title: MD simulations of P-glycoprotein started from three different crystal strucures: 3G5U, 4M1M and 4KSB
author: Karmen Condic-Jurkic
description: Molecular 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. 