failure or cure is related to the quantitative expression of determinate proteins. This work aimed to identify the proteins expressed in inflammatory exudates from CVUs and correlate them with reduction or increase in the wound size. For 90 days, 28 participants that received standard t...
  • Journal article

  • A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

    • Authors : Krasny, Lukas; Bland, Philip; Burns, Jessica (2020)

  • SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method ove...
  • Journal article

  • Glycoproteomic measurement of site-specific polysialylation

    • Authors : Pelingon, Ruby; Pegg, Cassandra L; Zacchi, Lucia F (2020)

  • Polysialylation is the enzymatic addition of a highly negatively charged sialic acid polymer to the non-reducing termini of glycans. Polysialylation plays an important role in development, and is involved in neurological diseases, neural tissue regeneration, and cancer. Polysialic acid (PSA) is also a biodegradable and non-immunogenic conjugate to therapeutic drugs to improve their pharmacokinetics. PSA chains vary in length, composition, and linkages, while the specif...