TITLE OF MANUSCRIPT: -------------------- Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase Lck AUTHOR LIST & AFFILIATION: ------------------------- Dheeraj Prakaash (1,2) Charline Fagnen (1,2) Graham P. Cook (3) Oreste Acuto (4) Antreas C. Kalli (1,2)* 1. Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, LS2 9DA, United Kingdom. 2. Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom. 3. Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, LS9 7TF, United Kingdom. 4. Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom. Correspondence: Antreas C. Kalli Email: a.kalli@leeds.ac.uk -------------------------------------------------------- CONTENTS = zip files + README.txt + metadata spreadsheet -------------------------------------------------------- Each zip file corresponds to CGMD/ATMD simulation data of a protein system containing: MDP files (Molecular Dynamics Parameters) GRO files (Final snapshots of simulations) XTC files (Trajectories of simulations) TPR files (Binary files containing topology and coordinates) -------------------------------------------------------- FILENAME FORMAT for GRO, XTC, TPR, MDP files -------------------------------------------- FORMAT: [A]_ [B]_ [C]_ [D].[E] | | | | | Example: CGMD_Lck-SH2_prod-1us_r1.xtc DESCRIPTION of files / filenames: -------------------------------- [A] = CGMD / ATMD -------------------------------------------------------- CGMD = coarse-grained molecular dynamics simulations in a membrane environment (Martini 2.2 forcefield) ATMD = atomistic molecular dynamics simulations in solution (CHARMM36 forcefield) [B] = System -------------------------------------------------------- Lck-FL-open = Open/active conformation of full-length Lck (including post-translational modifications) in a complex symmetric membrane containing PIP lipids Lck-FL-closed = Closed/inactive conformation of full-length Lck (including post-translational modifications) in a complex symmetric membrane containing PIP lipids Lck-FL-open_without_PIP_lipids = Open/active conformation of full-length Lck (including post-translational modifications) in a complex symmetric membrane without PIP lipids Lck-FL-closed_without_PIP_lipids = Closed/inactive conformation of full-length Lck (including post-translational modifications) in a complex symmetric membrane without PIP lipids Lck-SH2 = only the SH2 domain of Lck Lck-SH3 = only the SH3 domain of Lck Lck-SH4U = only the SH4 (post-translational modifications) and the unique domain of Lck Lck-SH234U = the SH2, SH3, and SH4U domains combined [C] = Stage of simulation and timescale of simulation -------------------------------------------------------- prod = Production stage (the final stage of simulation following energy minimization and equilibration) 1us = 1 microsecond 5us = 5 microseconds 250ns = 250 nanoseconds Note: timescale is not mentioned in MDP filenames [D] = Simulation replica number -------------------------------------------------------- (r1 to r20) = 20 replicas of CGMD simulations of each protein system. (r1 to r3) = 3 replicas of ATMD simulations of Lck-FL-open and -closed each. Note: simulation replica number is not mentioned in MDP filenames [E] = File format -------------------------------------------------------- GRO = Final snapshots of simulations in Gromacs format XTC = Trajectories of simulations TPR = Binary files containing topology and coordinates MDP = Molecular Dynamics Parameters -------------------------------------------------------- NOTE: ---- All XTC trajectories are truncated: All CGMD simulation trajectories are skipped every 100 frames All ATMD simulation trajectories are skipped every 20 frames Total frames in original simulations (not uploaded): CGMD Lck-SH domain simulations (1us) = 2500 frames (each frame = 400 picoseconds) CGMD Lck-SH234U simulations (5us) = 25000 frames (each frame = 200 picoseconds) CGMD Lck-FL simulations (5us) = 12500 frames (each frame = 400 picoseconds) ATMD Lck-FL simulations (250ns) = 6250 frames (each frame = 40 picoseconds) -------------------------------------------------------- # README file updated: 2 November 2022