PlaF - FLD Simulations to study FFA Binding in the Water Phase to t-PlaF
| dc.contributor.author | Gentile, Rocco | |
| dc.date.accessioned | 2025-05-26T11:43:59Z | |
| dc.date.available | 2025-05-26T11:43:59Z | |
| dc.date.issued | 2023-03-17 | |
| dc.description.abstract | To build up and simulate systems that allow us to discriminate the effect of FFA on PlaF monomers when localised in the soluble fraction. | |
| dc.description.sponsorship | SFB1208/DFG | |
| dc.identifier.uri | https://researchdata.test.hhu.de/handle/entry/139 | |
| dc.language.iso | en | |
| dc.publisher | AG Gohlke | |
| dc.subject | NATURAL SCIENCES::Chemistry::Molecular biophysics | |
| dc.subject.ddc | 500 Naturwissenschaften und Mathematik::540 Chemie | |
| dc.title | PlaF - FLD Simulations to study FFA Binding in the Water Phase to t-PlaF | |
| dc.type | Dataset | |
| lister.experiment-info.context | [["", "metadata section", "Project", "", ""], ["", "Title", "CRC 1208: Identity and Dynamcis of Membrane Systems - from Molecules to Cellular Functions 2. Funding Phase", "", ""], ["", "Subproject (CPCLab)", "A03: Functional state modulation of membrane proteins by dynamic association and dissociation", "", ""], ["", "Type", "nichtwirtschaftliches Drittmittelprojekt", "", ""], ["", "Sponsor", "", "", ""], ["", "Cooperation partners", "", "", ""], ["", "AObj-Nr.", "", "", ""], ["", "Project manager", "Prof. Holger Gohlke", "", ""], ["", "Responsible in working group", "", "", ""], ["", "Project staff", "Rocco Gentile since 01/2020 Lisa Kersten since 09/2021", "", ""], ["", "Start", "01.01.2020", "", ""], ["", "End", "31.12.2023", "", ""], ["", "Status", "active", "", ""], ["", "Further informations", "", "", ""], ["", "metadata section", "Study", "", ""], ["", "Aim", "Molecular Mechanisms underlying Activity Regulation of the Phospholipase PlaF from P. aeruginosa by Free Fatty Acids", "", ""], ["", "Responsible", "Rocco Gentile", "", ""], ["", "Currently working on study", "Rocco Gentile", "", ""], ["", "Previously worked on system", "Stephan Schott Verdugo, Sabahuddin Ahmad", "", ""], ["", "Start", "01.01.2021", "", ""], ["", "End", "31.12.2023", "", ""], ["", "Further information", "", "", ""], ["", "Storage of research data", "", "", ""], ["", "Publication (DOI)", "", "", ""], ["", "metadata section", "System", "", ""], ["", "Title", "", "", ""], ["", "Responsible", "Rocco Gentile", "", ""], ["", "Currently working on system", "", "", ""], ["", "Previously worked on system", "", "", ""], ["", "Further informations", "", "", ""], ["", "metadata section", "Experiment Info", "", ""], ["", "title", "PlaF_FLD Simulations to study FFA Binding in the Water Phase to t-PlaF", "", ""], ["", "creation date", "2023-03-17 17:43:56", "", ""], ["", "category", "experiments", "", ""], ["", "author", "Rocco Gentile", "", ""], ["", "tags", "3_MD Simulation|1_Drylab|2_PlaF", "", ""], ["", "metadata section", "Experiment Context", "", ""], ["-", "section level 0", "Preparation and Environment", "", ""], [4, "PDB_ID", "6i8w", "", ""], [4, "alignment tool", "OPM", "", ""], [4, "protonation method", "pdb2pqr", "", ""], [4, "pH", "7.4", "", ""], [4, "pKa method", "PROPKA", "", ""], [5, "membrane packing tool", "PACKMOL-Memgen", "", ""], [5, "membrane protein orienting tool", "memembed", "", ""], [6, "lipid ratio", "3:1", "", ""], [6, "lipid composition", "DOPE:DOPG", "", ""], [6, "FFA concentration", "30mM", "", ""], [6, "lipid force field", "Lipid17", "", ""], [7, "salt concentration", "0.15M", "", ""], [7, "salt", "KCl", "", ""], [8, "salt", "KCl", "", ""], ["-", "section level 0", "Solvation", "", ""], [9, "box type", "rectangular", "", ""], [9, "water type", "OPC", "", ""], [9, "shell radius", "15 Å", "", ""], [10, "simulation type", "All-atom molecular dynamics", "", ""], [10, "MD suite", "AMBER22", "", ""], [10, "force field", "ff14SB", "", ""], [10, "force field", "Lipid14", "", ""], [10, "force field", "Lipid17", "", ""], [10, "force field", "TIP3P", "", ""], [10, "parameters", "Li and Merz 12-6", "", ""], [11, "dt_fs", "4 fs", "", ""], [12, "thermostat", "Langevin", "", ""], [12, "gamma_ln", "1 ps-1", "", ""], [12, "temp0", "300 K", "", ""], [13, "barostat", "Berendsen", "", ""], [13, "taup", "1 ps", "", ""], [15, "cut", "10 Å", "", ""], ["-", "section level 0", "Minimization", "", ""], [17, "restraint_wt", "25 kcal mol-1 Å-2", "", ""], [17, "restrained elements", "protein atoms/membrane atoms/ligand atoms", "", ""], ["-", "section level 0", "Thermalization and Relaxation", "", ""], [18, "simulation time", "25 ps", "", ""], [18, "ensemble", "NVT", "", ""], [18, "temp0", "300 K", "", ""], [18, "simulation time", "975 ps", "", ""], [18, "pres0", "1 bar", "", ""], [18, "temp0", "300 K", "", ""], [19, "restraint_wt", "10 kcal mol-1 Å-2", "", ""], [20, "simulation time", "4 ns", "", ""], [20, "ensemble", "NPT", "", ""], [21, "simulation time", "500 ps", "", ""], ["-", "section level 0", "Production", "", ""], [22, "replicates", "12", "", ""], [22, "simulation time", "1 μs", "", ""], [22, "ensemble", "NVT", "", ""], ["-", "section level 0", "Analysis", "", ""], [23, "trajectory processing tool", "cpptraj", "", ""], [23, "replicates", "12", "", ""], [24, "t3 entrance", "COM of residues K170,Q234,Y236", "", ""], [24, "trajectory processing tool", "cpptraj", "", ""], ["-", "section level 0", "DensityMaps", "", ""], [25, "function", "grid function", "", ""], [25, "trajectory processing tool", "cpptraj", "", ""], [25, "grid spacing", "1.5A", "", ""]] | en |
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