------------------- GENERAL INFORMATION 1. Title: Systematic simulation of the interactions of Pleckstrin homology domains with membranes: dataset 2. Description: Pleckstrin homology (PH) domains can recruit proteins to membranes by recognition of phosphatidylinositol phosphate (PIP) lipids. Several family members are linked to diseases including cancer. In Le Huray et al., "Systematic simulation of the interactions of Pleckstrin homology domains with membranes", Science Advances, 2022, we report the systematic simulation of the interactions of 100 mammalian PH domains with PIP-containing membranes. This dataset contains the raw coarse-grained molecular dynamics (CG MD) simulation data for all 100 individual PH domains reported in this publication. 3. Author information A. Principal Investigator Contact Information Name: Dr Antreas Kalli Institution: University of Leeds Email: a.kalli@leeds.ac.uk B. Dataset Creator Contact Information Name: Kyle Le Huray Institution: University of Leeds Email: bskipl@leeds.ac.uk ------------------- DATA & FILE OVERVIEW For convenience, the data has been divided into 10 zips, each containing the simulation data for 10 PH domains in 10 separate folders. [zip name] [description] PH_domain_simulations_part1.zip Simulation data for the PH domains of acap1, ADAP1 (PH1), ADAP1 (PH2), AFAP1L2, agap2, akap13, akt1, akt2, akt3 and anln PH_domain_simulations_part2.zip Simulation data for the PH domains of Apbb1ip, APPL1, APPL2, ARAP2, ARHGAP21, ARHGAP25, ARHGAP27, arhgap9, ARHGEF1 and Arhgef16 PH_domain_simulations_part3.zip Simulation data for the PH domains of Arhgef18, ARHGEF2, ARHGEF28, Arhgef3, ARHGEF4, Arhgef6, Arhgef9, asap1, Asap1 and BCR PH_domain_simulations_part4.zip Simulation data for the PH domains of btk, CADPS, CERT, cyth2, cyth3, dapp1, dnm1, DNM2, DNM3 and dock9 PH_domain_simulations_part5.zip Simulation data for the PH domains of dok2, Dok7, ELMO1, Exoc8, Farp2 (PH1), Fermt1, fermt2, FERMT3, FGD3 and Fgd6 PH_domain_simulations_part6.zip Simulation data for the PH domains of GRB10, GRB14, GRK2, inpp5b, ipcef1, IQSEC1, IRS1, Mcf2l, OCRL and OSBPL11 PH_domain_simulations_part7.zip Simulation data for the PH domains of OSBPL8, pdpk1, plcd1, Plcg1 (PH1), PLEK2, PLEKHA1 (PH2), Plekha2, PLEKHA3, plekha4 and PLEKHA5 PH_domain_simulations_part8.zip Simulation data for the PH domains of PLEKHA6, PLEKHA7, Plekhb1, Plekhb2, PLEKHM2, PLEK (PH1), PLEK (PH2), p-rex1, PREX2 and PRKD2 PH_domain_simulations_part9.zip Simulation data for the PH domains of PRKD3, Ralgps1, RAPH1, Rock2, Sbf1, Sh2b2, SKAP1, Skap2, Sos1 and sptbn1 PH_domain_simulations_part10.zip Simulation data for the PH domains of SPTBN2, stap1, SWAP70, TBC1D2, TEC, Tiam1 (PH1), Tiam2 (PH1), TRIO (PH1), TRIO (PH2) and VAV1 Folder architechture: The data for each PH domain is contained in a folder with the general naming convention Genename_StructurePDBcode_MembraneModel, e.g. DNM2_2ys1_PM for simulations of the DNM2 PH domain using protein structure 2ys1 and a plasma membrane inner leaflet model (note that all simulations in this dataset are run with the plasma membrane model as described in the related publication). Where a gene encodes multiple PH domains the number of the PH domain is added after the gene name, e.g. TRIO_PH1_1nty_PM or TRIO_PH2_6d8z_PM. Each PH domain folder contains a number of simulation files, as described in the example below for the acap1 PH domain. Equilibration (eq) and production (md) simulation files are named using the same naming convention as the folder system, prefixed by either eq or md and suffixed by replicate number in the case of production simulation files. [file name] [description] acap1_4nsw_input.pdb The atomistic protein structure model used for input to the CG simulation pipeline em.protein.gro Coordinates of the energy minimised CG protein em.protein.tpr Run input binary for CG protein energy minimisation em.protein+lipids+w+ions.gro Coordinates of the energy minimised CG simulation system em.protein+lipids+w+ions.tpr Run input binary for simulation system energy minimisation eq.acap1_4nsw_PM.gro Coordinates of the equilibrated simulation system, used as the initial positions for all production simulations eq.acap1_4nsw_PM.tpr Run input binary for equilibration of the simulation system md.acap1_4nsw_PM_1_thinned.xtc Production simulation replicate 1 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_1.gro Production simulation replicate 1 final frame coordinate file md.acap1_4nsw_PM_1.tpr Production simulation replicate 1 run input binary md.acap1_4nsw_PM_10_thinned.xtc Production simulation replicate 10 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_10.gro Production simulation replicate 10 final frame coordinate file md.acap1_4nsw_PM_10.tpr Production simulation replicate 10 run input binary md.acap1_4nsw_PM_11_thinned.xtc Production simulation replicate 11 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_11.gro Production simulation replicate 11 final frame coordinate file md.acap1_4nsw_PM_11.tpr Production simulation replicate 11 run input binary md.acap1_4nsw_PM_12_thinned.xtc Production simulation replicate 12 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_12.gro Production simulation replicate 12 final frame coordinate file md.acap1_4nsw_PM_12.tpr Production simulation replicate 12 run input binary md.acap1_4nsw_PM_13_thinned.xtc Production simulation replicate 13 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_13.gro Production simulation replicate 13 final frame coordinate file md.acap1_4nsw_PM_13.tpr Production simulation replicate 13 run input binary md.acap1_4nsw_PM_14_thinned.xtc Production simulation replicate 14 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_14.gro Production simulation replicate 14 final frame coordinate file md.acap1_4nsw_PM_14.tpr Production simulation replicate 14 run input binary md.acap1_4nsw_PM_15_thinned.xtc Production simulation replicate 15 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_15.gro Production simulation replicate 15 final frame coordinate file md.acap1_4nsw_PM_15.tpr Production simulation replicate 15 run input binary md.acap1_4nsw_PM_16_thinned.xtc Production simulation replicate 16 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_16.gro Production simulation replicate 16 final frame coordinate file md.acap1_4nsw_PM_16.tpr Production simulation replicate 16 run input binary md.acap1_4nsw_PM_17_thinned.xtc Production simulation replicate 17 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_17.gro Production simulation replicate 17 final frame coordinate file md.acap1_4nsw_PM_17.tpr Production simulation replicate 17 run input binary md.acap1_4nsw_PM_18_thinned.xtc Production simulation replicate 18 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_18.gro Production simulation replicate 18 final frame coordinate file md.acap1_4nsw_PM_18.tpr Production simulation replicate 18 run input binary md.acap1_4nsw_PM_19_thinned.xtc Production simulation replicate 19 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_19.gro Production simulation replicate 19 final frame coordinate file md.acap1_4nsw_PM_19.tpr Production simulation replicate 19 run input binary md.acap1_4nsw_PM_2_thinned.xtc Production simulation replicate 2 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_2.gro Production simulation replicate 2 final frame coordinate file md.acap1_4nsw_PM_2.tpr Production simulation replicate 2 run input binary md.acap1_4nsw_PM_20_thinned.xtc Production simulation replicate 20 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_20.gro Production simulation replicate 20 final frame coordinate file md.acap1_4nsw_PM_20.tpr Production simulation replicate 20 run input binary md.acap1_4nsw_PM_3_thinned.xtc Production simulation replicate 3 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_3.gro Production simulation replicate 3 final frame coordinate file md.acap1_4nsw_PM_3.tpr Production simulation replicate 3 run input binary md.acap1_4nsw_PM_4_thinned.xtc Production simulation replicate 4 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_4.gro Production simulation replicate 4 final frame coordinate file md.acap1_4nsw_PM_4.tpr Production simulation replicate 4 run input binary md.acap1_4nsw_PM_5_thinned.xtc Production simulation replicate 5 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_5.gro Production simulation replicate 5 final frame coordinate file md.acap1_4nsw_PM_5.tpr Production simulation replicate 5 run input binary md.acap1_4nsw_PM_6_thinned.xtc Production simulation replicate 6 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_6.gro Production simulation replicate 6 final frame coordinate file md.acap1_4nsw_PM_6.tpr Production simulation replicate 6 run input binary md.acap1_4nsw_PM_7_thinned.xtc Production simulation replicate 7 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_7.gro Production simulation replicate 7 final frame coordinate file md.acap1_4nsw_PM_7.tpr Production simulation replicate 7 run input binary md.acap1_4nsw_PM_8_thinned.xtc Production simulation replicate 8 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_8.gro Production simulation replicate 8 final frame coordinate file md.acap1_4nsw_PM_8.tpr Production simulation replicate 8 run input binary md.acap1_4nsw_PM_9_thinned.xtc Production simulation replicate 9 1 us trajectory, (thinned to 5% of original frames) md.acap1_4nsw_PM_9.gro Production simulation replicate 9 final frame coordinate file md.acap1_4nsw_PM_9.tpr Production simulation replicate 9 run input binary protein-cg_box.pdb Coordinate file of CG protein in simulation box protein-cg.pdb Coordinate file of CG protein topol.top Simulation system topology file ------------------- METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: These data were generated using coarse grained molecular dynamics simulations, based on protein structure models obtained from the protein databank and a model of the inner leaflet of the mammalian plasma membrane. These were run using v2.1 of the Martini CG force field and GROMACS 5.0.7. 2. Methods for processing the data: Due to storage limitations the trajectories have been thinned to 5% of their original frames. 3. This work was undertaken on ARC3 and ARC4, part of the High Performance Computing facilities at the University of Leeds, UK. ------------------- FUNDING INFORMATION 1. This work was funded by the Biotechnology and Biological Sciences Research Council (grant BB/M011151/1). 2. Dr. Antreas Kalli is also funded by the British Heart Foundation (grant PG/21/10515).