Simulation report
Technical information
General information
Name: Fzd5 (g180-c539) y470a (apoform)
PDB id: Homo
Description: The study investigated conformational/structural differences between wild-type FZD5 and single-point mutants with interesting characteristics as determined in wet-lab experiments. Equilibration was done separately for each replica. Coordinate file is after equilibration1. Unbiased MD, NPT ensemble
Submitted by: Magdalena Scharf, Karolinska Institute
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Chloride (188 mM), Sodium ion (147 mM)
Number of molecules:
Water: 16251
POPC: 148
Chloride: 55
Sodium ion: 43
Frizzled-5: 1
Total number of atoms: 74359
Simulation details
Software and version: GROMACS, 2021.3
Forcefield and version: CHARMM, 36m
Time step : 2.0 fs
Delta : 0.1 ns
Replicates: 3
Accumulated simulation time: 1.5003000000000002 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
. None. . . doi: Graetz-et-al.
GPCRmd publication page: 1496
Lukas Grätz, Maria Kowalski-Jahn, Magdalena M. Scharf, Pawel Kozielewicz, Michael Jahn, Julien Bous, Nevin A. Lambert, David E. Gloriam, Gunnar Schulte. 2023. Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations. Nature Communications 14. doi: https://doi.org/10.1038/s41467-023-40213-0. (https://www.nature.com/articles/s41467-023-40213-0)
GPCRmd publication page: 1502
Simulation components
Receptor
Mutations
Table of simulated mutations
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|
