Simulation report

Technical information

General information

Name: Frizzled-6 (apoform)

PDB id: HOMO

Submitted by: Schulte lab, Karolinska Institutet

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Chloride (572 mM), Sodium ion (517 mM)

Number of molecules:

Water: 10000

POPC: 300

Chloride: 103

Sodium ion: 93

Smothened agonist: 1

Frizzled-6: 1

Total number of atoms: 149367

Simulation details

Software and version: GROMACS, 2019.2

Forcefield and version: CHARMM36, GAFF2, CHARMM36, GAFF2

Time step : 2.0 fs

Delta : 0.3 ns

Replicates: 4

Accumulated simulation time: 1.2507000000000001 µs

Additonal parameters: Available at "Simulation protocol & starting files"



References

Ainoleena Turku; Hannes Schihada; Pawel Kozielewicz; Carl-Fredrik Bowin; Gunnar Schulte. 2021. Residue 6.43 defines receptor function in class F GPCRs. Nature communications 12 (1). doi: 10.1038/s41467-021-24004-z. (https://doi.org/10.1038/s41467-021-24004-z)


Simulation components

Receptor

PDB id: HOMO
Frizzled-6

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Mutations

Table of simulated mutations

Residue ID Residue seq. position Generic num. From To


Other molecules



Sodium ion

Specific State ID: 5016

(93 molecules)

Na+


Chloride

Specific State ID: 5017

(103 molecules)

Cl-


POPC

Specific State ID: 5018

(300 molecules)


Water

Specific State ID: 5019

(10000 molecules)

H2O


Smothened agonist

Specific State ID: 5167

(1 molecule)