This page is dedicated to our partnership with iGEM Team IISER Kolkata. It will tell you about what we did to help each other advance our projects over the course of the competition.
As none of our Drylab team members had experiences regarding molecular dynamics simulations and guides available online only helped us creating systems that weren’t in our interest, we were insecure about how to use and what could be archived by using Gromacs (originally developed by the University of Groningen, Netherlands; our molecular dynamics software of choice) 1 2 3 .
By coincidence, we got in contact with the iGEM Team IISERK from Kolkata, India.
Throughout several meetings we got to learn about each other’s projects, and by that, how we could help each other out.
Not only could they help us use Gromacs, but they also showed us different simulation software (e.g., AutoDock) to generate interesting data for our project.
Further, they built 6 different membrane models we later used for our all-atom simulations and explained which relevant information we could extract from these for analysis.
Our initial goal was creating a simulation consisting of one of our grafted cyclotides (later on called constructs) next to a membrane, expecting the cyclotide to get closer to the membrane and, through molecular attraction, stick to it and hopefully even deform it.
Thanks to the advice from team IISERK, we, later on, decided to analyze our simulation results with methods like e.g. computing the solvent accessible area, as well as others.
Later, they also advised us to try AutoDock, a software dedicated to simulating protein-ligand docking, which we used to test the docking behavior of our constructs to a single phospholipid.
Those simulations allowed us to compare our selection of antimicrobial peptides (AMPs) to our constructs, giving us an idea of which construct might be the best at disrupting a membrane.
While Kolkata built our membrane system, we went ahead and got in contact with Dr. Thiel, who works for the department of biomedical informatics at the Universitätsklinikum Tübingen, and has access to the supercomputer BinAC.
Through him, we were given accounts for BinAC and got the required documents to learn how to use it.
After adapting some Gromacs files and the run script needed for the supercomputer we went ahead and ran the simulations of team IISERK and the ones they prepared for us on an all-atom resolution, which wouldn’t have been possible within a reasonable timeframe using consumer-grade computers.
While the main goal of the partnership was to help each other regarding issues in Drylab, through our regular meetings we also exchanged further ideas regarding e.g., our social media work or current problems in Wetlab.
Thanks to the collaboration both teams pushed each other forwards and achieved their goals which otherwise wouldn’t have been possible within the few months of the iGEM competition.
1 E. Lindahl, B. H. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 306-317.
2 H. Bekker, H. B. (1993). Gromacs: A parallel computer for molecular dynamics simulations. Physics computing, 252–256.
3 H.J.C. Berendsen, D. v. (2001). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 306-317.