Genetically Encoded Red Fluorescent Indicators for Imaging Intracellular and Extracellular Potassium Ions

Below is the description of the deposited files. File Name Description RGEPO2-300-K.gif Short simulation video of free diffusion of a potassium ion at 300 mM ionic concentration in RGEPO2, in GIF format RGEPO2-300-K.mov Short simulation video of free diffusion of potassium ion at 300 mM ionic concentration in RGEPO2, in MOV format RGEPO1-300-K.gif Short simulation video of free diffusion of potassium ion at the main binding site, at 300 mM ionic concentration in RGEPO1, in GIF format RGEPO1-300-K.mov Short simulation video of free diffusion of potassium ion at the main binding site,at 300 mM ionic concentration in RGEPO1, in MOV format mdin.1 Script to minimize bad contacts in the structure mdin.2 to mdin.5 Scripts to equilibrate density, slowly lifting restraints, at low temperature mdin.6 Script to slowly heat the system to 300K, with restraints replaced mdin.7 to mdin.12 Scripts to equilibrate density again, slowly lifting restraints on protein and then chromophore mdin.prod Script to run standard molecular dynamics with Langevin thermostat regpo1-20mM-K_bound.pdb Potassium bound cooridnate file of RGEPO1 at the transient binding site, at 20 mM ionic concentration rgepo1-300mM-K_bound.pdb Potassium bound cooridnate file of RGEPO1 at the main binding site, at 300 mM ionic concentration rgepo2-20mM-K_bound.pdb Potassium bound cooridnate file of RGEPO2 at the binding site, at 20 mM ionic concentration rgepo2-300mM-K_bound.pdb Potassium bound cooridnate file of RGEPO2 at the binding site, at 300 mM ionic concentration rgepo1-20mM.parm7 Topology file of RGEPO1 free diffusion simulation at 20 mM ionic concentration rgepo1-20mM_init0.rst7 Initial restart file of RGEPO1 free diffusion simulation at 20 mM ionic concentration rgepo1-20mM_md100.rst7 Restart file of RGEPO1 free diffusion simulation at 20 mM ionic concentration after 100 ns rgepo1-20mM_md200.rst7 Restart file of RGEPO1 free diffusion simulation at 20 mM ionic concentration after 200 ns rgepo1-300mM.parm7 Topology file of RGEPO1 free diffusion simulation at 300 mM ionic concentration rgepo1-300mM_init0.rst7 Initial restart file of RGEPO1 free diffusion simulation at 300 mM ionic concentration rgepo1-300mM_md100.rst7 Restart file of RGEPO1 free diffusion simulation at 300 mM ionic concentration after 100 ns rgepo1-300mM_md200.rst7 Restart file of RGEPO1 free diffusion simulation at 300 mM ionic concentration after 200 ns rgepo2-20mM.parm7 Topology file of RGEPO2 free diffusion simulation at 20 mM ionic concentration rgepo2-20mM_init0.rst7 Initial restart file of RGEPO2 free diffusion simulation at 20 mM ionic concentration rgepo2-20mM_md100.rst7 Restart file of RGEPO2 free diffusion simulation at 20 mM ionic concentration after 100 ns rgepo2-300mM.parm7 Topology file of RGEPO2 free diffusion simulation at 300 mM ionic concentration rgepo2-300mM_init0.rst7 Initial restart file of RGEPO2 free diffusion simulation at 300 mM ionic concentration rgepo2-20mM_md100.rst7 Restart file of RGEPO2 free diffusion simulation at 300 mM ionic concentration after 100 ns rgepo1-300mM-K_bound_at_7pvc.parm7 Topology file of the RGEPO1 simulation at 300 mM ionic concentration, with potassium initially placed at the reported Kpb site (PDB ID: 7PVC) rgepo1-300mM-K_bound_at_7pvc_init0.rst7 Initial restart file of the RGEPO1 simulation at 300 mM ionic concentration, with potassium placed at the reported Kpb site (PDB ID: 7PVC) rgepo1-300mM-K_bound_at_7pvc_md100.rst7 Restart file after 100 ns of RGEPO1 simulation at 300 mM ionic concentration, with potassium initially placed at the reported Kpb site (PDB ID: 7PVC) rgepo2-300mM-K_bound_at_7pvc.parm7 Topology file of the RGEPO2 simulation at 300 mM ionic concentration, with potassium initially placed at the reported Kpb site (PDB ID: 7PVC) rgepo2-300mM-K_bound_at_7pvc_init0.rst7 Initial restart file of the RGEPO2 simulation at 300 mM ionic concentration, with potassium placed at the reported Kpb site (PDB ID: 7PVC) rgepo2-300mM-K_bound_at_7pvc_md100.rst7 Restart file after 100 ns of RGEPO2 simulation at 300 mM ionic concentration, with potassium initially placed at the reported Kpb site (PDB ID: 7PVC) Chromophore.frcmod Parameter modification file of the chromophore Chromophore.mol2 Mol2 file of the chromophore