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

<p>CB2 receptor signaling complexes with beta-arrestin-2 and Gi protein<br>Eun Ha Heo and Ravinder Abrol (CSUN)<br>11/27/2024 (Zenodo)</p> <p>System names as filename prefixes:</p> <p>CB2R-WT-NoPhosphoC_BARR2_*: wildtype CB2 receptor without phosphorylated C-terminus bound to beta-arrestin-2.<br>&nbsp;<br>CB2R-WT-NoPhosphoC_Gi-Empty_*: wildtype CB2 receptor without phosphorylated C-terminus bound to nucleotide-free Gi protein (no GDP).<br>&nbsp;<br>CB2R-WT-NoPhosphoC_Gi-GDP_*: wildtype CB2 receptor without phosphorylated C-terminus bound to Gi-GDP.<br>&nbsp;<br>CB2R-WT-PhosphoC_BARR2_*: wildtype CB2 receptor with a phosphorylated C-terminus bound to beta-arrestin-2.&nbsp;</p> <p>CB2R-Q63R-NoPhosphoC_BARR2_*: CB2 receptor mutant Q63R without phosphorylated C-terminus bound to beta-arrestin-2.</p> <p>CB2R-Q63R-NoPhosphoC_Gi-Empty_*: CB2 receptor mutant Q63R without phosphorylated C-terminus bound to nucleotide-free Gi protein (no GDP).</p> <p>CB2R-Q63R-NoPhosphoC_Gi-GDP_*: CB2 receptor mutant Q63R without phosphorylated C-terminus bound to Gi-GDP.</p> <p>CB2R-Q63R-PhosphoC_BARR2_*: CB2 receptor mutant Q63R with a phosphorylated C-terminus bound to beta-arrestin-2.&nbsp;</p> <p>CB2R-L133I-NoPhosphoC_BARR2_*: CB2 receptor mutant L133I without phosphorylated C-terminus bound to beta-arrestin-2.</p> <p>CB2R-L133I-NoPhosphoC_Gi-Empty_*: CB2 receptor mutant L133I without phosphorylated C-terminus bound to nucleotide-free Gi protein (no GDP).&nbsp;</p> <p>CB2R-L133I-NoPhosphoC_Gi-GDP_*: CB2 receptor mutant L133I without phosphorylated C-terminus bound to Gi-GDP.&nbsp;</p> <p>CB2R-L133I-PhosphoC_BARR2_*: CB2 receptor L133I mutant with a phosphorylated C-terminus bound to beta-arrestin-2.&nbsp;</p> <p><br>Different file types in following folders when uncompressed:</p> <p>Folder: PDB files for signaling complex starting and average structures<br>*_md.pdb: Solvated complex structures used as starting geometries.<br>*_avgframe#.pdb: PDB file of average frame given by #.</p> <p>Folder: MD simulation input files for Amber MD<br>*_md.inpcrd: input coordinates file for MD job<br>*_md.prmtop: parameter and topology file for MD job<br>Step1_mini_solv.in: mdin file for energy minimization of solvent keeping protein fixed.<br>Step2_equi_solv.in: mdin file for NPT equilibration of solvent while keeping protein fixed.<br>Step3_mini_full.in: mdin file for energy minimization of whole system.<br>Step4_heat_full.in: mdin file for heating system under NPT of whole system.<br>Step5_equi_full.in: mdin file for NPT equilibration of whole system.<br>Step6_prod_full.in: mdin file for 100ns production NPT equilibration of whole system.&nbsp;<br>Step7a_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.<br>Step7b_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.<br>Step7c_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.<br>Step7d_prod_full.in: mdin file for 500ns production NPT equilibration of whole system.</p> <p>Folder: MD trajectories<br>*_step7_ai_stride100.xtc: Trajectory file in Gromacs xtc format.</p>