Team:McMaster II/Collaborations
Oxford
The team at Oxford has been working on a method of cell-free detection of Chargas disease. Specifically, they are testing for the presence of cruzipain, which is known to cleave and release the peptide hirudin from the transmembrane OmpA precursor. To measure cruzipain activity, they are using the Spytag/Spycatcher system. First, they must attach Spytag, a short peptide, onto the OmpA protein. We have assisted the team by running a CG simulation of OmpA bilayer insertion and simulation with SpyTag/SpyCatcher. This simulation, performed on the supercomputer cluster at McMaster University, provided insight into protein conformations and system stability after the OmpA+Spytag fusion protein was inserted into a model membrane.
Collaboration on this project has involved sharing of information on the proteins involved. Below are the 3D images of the two proteins involved in the simulation, OmpA and SpyTag. Furthermore, communication has been required to create the most realistic bond between OmpA and Spytag on a computer. After discussing this issue, we reached the consensus that the optimal route would be to create a harmonic artificial potential between the two proteins.
Below, we have attached the molecular dynamics simulations we ran of their chimeric protein. We showed which residues may be potentially unstable in both the Spytag and SpyCatcher proteins. The root-mean squared fluctuations (RMSF) is proportional to protein stability, and is unique to SHARCNET supercomputer clusters in Ontario, Canada. With this, we were able to offer atomistic resolution.
Oxford provided us with the code for reaction kinetics, which we implemented heavily in our modelling section.
