Docking Assay For Transmembrane components (DAFT)
Interactions between membrane proteins are key in many biological processes, but the complex environment makes it difficult to explore these in high detail both in simulations and in experiments. In simulations, the time scales of binding and unbinding pose difficulties. By focusing on association simulations, the problem of unbinding is avoided, and detailed maps of the landscapes of association can be built. For this we recently developed the Docking Assay For transmembrane components (DAFT) to set up and run high-throughput coarse-grain association simulations. DAFT is build around a set of PBC layouts for optimal placement of the components in the starting configurations, and uses insane to build membrane and solvent, and martinate to run the simulations.
T.A. Wassenaar, K. Pluhackova, A. Moussatova, D. Sengupta, S.J. Marrink, D.P. Tieleman, R.A. Böckmann: High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. J. Chem. Theory Comput. 11:2278-2291 (2015) [link]
This original DAFT method was further extended to allow for studying adsorption of peptides and proteins to membrane surfaces. Therefore, schemes were added where one or more components are positioned in the solvent layer instead of within the lipid bilayer. For such solutes, two new rotational schemes are available; 3D rotation for spherical proteins and rotation around the helix axis of helical peptides, which is aligned with the membrane plane.
K. Pluhackova, T.A. Wassenaar, S. Kirsch, R.A. Böckmann: Spontaneous Adsorption of Coiled-Coil Model Peptides K and E to a Mixed Lipid Bilayer. J. Phys. Chem. B 119:4396-4408 (2015) [link]
LOPLS Force Field
Force Field Check