Simulation report
Technical information
General information
Name: Ffa2-bua
PDB id: 8T3S
Activation state: Active
Description: Simulation aims to observe the effects of orthosteric agonist butyrate on FFA2 activation without G-protein. It produced NPT ensemble from 3 replicas of 1000 ns Langevin dynamics (T=310.15K, gamma=1ps-1) with semi-isotropic Berendsen barostat (P=1bar, tau=1ps) and 9A noncovalent cutoff.
Submitted by: Abdul-Akim Guseinov, University of Glasgow
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Number of molecules:
Butyric acid: 1
Free fatty acid receptor 2: 1
Total number of atoms: 4650
Simulation details
Software and version: AMBER PMEMD.CUDA, 2020
Forcefield and version: ff19SB/lipid21/GAFF2, ff19SB/lipid21/
Time step : 2.0 fs
Delta : 0.1 ns
Replicates: 3
Accumulated simulation time: 3.0 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Xuan Zhang, Abdul-Akim Guseinov, Laura Jenkins, Alice Valentini, Sara Marsango, Katrine Schultz-Knudsen, Trond Ulven, Elisabeth Rexen Ulven, Irina G. Tikhonova, Graeme Milligan, Cheng Zhang. None. Allosteric modulation and biased signalling at free fatty acid receptor 2. None. doi: 10.1038/s41586-025-09186-6.
Find a list of all simulations published in this paper: 1561
Simulation components
Ligands
Receptor
Mutations
No mutations found
