A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1323902 As I’ve been having problems overexpression HTT properly in my cancer cell lines, I decided to continue looking at other proteins of interest using our best overexpression model so far, which is in HEK293T cells. Although it may not be a cancer Read More …
Hello again! Here is my first attempt to find an EZH1 antibody. I have mainly focused on EZH2 in the PRC2 complex as the methyltransferase responsible for the H3K27me3 mark. However, EZH1 can functionally substitute for EZH2 in PRC2. We have a good antibody to detect EZH2 levels in patient AML samples. However, for some Read More …
NSD3 is located on a region of chromosome 8 (8p11-12) that is frequently amplified in several forms of cancer. It has been suggested that NSD3 (WHSC1L1) may be a driver of tumorigenesis in this context (Mahmood et al. 2013). However, it is still unclear how amplification of NSD3 contributes to the disease and whether or not it Read More …
The ongoing quest for huntingtin interaction partners
Based on previous 19F NMR and SPR assay experiments, 4 compounds were used to set up co-crystallization experiments (Table 1). I was able to get co-crystal structures of 3 of the 4 compounds! You can see full experimental details on Zenodo. Table 1. USP5 Zf-UBD ligands Read More …
Starting new projects in huntingtin structural biology
It’s been a busy couple of weeks in and out of the lab for me which is why it’s been some time since my last post. I previously identified small molecule compounds of interest using a 19F NMR spectroscopy assay. To quantify and validate these small molecule compounds, I used a surface plasmon resonance (SPR) Read More …
As a last step, to check if the assay qualifies for the screening purposes, Z’-factor was calculated. The dataset can be viewed on Zenodo.
For the purpose of compound library screenings, the compounds would be made available in DMSO and thus, when they would be incubated with the protein, the protein solution will now contain DMSO as well. It is important to determine the concentration of DMSO that could be tolerated by the protein such that the protein stays Read More …
The presence of detergent can prevent the sticking of the fluorophore to the sides of the wells of the plate and thus improve the signals. Hence, the effect of detergent was observed on the overall signals and the activity of HDAC11. The dataset can be viewed on Zenodo.
