Structural Investigation of the DedA Protein YqjA

As the threat of antimicrobial resistance (AMR) intensifies, resulting in a growing number of deaths worldwide every year, there is an increasing pressure to find solutions. One possibility is to reverse the resistance by determining its cause. DedA proteins are membrane transporters and have been shown to confer resistance to a variety of antibiotics in many different pathogenic bacteria. This project focussed on the structure of the DedA protein YqjA from E. coli which will aid in future drug design to block the functioning of this protein. The 3D structure was predicted via the EVcouplings algorithm which was then biochemically tested using Substituted Cysteine Accessibility Methods (SCAM). This uses single cysteine mutants of YqjA and, through treating the cells with various thiol-binding reagents, the location of the Cys residue in relation to the membrane can be determined. 8 out of 12 results from the SCAM analysis agreed with the predicted EVfold model showing it to be a reliable prediction of the 3D structure of YqjA. However, a rescue assay that was carried out to assess the functionality of the cysteine mutants needs to be repeated in order to have full confidence in the accuracy of the SCAM data.