Model systems with GPCRs embedded in multicomponent membranes

Files required to run coarse-grained simulations on various lipid membranes with embedded adenosine A_2A and dopamine D_2 receptors. These simulations were performed to study the effect of the presence of polyunsaturated fatty acid on GPCR oligomerization. The detailed description of the aims, methodologies and results of this study are explained in the research paper [1]. The composition and purpose of each simulated system will also be explained in this paper [1].

The Martini force field [2,3] was employed in the study, and the simulations were performed with version 4.5.x of the GROMACS package [4].

For each system the following (in GROMACS compatible format) is provided:

1) Initial structure (*Start.gro)

2) Topology file (*.top)

3) Index file (*.ndx)

In addition, for systems other than those containing only one protein, the final structure is given (*End.gro).

Other files required to run the simulations, which are common for all the systems, are also provided:

4) Simulation parameter file (.mdp)

5) Force field parameters (.itp)

References:

[1] Guixà-González et al., Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors. Scientific Reports 6, Article number: 19839 (2016) DOI:10.1038/srep19839​

[2] Marrink et al., The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations. Journal of Physical Chemistry B 111, 7812–7824 (2007), DOI:10.1021/jp071097f

[3] Monticelli et al., The MARTINI Coarse-Grained Force Field: Extension to Proteins.   Journal of Chemical Theory and Computation 4, 819–834 (2008), DOI:10.1021/ct700324x

[4] Pronk et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29  845-854 (2013), DOI:10.1093/bioinformatics/btt055