Simulation report
Technical information
General information
Name: Ffa2_apo-empty (apoform)
PDB id: 8J23
Activation state: Active
Description: Simulation aims to observe structural features of FFA2 in the absence of G-protein and any ligands. It will be used for comparison to docking-based simulations. 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:
Free fatty acid receptor 2: 1
Total number of atoms: 4529
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
Receptor
Mutations
Table of simulated mutations
(Mutations shown in blue at the viewer)
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | V | - |
| 275 | 275 | 7x55 | V | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | A | - |
| 275 | 275 | 7x55 | F | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | L | - |
| 275 | 275 | 7x55 | Q | - |
| 275 | 275 | 7x55 | V | - |
| 275 | 275 | 7x55 | L | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | N | - |
| 275 | 275 | 7x55 | Q | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | L | - |
| 275 | 275 | 7x55 | L | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | K | - |
| 275 | 275 | 7x55 | D | - |
| 275 | 275 | 7x55 | T | - |
| 275 | 275 | 7x55 | A | - |
| 275 | 275 | 7x55 | E | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | T | - |
| 275 | 275 | 7x55 | N | - |
| 275 | 275 | 7x55 | E | - |
| 275 | 275 | 7x55 | D | - |
| 275 | 275 | 7x55 | R | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | V | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | Q | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | E | - |
| 275 | 275 | 7x55 | G | - |
| 275 | 275 | 7x55 | M | - |
| 275 | 275 | 7x55 | P | - |
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | S | - |
| 275 | 275 | 7x55 | D | - |
| 275 | 275 | 7x55 | F | - |
| 275 | 275 | 7x55 | T | - |
| 275 | 275 | 7x55 | T | - |
