A2aR Oligomeric assemblies identified from coarse-grained simulations using large complex membranes

This deposit contains the oligomeric assemblies of A2a receptor sampled using coarse-grained simulations in different membrane environments. The molecular dynamics simulations studied how A2aR oligomerization was affected by i/ different receptor conformations (inactive/active); ii/ different protein densities (9 copies or 16 copies in a 45nm x 45 nm complex membrane); and iii/ the presence of PIP2 lipids (9-copy and 9copy NoPIP2). ############################################### Each tar.gz (a compressed file format) contains the oligomeric assemblies sampled in the simulations condition indicated by its file name. The tar.gz file was named as: <em>{Density}_{Presence of PIP2}_{Receptor Conformation}_{Oligomeric Order}.tar.gz</em><strong> </strong> where <em>{Density}</em> denotes whether 9 or 16 copies of the receptor in the simulations system; <em>{Presence of PIP2}</em> denotes whether PIP2 lipids were included in the membrane; <em>{Receptor Conformation}</em> denotes whether the receptor in the simulations was in the inactive or active states; and <em>{Oligomeric Order}</em> denotes the number of protomers in the oligomeric assemblies, i.e. OS2 denotes dimers, OS3 denotes trimers, OS4 denotes tetramers, etc. ############################################### Once decompressed, each tar.gz contains three directories: pdb, gro and tiff. The pdb directory contains the atomistic coordinates of oligomeric assemblies in the pdb format. The pdb file is named as <em>cl{NUM}_frameidx{IDX}_AA_charmm.pdb </em> where cl{num} denotes cluster id from which the structure was taken. All the oligomers of the same oligomeric order were put together and then clustered using K-means to identify different oligomeric assemblies; frameidx{IDX} denotes the frame idx from which the structure was taken. 100 structures were randomly each cluster if the cluster contained more than 100 structures otherwise all the structures in the cluster were written out. These structures were identified by their frame idx; and AA_charmm denotes that the structure is in atomistic model that was converted from coarse-grained modelled using CHARMM force field. The gro directory contains the same atomistic coordinates of the oligomeric assemblies in the gromos format (used in GROMACS simulation software). The tiff directory contains snapshots of the oligomeric assemblies, in the tiff format. These snapshots files were named as <em>{Oligomeric Order}.{Cluster id}_{View Direction}.tiff </em> where {Oligomeric Order} denotes the oligomeric order; {Cluster id} denotes the cluster id; and {View Direction} denotes the direction from which the snapshot was taken. "top" means the snapshot was taken from the extracellular side and "bottom" from the intracellular side.