Cryo-EM of the eukaryotic purine transporter UapA demonstrates intramolecular and lipid regulation of transport.

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The data uploaded are in-silico calculations performed for the manuscript entitled "Cryo-EM of the eukaryotic purine transporter UapA demonstrates intramolecular and lipid regulation of transport." The uploaded compressed folders contain data for calculations described in the article. More specifically: 1. MOLECULAR DYNAMICS SIMULATIONS MD Simulation performed on the Cryo-EM UapA Inward Facing structure as well as the UapA Occluded and Outward Facing models using GROMACS. Each one of the compressed folders uploaded to Zenodo contains the .tpr input files for all phases (Minimization, Equilibration and Production) for each of the MD Simulations performed, as well as 2 to 3 frames illustrating the whole system at the beginning and end of the calculation in .pdb format. The systems were built using CHARMM-GUI as described in the PNAS manuscript. The .tpr files included in each one of the folders are described below. step6.0_minimization.tpr: Input file for the energy minimization phase. Used to remove steric clashes and contains restraints. (-DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0) step6.1_equilibration.tpr: Input file for the 1st Equilibration step (NVT Ensemble). Initial heating phase with strong position restraints. (-DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0) step6.2_equilibration.tpr: Input file for the 2nd Equilibration step (NVT ensemble). Slightly reduced position restraints. (-DPOSRES -DPOSRES_FC_BB=2000.0 -DPOSRES_FC_SC=1000.0 -DPOSRES_FC_LIPID=400.0 -DDIHRES -DDIHRES_FC=400.0) step6.3_equilibration.tpr: Input file for the 3rd Equilibration step (NPT ensemble). introduction of pressure coupling. (-DPOSRES -DPOSRES_FC_BB=1000.0 -DPOSRES_FC_SC=500.0 -DPOSRES_FC_LIPID=400.0 -DDIHRES -DDIHRES_FC=200.0) step6.4_equilibration.tpr: Input file for the 4th Equilibration step (NPT ensemble). Further reduction of restraints. (-DPOSRES -DPOSRES_FC_BB=500.0 -DPOSRES_FC_SC=200.0 -DPOSRES_FC_LIPID=200.0 -DDIHRES -DDIHRES_FC=200.0) step6.5_equilibration.tpr: Input file for the 5th Equilibration step (NPT ensemble). Final relaxation of restraints. (-DPOSRES -DPOSRES_FC_BB=200.0 -DPOSRES_FC_SC=50.0 -DPOSRES_FC_LIPID=40.0 -DDIHRES -DDIHRES_FC=100.0) step6.6_equilibration.tpr: Input file for the 6th Equilibration step (NPT ensemble). Final pre-production phase (-DPOSRES -DPOSRES_FC_BB=50.0 -DPOSRES_FC_SC=0.0 -DPOSRES_FC_LIPID=0.0 -DDIHRES -DDIHRES_FC=0.0) step7.tpr: Input file for the main Production MD phase (No position restraints applied). The final production step7.tpr files were created after extending the original .tpr files. MD Simulation Data Description UapA_apo-Inward.zip MD Simulation performed in the AupA Inward cryo-EM structure in the apo state. The folder contains all the .tpr files described above as well as 2 frames in .pdb format. frame_1.pdb: first frame of the MD Simulation frame_3365.pdb: Last frame of the MD Simulation UapA_apo-Occluded.zip MD Simulation performed in the AupA Occluded model in the apo state. The folder contains all the .tpr files described above as well as 2 frames in .pdb format. frame_1.pdb: first frame of the MD Simulation frame_2017.pdb: Last frame of the MD Simulation UapA_apo-Outward.zip MD Simulation performed in the AupA Occluded model in the apo state. The folder contains all the .tpr files described above as well as 2 frames in .pdb format. frame_1.pdb: first frame of the MD Simulation frame_2500.pdb: Last frame of the MD Simulation UapA_xanthine-Inward.zip MD Simulation performed in the AupA Inward structure in complex with xanthine. The folder contains all the .tpr files described above as well as 3 frames in .pdb format. frame_1.pdb: first frame of the MD Simulation frame_452.pdb: frame depicting the first xanthine exiting the UapA pore frame_629.pdb: frame showing the second xanthine leaving the UapA pore. UapA_xanthine_waters-Inward.zip MD Simulation performed in the AupA Inward structure in complex with xanthine as well as 3 stable cryo-EM waters. The folder contains all the .tpr files described above as well as 2 frames in .pdb format. frame_1.pdb: first frame of the MD Simulation frame_3790.pdb: frame illustrating that the first xanthine exited the UapA pore. 2. UAPA - HYPOXANTHINE STRUCTURES Structures Description Hypoxathine_structures.zip 3 top ranked docking structures of wild type UapA as well as Q408E UapA in complex with hypoxanthine, described in the manuscript are included in the folder. 3. Solvent Mapping Calculations Structures Description Solvent_Maps.zip UapA_Xanthine-Inward_HighEnergy_waters.pdb: Water map depicting the high energy waters calculated in the pore of UapA inward cryo-EM structure. UapA_Xanthine-Inward_LowEnergy_waters.pdb: Water map depicting the low energy waters calculated in the pore of UapA inward cryo-EM structure.

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