A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
This is an excerpt from my PhD thesis where I investigated 13 human PR/SET domains from the PRDM protein family and assessed their ability to bind to a fluorinated SAH analog. The research helps to identify which of the PRDMs could be methyltransferases. This work was carried out in the laboratory of Dr. Cheryl Arrowsmith Read More …
Production and purification of Ectodomain of SARS-CoV-2 Spike (S) protein Two different expression plasmids for prefusion S ectodomain residues 1−1208 of 2019-nCoV S (GenBank: MN908947) with proline substitutions (2P) at residues 986 and 987(1) and with six proline substitutions (HexaPro (at residues 817, 892, 899, 942, 986 and 987 (2), a “GSAS” substitution at the Read More …
In a previous post, I described a ubiquitin-rhodamine110 (UbRho110) assay, and showed that a ZnF-UBD ligand antagonizes USP5 catalytic activity. UbRho110 is not a native substrate, and validation with native polyubiquitin species in an orthogonal assay is required. To address this, I developed and optimized an internally quenched fluorophore pair (IQF) assay. You can see Read More …
SARS-CoV-2 is a positive-strand RNA virus, depending on its multi-subunit machinery to replicate its RNA. This machinery is known as RNA-dependent RNA polymerase (RdRp). The catalytic subunit of RdRp, which is the core component of this machinery, is called nsp12. Nsp12 has little catalytic activity on its own and relies on accessory subunits to have Read More …
Background The SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase is a complex of proteins that helps facilitate the ubiquitination of substrates for targeted proteasomal degradation. FBXW11 is F-box containing protein that has 11 WD-repeats and is a substrate recognition component of the SCF complex. FBXW11 recognizes and binds its substrates, including beta-catenin, at phosphorylated sites or Read More …
Background The SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase is a complex of proteins that helps facilitate the ubiquitination of substrates for targeted proteasomal degradation. FBXW7 (F-box/WD repeat-containing protein 7) is an F-box protein component of the SCF complex and is involved in substrate recognition. The F-box domain tethers FBXW7 to the SCF complex by interacting Read More …
Production and purification of recombinant SARS COV-2 RBDSD1-Fc protein from a transiently transfected EXPI293 mammalian cells. Expression plasmid for CoV-9-RBDSD1, residues of RBD R319−S591 with a C-terminal HRV3C protease cleavage site, a monomeric Fc tag and an 8XHisTag was generously gifted by Dr. McLellan’s lab (1). Secreted proteins were purified from a suspension culture cell Read More …
Over the last few months, we have all become familiar with the COVID-19 global pandemic. The coronavirus is “decorated” with the Spike (S) protein, one of the 25 proteins of SARS-CoV-2 that are encoded in the viral genome. The infection starts with the attachment of the virus to the cell membrane to enter host cells. Read More …
In my previous post 19, I showed how we assessed the druggability of the remdesivir-binding site of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and determined the residues lining that site. In this post, we analyze the genetic diversity of RdRp catalytic site across Alpha- and Betacoronavirus entries from UniProt and among SARS-CoV-2 samples. In the context Read More …
Previously we reported our analysis on the structural diversity of binding pockets found on the SARS-CoV-2 main protease, methyltransferase, and papain-like protease, macrodomain. We then shifted our focus on the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). SARS-CoV-2 is a positive-strand RNA virus, depending on its multi-subunit machinery to replicate its RNA. The catalytic subunit of RdRp Read More …
