Data
Limited proteolysis of full-length huntingtin with chymotrypsin
I have received data from SPARC, Sick Kids Hospital Toronto, for the limited digest experiment I previously wrote about. This experiment aims to work out where the flexible linker regions of the protein structure are, therefore predicting which regions of the protein sequence correspond to folded domains.All of the experimental data is uploaded onto Zenodo. Very Read More …
Huntingtin linker sequence determination by computational methods - correspondence with Alex Holehouse
I firmly believe that the more scientists discuss their data with experts both within their field and outside of it, the better! Without peer review, constructive criticism and comprehensive evaluation of the data we all generate, we can not understand its limitations nor its value to others working in the same field. In this vein, Read More …
Domain mapping of full-length huntingtin by limited proteolysis with chymotrypsin
I am continuing to try and understand the domain architecture of the huntingtin protein. In a bid to validate my previous limited proteolysis/mass spectrometry experiment, I wanted to see if I could get similar proteolytically stable fragments by digesting my remaining aliquot (courtesy of the generous Stefan Kochanek and Bin Huang) of full-length huntingtin protein Read More …
Structure prediction analysis of huntingtin using Phyre2
The fundamental goal of this project is to try and understand more about the structure of the huntingtin protein molecule i.e. what does this long chain of amino acids look like in three dimensions in the cells of our bodies? By understanding more about what this protein looks like, we may be able to make Read More …
Domain mapping of full-length Q17 huntingtin - summary so far
Over the past week, I have continued to analyze the mass spectrometry (MS) data from the limited proteolysis experiment, performed on the full-length Q17 Huntingtin protein sample from Stefan Kochanek’s lab, and also assessed how this data tallies with previously published studies. To pull all of this analysis together from the past few blog posts, I Read More …
Literature review of huntingtin proteolysis
The cutting of huntingtin protein by enzymes in the cell into shorter fragments is linked to cellular toxicity and therefore is thought to contribute to the phenotype and symptoms of Huntington’s disease. By searching through Pubmed, I have found a number of published papers which detail the sites at which this happens in the huntingtin Read More …
Mass Spectrometry Data
Currently, I am continuing to work on the domain mapping experiments with huntingtin (HTT) protein. I hope that by working out more about the domain organisation of this protein, I will be able to infer information about its 3-dimensional structure (what does it look like?) and maybe its functions in the cell (what is it Read More …
First installment
Over the past few weeks, I have been working on how best to disperse the scientific data I have with as many people as possible in the most effective way, as well as getting this blog up and running. I have decided to deposit all of my methods and data, in real-time, on Zenodo. This Read More …