A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
Hi Here are the details of the assay I developed to measure interaction between USP5 and ubiquitin in cells. Ubiquitin specific peptidase 5 (USP5) belongs to the largest ubiquitin-specific protease (USP) subfamily and has a zinc finger at its N-terminal portion and two ubiquitin-associated domains in the large catalytic region that mediate polyubiquitin binding (PMID:28923280, Read More …
Hi all! Hope everyone is staying safe and practising social distancing during these difficult times. Working from home, I’ve decided to catch up on my open notebook. In a previous post, I purified various full length USP5 constructs and determined the binding affinity of ubiquitin to these constructs. I wanted to determine the stoichiometry of Read More …
In a previous post, we solved the co-crystal structure of the USP5 zinc finger ubiquitin-binding domain (ZnF-UBD) with a promising compound, UBTR012574, which had a potency of approximately 10 µM (Figure 1). W expanded the chemical series of UBTR012574 by docking analogue compounds from the Enamine REAL database and Scifinder. We decided to order 17 Read More …
When I was a kid, I used to have a spinning globe lamp in my bedroom. What can I say? I was a big nerd child (I also had a passion for stamp collecting and making model airplanes, but thats a tale for another time). I loved plugging it in and when it lit up Read More …
Written in collaboration with Tigran M. Abramyan (Alexander Tropha’s lab at UNC Chapel Hill) In my previous open lab notebook entry I described the in silico approach using the program SparkTM to grow fragments found to co-crystallize within binding site A of the transcription factor brachyury to compounds with hopefully higher binding potency. The overall aim Read More …
Previously in our lab, Jiayan Wang et al. worked on a project related to the druggable genome. In her project, she evaluated the druggability of protein domains found in the human genome using protein structures bound to druglike ligands. The left panel in Figure 1 demonstrates her workflow to define ligand binding pockets. To build Read More …
Grin1 p.Tyr647Ser Project Background. Grin genes across species encode for proteins that make up the different NMDA receptor subunits. GRIN1 mutations (usually heterozygous) are associated with intellectual disability with epilepsy in humans, including the rare p.Tyr647Ser (Y647S) variant. This missense mutation occurs in the M3 helix of the transmembrane domain of GRIN1 which, importantly, is conserved between human GRIN1 and mouse Read More …
Do you know what the image above represents? I will give you a clue, it relates to lab safety. Any takers? Still nothing? Well, this my friends represents corrosive materials. This group includes many strong acids and bases and was a question I got wrong in my safety exam today (gasp, shock, you failed Tom). Read More …
In my previous purification of the HTT N-HEAT_81-1643 construct, I showed that an additional heparin step did not remove any traces of nucleic acid material, changed purity or oligomeric state of the sample. Additionally, my DLS results showed that this construct forms large particles in solution. Thus, the DLS results in combination with the gel filtration Read More …
Last week this was my view. This week nothing but wintry snow and cold everywhere. Oh, how I miss the sunnier climes of San Diego. I think I will add one more resolution to my first blog, spend some time every winter somewhere sunny, as this cold really gets into the bones. Anyways, I wasn’t Read More …
