Genetically Encoded Red Fluorescent Indicators for Imaging Intracellular and Extracellular Potassium Ions
Creators: name: Pathiranage, Vishaka
name: Walker, Alice R.
Publisher: name: Zenodo
Year: 2024

description: 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