CB2 Receptor Signaling Complexes with Beta-Arrestin-2 and Gi Protein

CB2 receptor signaling complexes with beta-arrestin-2 and Gi protein
Eun Ha Heo and Ravinder Abrol (CSUN)
11/27/2024 (Zenodo)

System names as filename prefixes:

CB2R-WT-NoPhosphoC_BARR2_*: wildtype CB2 receptor without phosphorylated C-terminus bound to beta-arrestin-2.
 
CB2R-WT-NoPhosphoC_Gi-Empty_*: wildtype CB2 receptor without phosphorylated C-terminus bound to nucleotide-free Gi protein (no GDP).
 
CB2R-WT-NoPhosphoC_Gi-GDP_*: wildtype CB2 receptor without phosphorylated C-terminus bound to Gi-GDP.
 
CB2R-WT-PhosphoC_BARR2_*: wildtype CB2 receptor with a phosphorylated C-terminus bound to beta-arrestin-2. 

CB2R-Q63R-NoPhosphoC_BARR2_*: CB2 receptor mutant Q63R without phosphorylated C-terminus bound to beta-arrestin-2.

CB2R-Q63R-NoPhosphoC_Gi-Empty_*: CB2 receptor mutant Q63R without phosphorylated C-terminus bound to nucleotide-free Gi protein (no GDP).

CB2R-Q63R-NoPhosphoC_Gi-GDP_*: CB2 receptor mutant Q63R without phosphorylated C-terminus bound to Gi-GDP.

CB2R-Q63R-PhosphoC_BARR2_*: CB2 receptor mutant Q63R with a phosphorylated C-terminus bound to beta-arrestin-2. 

CB2R-L133I-NoPhosphoC_BARR2_*: CB2 receptor mutant L133I without phosphorylated C-terminus bound to beta-arrestin-2.

CB2R-L133I-NoPhosphoC_Gi-Empty_*: CB2 receptor mutant L133I without phosphorylated C-terminus bound to nucleotide-free Gi protein (no GDP). 

CB2R-L133I-NoPhosphoC_Gi-GDP_*: CB2 receptor mutant L133I without phosphorylated C-terminus bound to Gi-GDP. 

CB2R-L133I-PhosphoC_BARR2_*: CB2 receptor L133I mutant with a phosphorylated C-terminus bound to beta-arrestin-2. 

Different file types in following folders when uncompressed:

Folder: PDB files for signaling complex starting and average structures
*_md.pdb: Solvated complex structures used as starting geometries.
*_avgframe#.pdb: PDB file of average frame given by #.

Folder: MD simulation input files for Amber MD
*_md.inpcrd: input coordinates file for MD job
*_md.prmtop: parameter and topology file for MD job
Step1_mini_solv.in: mdin file for energy minimization of solvent keeping protein fixed.
Step2_equi_solv.in: mdin file for NPT equilibration of solvent while keeping protein fixed.
Step3_mini_full.in: mdin file for energy minimization of whole system.
Step4_heat_full.in: mdin file for heating system under NPT of whole system.
Step5_equi_full.in: mdin file for NPT equilibration of whole system.
Step6_prod_full.in: mdin file for 100ns production NPT equilibration of whole system. 
Step7a_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.
Step7b_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.
Step7c_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.
Step7d_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.

Folder: MD trajectories
*_step7_ai_stride10.xtc: Trajectory file in Gromacs xtc format.