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Simulation report

Technical information

General information

Name: Dopamine d2 receptor (apoform) (apoform)

PDB id: 6CM4

Activation state: Inactive

Description: Production simulations for each replica were run for 1 µs each, at constant volume (NVT ensemble), 1013 bar and 310 K

Submitted by: Ramon Guixà-González, Paul Scherrer Institut

System setup

Solvent type: Implicit

Membrane type: Heterogeneous

Membrane composition: PSM (23.7%), SDPC (13.0%), CHL1 (33.1%), DOPC (10.7%), DSPC (5.3%), DPPC (14.2%)

Number of molecules:

Cholesterol: 112

N-palmitoylsphingomyelin: 80

1,2-dipalmitoylphosphatidylcholine: 48

1-stearoyl-2-docosahexanoyl-sn-glycero-3-phosphocholine: 44

DOPC: 36

DSPC: 18

D(2) dopamine receptor: 1

Total number of atoms: 42931

Simulation details

Software and version: ACEMD, 3.3.0

Forcefield and version: CHARMM, CHARMM36m

Time step : 4.0 fs

Delta : 1.0 ns

Replicates: 4

Accumulated simulation time: 3.735 µs

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

Simulation protocol & starting files

References

Marie-Lise Jobin, Véronique De Smedt-Peyrusse, Fabien Ducrocq, Rim Baccouch, Asma Oummadi, Maria Hauge Pedersen, Brian Medel-Lacruz, Maria-Florencia Angelo, Sandrine Villette, Pierre Van Delft, Laetitia Fouillen, Sébastien Mongrand, Jana Selent, Tarson Tolentino-Cortez, Gabriel Barreda-Gómez, Stéphane Grégoire, Elodie Masson, Thierry Durroux, Jonathan A. Javitch, Ramon Guixà-González, Isabel D. Alves, Pierre Trifilieff. 2023. Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling. Molecular Psychiatry. doi: 10.1038/s41380-022-01928-6.



GPCRmd publication page: 1495

Simulation components

Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue ID Residue seq. position Generic num. From To
397 222 5x71 V -
397 222 5x71 N -
397 222 5x71 T -
397 222 5x71 K -
397 222 5x71 R -
397 222 5x71 S -
397 222 5x71 S -
397 222 5x71 R -
397 222 5x71 A -
397 222 5x71 F -
397 222 5x71 R -
397 222 5x71 A -
397 222 5x71 H -
397 222 5x71 L -
397 222 5x71 R -
397 222 5x71 A -
397 222 5x71 P -
397 222 5x71 L -
397 222 5x71 K -
397 222 5x71 G -
397 222 5x71 N -
397 222 5x71 C -
397 222 5x71 T -
397 222 5x71 H -
397 222 5x71 P -
397 222 5x71 E -
397 222 5x71 D -
397 222 5x71 M -
397 222 5x71 K -
397 222 5x71 L -
397 222 5x71 C -
397 222 5x71 T -
397 222 5x71 V -
397 222 5x71 I -
397 222 5x71 M -
397 222 5x71 K -
397 222 5x71 S -
397 222 5x71 N -
397 222 5x71 G -
397 222 5x71 S -
397 222 5x71 F -
397 222 5x71 P -
397 222 5x71 V -
397 222 5x71 N -
397 222 5x71 R -
397 222 5x71 R -
397 222 5x71 R -
397 222 5x71 V -
397 222 5x71 E -
397 222 5x71 A -
397 222 5x71 A -
397 222 5x71 R -
397 222 5x71 R -
397 222 5x71 A -
397 222 5x71 Q -
397 222 5x71 E -
397 222 5x71 L -
397 222 5x71 E -
397 222 5x71 M -
397 222 5x71 E -
397 222 5x71 M -
397 222 5x71 L -
397 222 5x71 S -
397 222 5x71 S -
397 222 5x71 T -
397 222 5x71 S -
397 222 5x71 P -
397 222 5x71 P -
397 222 5x71 E -
397 222 5x71 R -
397 222 5x71 T -
397 222 5x71 R -
397 222 5x71 Y -
397 222 5x71 S -
397 222 5x71 P -
397 222 5x71 I -
397 222 5x71 P -
397 222 5x71 P -
397 222 5x71 S -
397 222 5x71 H -
397 222 5x71 H -
397 222 5x71 Q -
397 222 5x71 L -
397 222 5x71 T -
397 222 5x71 L -
397 222 5x71 P -
397 222 5x71 D -
397 222 5x71 P -
397 222 5x71 S -
397 222 5x71 H -
397 222 5x71 H -
397 222 5x71 G -
397 222 5x71 L -
397 222 5x71 H -
397 222 5x71 S -
397 222 5x71 T -
397 222 5x71 P -
397 222 5x71 D -
397 222 5x71 S -
397 222 5x71 P -
397 222 5x71 A -
397 222 5x71 K -
397 222 5x71 P -
397 222 5x71 E -
397 222 5x71 K -
397 222 5x71 N -
397 222 5x71 G -
397 222 5x71 H -
397 222 5x71 A -
397 222 5x71 K -
397 222 5x71 D -
397 222 5x71 H -
397 222 5x71 P -
397 222 5x71 K -
397 222 5x71 I -
397 222 5x71 A -
397 222 5x71 K -
397 222 5x71 I -
397 222 5x71 F -
397 222 5x71 E -
397 222 5x71 I -
397 222 5x71 Q -
397 222 5x71 T -
397 222 5x71 M -
397 222 5x71 P -
397 222 5x71 N -
397 222 5x71 G -
397 222 5x71 K -
397 222 5x71 T -
397 222 5x71 R -
397 222 5x71 T -
397 222 5x71 S -
397 222 5x71 L -
397 222 5x71 K -
397 222 5x71 T -
397 222 5x71 M -
397 222 5x71 S -
397 222 5x71 R -
397 222 5x71 R -
397 222 5x71 K -
397 222 5x71 L -

Other molecules



N-palmitoylsphingomyelin

Specific State ID: 5328

(80 molecules)


1-stearoyl-2-docosahexanoyl-sn-glycero-3-phosphocholine

Specific State ID: 5329

(44 molecules)


Cholesterol

Specific State ID: 5166

(112 molecules)


DOPC

Specific State ID: 5324

(36 molecules)


DSPC

Specific State ID: 5327

(18 molecules)


1,2-dipalmitoylphosphatidylcholine

Specific State ID: 5325

(48 molecules)


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