Introducing the team: The Gileadi Group in Oxford.

Hi! I’m Opher Gileadi, I head a group at the Structural Genomics Consortium (SGC) in Oxford. For many years, we’ve been looking at proteins involved in human. We’ve looked at a wide variety of proteins: from DNA repair enzymes and transcription factors to enzymes involved in signalling. In most cases, we focus on early work: Read More …

Update on crystal hits, XChem and more purification

Things have been really busy in the lab the last few weeks. I’ve done a couple of purifications of ACVR1 (ALK2), which I’ll post in Zenodo (getting loads of protein now), but probably won’t write up the details of every purification every single time anymore, as it’s the same process every time for this construct. Read More …

Development of a Mass Spectrometry USP5 Catalytic Activity Assay

Now that I’ve got my biophysical screening assays developed (19F NMR, SPR), as well as my hit expansion campaign started for small molecule inhibitors against the USP5 Zf-UBD, I need to be able to test if these small molecule inhibitors will antagonize the catalytic activity of USP5. It has been speculated in literature that the Read More …

Generating mutations in the GS domain of ALK2

This week one of the things I’ve been working on is the final set of mutations in the GS domain of Alk2 to help us unpick the influence of phosphorylation on function. That, however, is a bit of a mouthful so let’s unpack it a bit. I said in my last blog post that we Read More …

Reduction of HTT Protein through Chemical Inhibition

The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1495129. Apologies for the long delay between this post and my last post, it really has been quite some time! As postdocs, we generally have several projects running simultaneously and we have to split our time between these projects. I am no Read More …

Checking expression and localization of split-SCN1A constructs in HEK293 cells

In my last posts, I have constructed a pair of split-SCN1A constructs (split- SCN1A-GFP(1-10) and SCN1A-GFP(11)). Here, I tested the functionality of these constructs by looking at whether these split- constructs reconstitute into a full-length SCN1A and generate a fluorescent signal when co-transfected in HEK293 cells, and if so, do the reconstituted SCN1A (with an Read More …

Hit Expansion using Substructure Search, Virtual Screening & Free Energy Perturbation

Molecular dynamic simulations are a powerful tool for modeling biomolecular systems such as ligand binding to proteins. In a previous post I was able to get co-crystal structures of ligands which bind to the USP5 zinc finger ubiquitin binding domain (Zf-UBD). In order to explore the structure activity relationship (SAR) of the chemical series, so Read More …

Some structure pictures for your viewing pleasure

So I reported here a couple of weeks ago that I’d obtained datasets for ACVR1 bound to M4K2117 and M4K2121, at 1.25 and 2 Å resolution, respectively, and I put up a link to the data. I’m now refining the data and got some pretty good structures so far. These are what the current stats look Read More …

Phosphorylation of SMAD1 – rates as a function of Alk2 mutations and type II association.

One of the questions to be asked when looking at the mutation in ALK2 that causes FOP, is how exactly does that mutation cause the disease. ALK2 we know is part of the BMP signalling pathway responsible for bone formation and the mutation results in excess bone formation – thus we can summarise that somehow Read More …