Role of lipid nanodomains for inhibitory FcγRIIb function

Dataset repository - Role of lipid nanodomains for inhibitory FcγRIIb function

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The repository contains setup files and parameter files for atomistic molecular dynamics (MD) simulations performed with the GROMACS 2021/2022 series. Modified trajectories for the post-processing analysis are further included. The repositiory corresponds to the following manuscript:

Franziska Spiegel, Marius F.W. Trollmann, Sibel Kara, Matthias Pöhnl, Astrid F. Brandner, Falk Nimmerjahn, Anja Lux, Rainer A. Böckmann bioRxiv 2023.05.09.540011; doi: https://doi.org/10.1101/2023.05.09.540011

Corresponding authors:

* Rainer A. Böckmann (rainer.boeckmann@fau.de)

* Anja Lux (anja.lux@fau.de)

### XTC/TPRs

Directories contain:

    * md.tpr: GROMACS run file for the whole system

    * md_nonsolvent.tpr: GROMACS run file for the non-solvent selection (Membrane-Protein only)

    * md_mol_center_dt10ns.xtc: GROMACS trajectories used during post-processing with a slightly larger spacing (10ns instead of 1ns).

    * topol.top: GROMACS topology file used for simulations

    * index.ndx: GROMACS index file used for simulations

    * toppar: Contains CHARMM36 forcefield parameters for lipids, protein and glycans in GROMACS readable format (.itp) 

    * step6.6_equilibration.gro: Input structure of the last equilibration step (see step6.6_equilibration.mdp) that was used as inital structure for the production simulation

    * last_frame.gro: Output structure of the production simulation

The preparation of the raw trajectories for post-processing was done with GROMACS using the commands:

>> gmx trjconv -f md.xtc -s md.tpr -pbc mol -center -n md_traj.ndx -dt 1000 -o md_mol_center.xtc

>> gmx trjconv -f md_mol_center.xtc -s md_nonsolvent.tpr -o md_mol_center_dt10ns.xtc -dt 10000

The group for centering was the transmembrane domain of the Fcg receptor, as output only the protein and the membrane was chosen. 

#### Wild type simulations (No Glycans)

* wt_replica_0

* wt_replica_1

* wt_replica_2

* wt_replica_3

* wt_replica_4

* wt_replica_5

* wt_replica_6

* wt_replica_7

* wt_replica_8

#### Mutant simulations (No Glycans)

* mut_replica_0

* mut_replica_1

* mut_replica_2

#### Wild type simulations (Glycans)

* wt_glycan_replica_0

* wt_glycan_replica_1

* wt_glycan_replica_2

* wt_glycan_replica_3

### Parameters

Simulation parameter files (.mdp) are given for each equilibration step and the final production simulation. Initial input files are obtained from the CHARMM-GUI webserver.

* simulation_parameters

    * mut_wt_no_glycans

    * wt_glycans

### Copyright

This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.