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MD simulations of P-glycoprotein started from three different crystal strucures: 3G5U, 4M1M and 4KSB
Version 4 2018-01-10, 06:17
Version 3 2017-09-29, 05:00
Version 2 2017-04-10, 01:37
Version 1 2017-03-31, 08:32
dataset
posted on 2018-01-10, 06:17 authored by Karmen Condic-JurkicKarmen Condic-JurkicMolecular simulations of mouse P-glycoprotein started from three different crystal structures with PDB IDs corresponding to 3G5U, 4KSB and 4M1M. The protein was transferred to POPC/cholesterol bilayer, followed by energy minimization and 10 ns equilibration period. All the simulations were performed in Gromacs 3.3.3 in conjunction with GROMOS54a7 force field at 300 K and pressure of 1 bar. Each system was run in triplicates for 200 ns.
The uploaded fileset contains:
- MD protocol used to run simulations for 3G5U, 4M1M and 4KSB systems;
- Example input file for a production run for each system (3G5U_run1.mdp, 4M1M_run1.mdp, 4KSB_run1.mdp);
- System topologies (3G5U_memb.top, 4M1M_memb.top, 4KSB_memb.top) and relevant parameter files (3g5u.itp, 4m1m.itp, 4ksb.itp, CLR.itp, POPC.itp, vdw_OML_CH3L.itp);
- Set of three trajectories containing membrane-embedded P-glycoprotein with 1000 frames for each simulated system (snapshots printed every 200 ps);
- Movies generated from each trajectory with a more detailed description provided in Movie_Legends.pdf;
- Model data calculated using principal component analysis method, including the covariance matrices, for each replica (3G5U1-3.eda.npz, 4KSB1-3.eda.npz, 4M1M1-3.eda.npz) and for the concatenated trajectory containing all 9 replicas (3G5U_4KSB_4M1M.eda.npz). The files containing data for the transmembrane domain only have the tmd prefix. These models can be further explored in ProDy package by using loadModel() function.
- Figures representing cholesterol distributions in the upper (dark violet) and lower leaflets (light violet) in all three systems at the beginning and at the end of each simulation.
The uploaded fileset contains:
- MD protocol used to run simulations for 3G5U, 4M1M and 4KSB systems;
- Example input file for a production run for each system (3G5U_run1.mdp, 4M1M_run1.mdp, 4KSB_run1.mdp);
- System topologies (3G5U_memb.top, 4M1M_memb.top, 4KSB_memb.top) and relevant parameter files (3g5u.itp, 4m1m.itp, 4ksb.itp, CLR.itp, POPC.itp, vdw_OML_CH3L.itp);
- Set of three trajectories containing membrane-embedded P-glycoprotein with 1000 frames for each simulated system (snapshots printed every 200 ps);
- Movies generated from each trajectory with a more detailed description provided in Movie_Legends.pdf;
- Model data calculated using principal component analysis method, including the covariance matrices, for each replica (3G5U1-3.eda.npz, 4KSB1-3.eda.npz, 4M1M1-3.eda.npz) and for the concatenated trajectory containing all 9 replicas (3G5U_4KSB_4M1M.eda.npz). The files containing data for the transmembrane domain only have the tmd prefix. These models can be further explored in ProDy package by using loadModel() function.
- Figures representing cholesterol distributions in the upper (dark violet) and lower leaflets (light violet) in all three systems at the beginning and at the end of each simulation.
