PlaF - Simulated Extraction of Fatty Acid Throgh T3
| dc.contributor.author | Gentile, Rocco | |
| dc.date.accessioned | 2025-05-26T11:53:04Z | |
| dc.date.available | 2025-05-26T11:53:04Z | |
| dc.date.issued | 2023-03-17 | |
| dc.description.abstract | Simulation to build up and simulate the extraction of FFA from the bound state with t-PlaF back in the soluble fraction. | |
| dc.description.sponsorship | SFB1208/DFG | |
| dc.identifier.uri | https://researchdata.test.hhu.de/handle/entry/143 | |
| dc.language.iso | en | |
| dc.publisher | AG Gohlke | |
| dc.subject | NATURAL SCIENCES::Chemistry::Molecular biophysics | |
| dc.title | PlaF - Simulated Extraction of Fatty Acid Throgh T3 | |
| dc.type | Dataset | |
| lister.experiment-info.context | [["", "metadata section", "Project", "", ""], ["", "Title", "CRC 1208: Identity and Dynamcis of Membrane Systems - from Molecules to Cellular Functions 3. Funding Phase", "", ""], ["", "Subproject (CPCLab)", "", "", ""], ["", "Type", "nichtwirtschaftliches Drittmittelprojekt", "", ""], ["", "Sponsor", "", "", ""], ["", "Cooperation partners", "", "", ""], ["", "AObj-Nr.", "", "", ""], ["", "Project manager", "Prof. Holger Gohlke", "", ""], ["", "Responsible in working group", "", "", ""], ["", "Project staff", "Rocco Gentile Lisa Kersten", "", ""], ["", "Start", "in planning from 01.01.2024", "", ""], ["", "End", "", "", ""], ["", "Status", "Project proposal in preparation", "", ""], ["", "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_Simulated Extraction of Fatty Acid through T3", "", ""], ["", "creation date", "2023-03-17 17:45:51", "", ""], ["", "category", "experiments", "", ""], ["", "author", "Rocco Gentile", "", ""], ["", "tags", "3_MD Simulation|1_Drylab|2_PlaF|3_Umbrella Sampling", "", ""], ["", "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", "Lipid21", "", ""], [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", " [A]SMD ", "", ""], [23, "velocity", "1", "", "Å ns−1"], [23, "reaction_coordinate", "reaction_coordinate", "", ""], [23, "fxyz", "x,y,z axis/the reaction coordinate", "", ""], [23, "force_constant", "5", "", "kcal mol−1 Å−2"], [23, "No of_Stages", "5", "", ""], [23, "No_Replicas_per_Stage", "50", "", ""], [23, "Simulation_time_per_Stage", "1", "", "ns"], ["-", "section level 0", "Umbrella sampling", "", ""], [24, "US force constant", "5 kcal mol–1 Å–2", "", ""], [24, "US windows", "28", "", ""], [24, "US record time", "2 ps", "", ""], [24, "PMF method", "Weighted Histogram Analysis Method", "", ""], [24, "US equilibration time", "100 ns", "", ""], [24, "US distribution overlap", "33.6±3.1%", "", ""], [24, "PMF_convergence_step", "20 ns", "", ""], [24, "US independent chunk", "20 ns", "", ""]] | en |
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