- Journal Article
Authors : Ketaren, Natalia E. (2023) - SARS-CoV-2 has infected >40% of the world’s population (Collaborators 2022) resulting in
a devastating loss of life. As the SARS-CoV-2 pandemic enters its endemic phase (Meng,
Irwin et al. 2023, Pilz and Ioannidis 2023), multiple new variants continue to circulate. Since
its initial spread, the rapid adaptation of the virus to selective pressures continues to
produce variants of concern (VoC), of which the omicron variants presently ...
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- Journal article
Authors : Samant, Rahul S. (2023) - works in concert with co-chaperones to stabilize its client
proteins, which include multiple drivers of oncogenesis
and malignant progression. Pharmacologic inhibitors of
HSP90 have been observed to exert a wide range of
effects on the proteome, including depletion of client
proteins, induction of heat shock proteins, dissociation
of co-chaperones from HSP90, disruption of client protein
signaling networks, and recruitment of the protein
...
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- Journal article
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...
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- Journal article
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-...
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- Journal article
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...
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- Journal Article
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&#...
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- Journal article
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&...
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- Journal article
Authors : Nawaz, Mudassar (2021) - Soybean is a legume crop enriched with proteins and oil. It is frequently exposed to anthropogenic and natural flooding that limits its growth and yield. Current study applied gel free proteomic techniques to unravel soybean response mechanism to flooding stress. Two-days 44 old soybeans were flooded for 4 days continuously and root samples were collected at days 2 to 6 for proteomic and enzymatic analyses. Age-matched untreated soybeans ...
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- Journal Article
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...
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- Journal Article
Authors : Chesney, Andrew D (2023) - Parkinson’s Disease is accompanied by presence of amyloids in the brain formed of α-synuclein
chains. Correlation between COVID-19 and the onset of Parkinson’s disease let to the idea that
amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of α-synuclein. Using
molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein,
which is unique for SARS-COV-2, shifts preferentially the ensemble of α-synuclein&#x...
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- Journal article
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,&#...
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- Journal article
Authors : Buscagan, Trixia M. (2023) - The nitrogenase Fe protein mediates ATP-dependent electron transfer to the nitrogenase MoFe
protein during nitrogen fixation, in addition to catalyzing MoFe protein independent substrate
(CO2) reduction and facilitating MoFe protein metallocluster biosynthesis. The precise role(s) of
the Fe protein Fe4S4 cluster in some of these processes remains ill-defined. Herein, we report
crystallographic data demonstrating ATP-dependent chalcogenide exchange at the Fe4S4 clus...
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- Journal article
Authors : Noort, Marco van den (2021) - Our understanding of what determines ligand affinity of proteins is poor, even with highresolution structures available. Both the non-covalent ligand-protein interactions and the
relative free energies of available conformations contribute to the affinity of a protein for a
ligand. Distant, non-binding site residues can influence the ligand affinity by altering the free
energy difference between a ligand-free and ligand-bound conformation. Our hypothesis isthat...
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- Journal article
Authors : Chafiaa, Bouguechtouli (2023) - The combined expression of a handful of pluripotency transcription factors (PluriTFs) in
24 somatic cells can generate induced pluripotent stem cells (iPSCs). Here, we report the
25 structural characterization of disordered regions contained in four important PluriTFs, namely
26 Oct4, Sox2, Nanog and Esrrb. Moreover, many post-translational modifications (PTMs) have
27 been detected on PluriTFs, whose roles are not yet characterized. To help in ...
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- Journal article
Authors : Fürsch, Julius (2021) - Small heat-shock proteins (sHSP) are important members of the cellular stress response
in all species. Their best described function is the binding of early unfolding states and
the resulting prevention of protein aggregation. Most sHSPs exist as oligomers but vary
in size and subunit organization. Many sHSPs exist as a polydisperse composition of
oligomers which undergoes changes in subunit composition, folding status and rel...
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- Journal Article
Authors : Kind, Laura (2023) - Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, ...
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- Journal Article
Authors : chechik, Maria (2023) - The large group of dsDNA viruses comprising tailed bacteriophages and herpesviruses assemble by
packaging their DNA into preformed procapsids. The key component ensuring specific recognition of
bacteriophage DNA from the mixture of all the nucleic acids contained in the host cell, and initiating
its packaging is the small terminase protein. The nascent genome is usually produced as multiple copies, joined head-to-tail, in long concatemers of dsDN...
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- Journal article
Authors : Birke, Ramona (2021) - Sulfonated rhodamines that endow xanthene dyes with cellular impermeability are presented. We
fuse charged sulfonates to red and far-red dyes to obtain Sulfo549 and Sulfo646, respectively, and
further link these to SNAP- and Halo-tag substrates for protein self-labelling. Cellular
impermeability is validated in live cell imaging experiments in transfected HEK cells and neurons
derived from induced pluripotent stem cells (iPSCs). Lastly, we show that&...
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- Journal article
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...
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- Journal article
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...
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