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Showing results 39 to 58 of 87
  • OER000003033.pdf.jpg
  • 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...
  • OER000002456.pdf.jpg
  • Journal Article

  • Identification of the bacteriophage nucleus protein interaction network

    • Authors : Enustun, Eray (2023)

  • In the arms race between bacteria and bacteriophages (phages), some large-genome jumbo phages have evolved a protein shell that encloses their replicating genome to protect it against DNA-targeting immune factors. By segregating the genome from the host cytoplasm, however, the “phage nucleus” introduces the need to specifically transport mRNA and proteins through the nuclear shell, and to dock capsids on the shell for genome packaging. �...
  • OER000002332.pdf.jpg
  • 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...
  • OER000002731.pdf.jpg
  • Journal article

  • In-silico identification of Tyr232 in AMPKα2 as a dephosphorylation site for the protein tyrosine phosphatase PTP-PEST

    • Authors : Manikandan, Amrutha (2023)

  • The AMP-activated protein kinase (AMPK) is known to be activated by the protein tyrosine phosphatase non-receptor type 12 (PTP-PEST) under hypoxic conditions. This activation is mediated by tyrosine dephosphorylation of the AMPKα subunit. However, the identity of the phosphotyrosine residues remains unknown. In this study we first predicted the structure of the complex of the AMPKα2 subunit and PTP-PEST catalytic domain using bioinformatics too...
  • OER000003006.pdf.jpg
  • Journal article

  • Influence of the TorD signal peptide chaperone on Tat-dependent protein translocation

    • Authors : Bageshwar, Umesh K. (2021)

  • The twin-arginine translocation (Tat) pathway transports folded proteins across energetic membranes. Numerous Tat substrates contain co-factors that are inserted before transport with the assistance of redox enzyme maturation proteins (REMPs), which bind to the signal peptide of precursor proteins. How signal peptides are transferred from a REMP to a binding site on the Tat receptor complex remains unknown. Since the signal peptide mediates both ...
  • OER000002987.pdf.jpg
  • 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 ...
  • OER000002405.pdf.jpg
  • Journal Article

  • Label-free quantification LC-mass spectrometry proteomic analysis of blood plasma in healthy dogs

    • Authors : Doulidis, Pavlos G. (2023)

  • Bloodwork is a widely used diagnostic tool in veterinary medicine, as diagnosis and therapeutic 15 interventions often rely on blood biomarkers. However, biomarkers available in veterinary medicine 16 often lack sensitivity or specificity. Mass spectrometry (MS)-based proteomics technology has been 17 extensively used in biological fluids and offers excellent potential for a more comprehensive 18 characterization of the plasma proteome in veterinary medicine. In this&#...
  • OER000002480.pdf.jpg
  • Journal Article

  • Label-free Quantification of Host-Cell Protein Impurity in a Recombinant Hemoglobin Reference Material

    • Authors : Henrion, André (2023)

  • Quantitative analysis depends on pure-substance primary calibrators with known mass fractions of impurity. Here, label-free quantification (LFQ) is being evaluated as a readily available, reliable method for determining the mass fraction of host-cell proteins (HCPs) in bioengineered proteins. For example, hemoglobin-A2 (HbA2) is being used as obtained through overexpression in E.coli. Two different materials had been produced: natural, and U-15N-labeled HbA2. For quantification&...
  • OER000002611.pdf.jpg
  • Journal article

  • Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins

    • Authors : Cannon, Kevin S. (2023)

  • processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported highresolution stru...
  • OER000002555.pdf.jpg
  • Journal article

  • Phase Separation and Ageing of Glycine-Rich Protein from Tick Adhesive

    • Authors : Ganar, Ketan A. (2023)

  • Hard ticks feed on their host for multiple days. To ensure firm attachment, they secrete a protein-rich saliva that eventually forms a solid cement cone. The underlying mechanism of this liquid-to-solid transition is not yet understood. This study focuses on the phase transitions of a disordered glycine- rich protein (GRP) that is prominent in tick saliva. We show that GRP undergoes liquid-liquid phase separation via simple coacervatio...
  • OER000002746.pdf.jpg
  • Journal article

  • Phenotyping technology for assessing protein content in seaweed by field spectroscopy and a machine learning algorithm

    • Authors : Shalev, Niva Tadmor (2023)

  • Determining seaweed protein concentration and the associated phenotype is critical for food industries that require precise tools to moderate concentration fluctuations and attenuate risks. Algal protein extraction and profiling have been widely investigated, but content determination involves a costly, time-consuming, and high-energy, laboratory-based fractionation technique. The present study examines the potential of field spectroscopy technology as a precise, high-...
  • OER000002749.pdf.jpg
  • Journal article

  • Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

    • Authors : Gegner, Hagen M. (2023)

  • Metabolomic and proteomic analyses of human plasma and serum samples harbour the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implement a unified proteomic and...
  • OER000002283.pdf.jpg
  • Journal Article

  • Protein Ensemble Generation through Variational Autoencoder Latent Space Sampling

    • Authors : Mansoor, Sanaa (2023)

  • Mapping the ensemble of protein conformations that contribute to function and can be targeted by small molecule drugs remains an outstanding challenge. Here we explore the use of soft-introspective variational autoencoders for reducing the challenge of dimensionality in the protein structure ensemble generation problem. We convert high-dimensional protein structural data into a continuous, low-dimensional representation, carry out search in this space guided&#...
  • OER000002765.pdf.jpg
  • Journal article

  • Protein-Peptide Turnover Profiling reveals wiring of phosphorylation during protein maturation

    • Authors : Hammarén, Henrik M. (2023)

  • Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods that rely on pulsed metabolic labeling are very popular to quantify turnover rates on a proteome-wide scale. Such data have often been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture&...
  • OER000002407.pdf.jpg
  • Journal Article

  • SARS-CoV-2 Nonstructural Proteins 3 and 4 tune the Unfolded Protein Response

    • Authors : Davies, Jonathan P. (2023)

  • Coronaviruses (CoV), including SARS-CoV-2, modulate host proteostasis through activation of stress-responsive signaling pathways such as the Unfolded Protein Response (UPR), which remedies misfolded protein accumulation by attenuating translation and increasing protein folding capacity. While CoV nonstructural proteins (nsps) are essential for infection, little is known about the role of nsps in modulating the UPR. We characterized the impact of SARS-CoV-2 ns...