- Journal article
Authors : Roy, Urmi (2023) - Among the multiple SARS-CoV-2 variants recently reported, the Delta variant has generated most perilous and widespread effects. Another variant, Omicron, has been identified specifically for its high transmissibility. Omicron contains numerous spike (S) protein mutations and in numbers much larger than those of its predecessor variants. In this report we discuss some essential structural aspects and time-based structure changes of a selected set of spike protein&#...
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- Journal article
Authors : Yadav, Ruchi (2023) - SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19
34 pandemic. Its ~30 kb RNA genome is translated into two large polyproteins subsequently cleaved
35 by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential
36 yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11
37 polyprotein, whose mature products are cofactors of the viral replicase, identifying the&#...
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- Journal Article
Authors : Baboo, Sabyasachi (2023) - UBR4 is an E3 ligase (E3) of the N-degron pathway and is involved in
neurodevelopment, age-associated muscular atrophy and cancer progression. The location
and mechanistic classification of the E3 module within the 600 kDa protein UBR4 remains
unknown. Herein, we identify and characterize, at a biochemical and structural level, a distinct
E3 module within human UBR4 consisting of a novel “hemiRING” zinc finger, a helical-rich
UBR ...
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- Journal article
Authors : Aguilera, David (2023) - Antiviral compounds are crucial to controlling the SARS-CoV-2 pandemic. Approved drugs have been tested for their efficacy against COVID-19, and new pharmaceuticals are being developed as a complementary tool to vaccines However, there are not any effective treatment against this disease yet. In this work, a cheap and fast purification method of natural tyrosinase from Agaricus bisporus fresh mushrooms was developed in order to evaluate the potential of&...
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- Journal article
Authors : Zaidman, Daniel; Gehrtz, Paul; Filep, Mihajlo (2020) - Present covalentizer, a computational pipeline for creating irreversible inhibitors based on complex structures of targets with known reversible binders. For each ligand, we create a custom-made focused library of covalent analogs. We use covalent docking, to dock these tailored covalent libraries and to find those that can bind covalently to a nearby cysteine while keeping some of the main interactions of the original molecule. We found ~11,000 cysteine...
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- Journal article
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 ...
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- Journal article
Authors : Laffeber, Charlie (2021) - Rapidly spreading new variants of SARS-CoV-2 carry multiple mutations in the viral spike
protein which attaches to the angiotensin converting enzyme 2 (ACE2) receptor on host cells.
Among these mutations are amino acid changes N501Y (lineage B.1.1.7, first identified in the
UK), and the combination N501Y, E484K, K417N (B.1.351, first identified in South Africa),
all located at the interface on the receptor binding domain (RBD). We expe...
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- Periodicals (Báo – Tạp chí)
Authors : Rangan, Ramya (2020) - he rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta’s FARFAR2 algorithm ...
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- Journal article
Authors : Almasy, Katherine M. (2021) - Human coronaviruses have become an increasing threat to global health; three highly pathogenic strains have emerged since the early 2000s, including most recently SARS-CoV-2, the cause of COVID-19. A better understanding of the molecular mechanisms of coronavirus pathogenesis is needed, including how these highly virulent strains differ from those that cause milder, common-cold like disease. While significant progress has been made in understanding how SARS-CoV-2 ...
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- Journal article
Authors : Fleming, Aaron M. (2021) - Nanopore devices can directly sequence RNA, and the method has the potential to determine
locations of epitranscriptomic modifications that have grown in significance because of their roles
in cell regulation and stress response. Pseudouridine (Ψ), the most common modification in RNA,
was sequenced with a nanopore system using a protein sensor with a helicase brake in synthetic
RNAs with 100% modification at 18 known human pseudouridinylati...
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