Engineering
To achieve our goal of engineering a recombinant gastric intrinsic factor (BiG-IF), mutant candidates were designed based on the rationale of preserving the structure as much as possible. They were further screened using an in silico modelling pipeline, composed of different techniques, to select the ones to be tested in wet lab experiments. Corresponding primers for site-directed mutagenesis as well as plasmids for protein production were designed.
Model
No successful wet lab experiment can be performed without proper modelling. A multistep modelling pipeline was built to get insights into how desired mutations will affect the structure of IF and its binding properties with B12 and cubilin. Starting with protein structure predictions of all possible mutants to docking, molecular dynamics and immunogenicity studies, we used this rigorous approach to pick only the best out of the best ones.
Software
Introducing ProMutor - Protein Mutant Generator, a user-friendly web-tool for selecting potent mutants of your choice. Given a nucleotide or amino acid sequence, the tool suggests a list of mutants, scored based on epistatic relationships between amino acids as well as their conservation. It enables direct assessment of mutation effect on the protein. The tool also provides a direct access to tools for further protein mutants investigation.
Wikipage
Priority has been the user-friendly experience and accessibility of the information. Subpages organized in a logical order are accessible by using the menu with only 1 click or by reading the wikipage from start to end using the “previous/next” buttons at the bottom of every page. The side menu allows the user to navigate through the page or simply jump to a specific section of interest. The non-overwhelming organization of the references into a dropdown allows the most agreeable experience. "Inclusive and accessible" is the page's motto primarily achieved by the pleasant and sober font style, the color choice that allows colorblind people to detect shapes in both dark and light modes, particular font style and size make the wiki dyslexic-friendly and descriptive figure captions allow for screen-reader usage. The dynamic elements integrated successfully add life to the wikipage which keeps the user engaged!