Research Data Leeds Repository

Systematic simulation of the interactions of Pleckstrin homology domains with membranes: dataset

Le Huray, Kyle I.P. and Kalli, Antreas C. (2022) Systematic simulation of the interactions of Pleckstrin homology domains with membranes: dataset. University of Leeds. [Dataset] https://doi.org/10.5518/1085

Dataset 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 raw coarse-grained molecular dynamics (CG MD) simulation data for all 100 individual PH domains.

Keywords:	molecular dynamics simulations, membrane proteins, cell signalling, biochemistry, biophysics, computational biochemistry
Subjects:	C000 - Biological sciences > C700 - Molecular biology, biophysics & biochemistry
Divisions:	Faculty of Biological Sciences > Astbury Centre for Structural Molecular Biology
Related resources:	Location Type http://doi.org/10.1126/sciadv.abn6992 Publication https://eprints.whiterose.ac.uk/186303/ Publication
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	30 Jun 2022 20:07
URI:	http://archive.researchdata.leeds.ac.uk/id/eprint/992
Additional details Additional details Creators: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Le Huray, Kyle I.P. https://orcid.org/0000-0002-7518-5666 University Of Leeds https://ror.org/024mrxd33 ROR Kalli, Antreas C. https://orcid.org/0000-0001-7156-9403 University Of Leeds https://ror.org/024mrxd33 ROR Type of data: Dataset Research funders: BBSRC, British Heart Foundation Grant numbers: BB/M011151/1, PG/21/10515 Publication date: 2022 Data collection method: Molecular dynamics simulations Resource language: English Metadata language: English Research project title: White Rose Doctoral Training Partnership in Mechanistic Biology and its Strategic Application Publisher: University of Leeds Contact Email Address: bskipl@leeds.ac.uk Last Modified: 01 Jul 2022 13:08

Files

Documentation

Readme [11kB] Readme [11kB] Readme [11kB] Visible to: Anyone File name: readme.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 11kB

Data

PH_domain_simulations_part1 [6GB] PH_domain_simulations_part1 [6GB] PH_domain_simulations_part1 [6GB] Visible to: Anyone File name: PH_domain_simulations_part1.zip Content type: Data Description: Simulation data for the PH domains of acap1, ADAP1 (PH1), ADAP1 (PH2), AFAP1L2, agap2, akap13, akt1, akt2, akt3 and anln Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part2 [6GB] PH_domain_simulations_part2 [6GB] PH_domain_simulations_part2 [6GB] Visible to: Anyone File name: PH_domain_simulations_part2.zip Content type: Data Description: Simulation data for the PH domains of Apbb1ip, APPL1, APPL2, ARAP2, ARHGAP21, ARHGAP25, ARHGAP27, arhgap9, ARHGEF1 and Arhgef16 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part3 [6GB] PH_domain_simulations_part3 [6GB] PH_domain_simulations_part3 [6GB] Visible to: Anyone File name: PH_domain_simulations_part3.zip Content type: Data Description: Simulation data for the PH domains of Arhgef18, ARHGEF2, ARHGEF28, Arhgef3, ARHGEF4, Arhgef6, Arhgef9, asap1, Asap1 and BCR Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part4 [6GB] PH_domain_simulations_part4 [6GB] PH_domain_simulations_part4 [6GB] Visible to: Anyone File name: PH_domain_simulations_part4.zip Content type: Data Description: Simulation data for the PH domains of btk, CADPS, CERT, cyth2, cyth3, dapp1, dnm1, DNM2, DNM3 and dock9 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part5 [6GB] PH_domain_simulations_part5 [6GB] PH_domain_simulations_part5 [6GB] Visible to: Anyone File name: PH_domain_simulations_part5.zip Content type: Data Description: Simulation data for the PH domains of dok2, Dok7, ELMO1, Exoc8, Farp2 (PH1), Fermt1, fermt2, FERMT3, FGD3 and Fgd6 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part6 [6GB] PH_domain_simulations_part6 [6GB] PH_domain_simulations_part6 [6GB] Visible to: Anyone File name: PH_domain_simulations_part6.zip Content type: Data Description: Simulation data for the PH domains of GRB10, GRB14, GRK2, inpp5b, ipcef1, IQSEC1, IRS1, Mcf2l, OCRL and OSBPL11 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part7 [6GB] PH_domain_simulations_part7 [6GB] PH_domain_simulations_part7 [6GB] Visible to: Anyone File name: PH_domain_simulations_part7.zip Content type: Data Description: Simulation data for the PH domains of OSBPL8, pdpk1, plcd1, Plcg1 (PH1), PLEK2, PLEKHA1 (PH2), Plekha2, PLEKHA3, plekha4 and PLEKHA5 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part8 [6GB] PH_domain_simulations_part8 [6GB] PH_domain_simulations_part8 [6GB] Visible to: Anyone File name: PH_domain_simulations_part8.zip Content type: Data Description: Simulation data for the PH domains of PLEKHA6, PLEKHA7, Plekhb1, Plekhb2, PLEKHM2, PLEK (PH1), PLEK (PH2), p-rex1, PREX2 and PRKD2 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part9 [6GB] PH_domain_simulations_part9 [6GB] PH_domain_simulations_part9 [6GB] Visible to: Anyone File name: PH_domain_simulations_part9.zip Content type: Data Description: Simulation data for the PH domains of PRKD3, Ralgps1, RAPH1, Rock2, Sbf1, Sh2b2, SKAP1, Skap2, Sos1 and sptbn1 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

PH_domain_simulations_part10 [6GB] PH_domain_simulations_part10 [6GB] PH_domain_simulations_part10 [6GB] Visible to: Anyone File name: PH_domain_simulations_part10.zip Content type: Data Description: Simulation data for the PH domains of SPTBN2, stap1, SWAP70, TBC1D2, TEC, Tiam1 (PH1), Tiam2 (PH1), TRIO (PH1), TRIO (PH2) and VAV1 Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB