Co-Crystallisation of the ALK2/FKBP12 complex with compounds from M4K and others.

New compounds developed by Meds4Kids (M4K) and other collaborators against ALK2 would benefit from being crystallised so we can look at the structure of the complex and explain exactly how these compounds bind. This helps us work out how to improve them for both potency and selectivity and explain why some bind better than others. Read More …

Following Up on NSD3’s Involvement in Epithelial to Mesenchymal Reprogramming

In my last blog post, I observed morphological changes that were indicative of an epithelial to mesenchymal transition (EMT) when NSD3short was overexpressed from a stably integrated transgene in the cancer cell line H1299. Importantly, NSD3 has been identified as amplified in a number of cancer types, including lung (Figure 1) (cBioPortal: Cerami et al., Cancer Discov. 2012 Read More …

Project overview: New compounds for FOP and the role of mutation on protein function.

Hi, my name is Ellie Williams and I’ve been working at the SGC since 2010 in the lab of Alex Bullock. I’m funded by FOP Friends to look at the development of new drugs that target ALK2 and to study the disease Fibrodysplasia Ossificans Progressiva (or FOP). In the last couple of years a new Read More …

Overexpression of Expanded HTT

The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1218375 The etiology of HD is the expansion of Q repeats or CAG repeats in the HTT gene, which produces the huntingtin protein. This causes improper folding of the protein and leads to protein aggregation in neuronal cells, which ultimately causes the Read More …

Crystallization of USP5 Zf-UBD #2

In my last post, I analyzed a structure of USP5 zinc-finger ubiquitin binding domain with a cysteine-glutathione disulphide bond. These crystals were not suitable for ligand soaking due to the formation of a disulphide bond at Cys195 with a glutathione additive that occupies the ubiquitin binding pocket in the adjacent molecule in the crystal lattice. Read More …

Purification of ACVR1 for co-crystallisation with new compounds and for fragment screening crystals

I was away on leave last week, but happily, before I left, I set up 25 crystal plates of ACVR1 with various compounds. The details of the protein purification, the compounds used and some of the crystals obtained are here, on Zenodo. So I was able to at least come back to something after my Read More …

Compound 11 update (SNS-032 analogues)

Following previous post, https://openlabnotebooks.org/sns-032-analogues-update/, compound 11 was chosen to further investigate the structure activity relationships (SAR) of the oxazole ring system with the hope to enhance potency and improve selectivity towards each respective target. The criteria to pick the building blocks to further study the SAR is based on electronics, size and shape. I have Read More …

Determining the plasticity of CD34 expression

Previously, we established that OCI-AML-20 requires stroma to maintain CD34 expression (https://zenodo.org/record/1187083#.Wr5-1C7wbIV). In this experiment, we wanted to see whether those cells grown in suspension are able to regain CD34 expression when cells are reintroduced to stroma. We find that OCI-AML-20 regains CD34 expression when put back on to stroma (either MS5 or OP9). Full Read More …

Structural Analysis of USP5 Zf-UBD

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 …