A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
In a previous post, I determined a crystallization condition that produced nice 3D crystals of USP5 Zf-UBD that diffracted well. Rachel Harding, a postdoc at the SGC collected data images for these crystals and solved the structure using computational techniques. You can see the solved crystal structure and a more detailed analysis of the structure Read More …
Several compounds derived from thienopyrimidine scaffolds were recently synthesized to be tested as inhibitors of DRAK2/STK17B kinase. Among these, a set of 12 were selected to determine their potency as IC50 values on a DRAK2 cellular assay. These compounds have different functional groups around the phenyl ring and variation in the position of the sulfur Read More …
Over the past few weeks I’ve been perfecting a method for screening a small set of therapeutic compounds on DIPG cell lines. Before starting I made sure to discuss the techniques used in other groups to make sure that I design an assay that is comparable to theirs, although I may make my own changes Read More …
I wanted to determine whether USP5 Zf-UBD is a monomer or a dimer in solution as some known USP5 structures have shown that there is a cysteine surface residue that is not involved in Zn-coordination but forms disulfide bonds (2G43, 2G45, 3IHP). I used size exclusion chromatography with multiple angle light scattering (SEC-MALS) to determine Read More …
A follow-up to check the increased fluorescence signals at 0 min of the HDAC11 reaction with its substrate was performed. The data is uploaded on Zenodo.
I’ve put the Molprobity stats for the model I have refined to run my fragment screening datasets against in Zenodo. It looks pretty good, and I was happy when the parameters finally all went into the green. I have about 90 datasets with resolution lower than 2.6 Å, so hopefully I’ll get at least one Read More …
The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1202292 In my previous post, I used baculovirus to overexpress HTT in mammalian cells. Although I managed to overexpress HTT, this HTT is actually FLAG-tagged, and very strangely, I could not detect FLAG! Let me first explain what a FLAG-tag is. FLAG is Read More …
Recently, a study of cancer-focused protein-protein interactions identified a direct interaction between NSD3 and the oncoprotein Myc in the non-small cell lung cancer cell line H1299 (Li, Z et al. 2017). Importantly, the study found that increased NSD3 expression levels can activate Myc in H1299 cells as measured by an E-box luciferase reporter. However, the functional significance of Read More …
As mentioned in my Zenodo post here, I fine screened ACVR1 with the three compounds in the title. I got loads of hits for co-crystallisation with K62821a. I mounted almost two pucks’ worth of crystals (31 crystals) and sent them to Diamond for Monday’s run. Unfortunately, none of them diffracted better than 3.5 Å, so Read More …
Whether or not a cell line can be transfected efficiently is an important factor to consider when designing experiments. Often times scientists would like to deliver into the cells DNA or RNA with the instructions to produce specific proteins or to delete away specific proteins. Transfection via liposome (eg: Lipofectamine 2000) is a relatively simple Read More …
