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2 results for “ligand coupling”
The coupling mechanism of ligands with SERT distinguishes substrates from inhibitors (raw data)
<p>Raw data of the manuscript: Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors</p> <p><strong>Abstract:</strong></p> <p>The presynaptic serotonin transporter (SERT) reuptakes the serotonin (5HT) released into the synaptic cleft, thus ensuring temporal and spatial regulation of serotonergic signalling. Clinically approved drugs used for the treatment of neurological disorders, including depression and anxiety modulate SERT by trapping the transporter in the outward-open conformation. Illicit drugs of abuse as amphetamines act as substrates but reverse the transport direction, thereby releasing intracellular accumulated 5HT. Both mechanisms increase extracellular 5HT levels. Stoichiometry of the transport cycle has been described by kinetic schemes, the structures of the main conformations within the transport cycle revealed static coordinates. By combining <em>in-silico</em> approaches with <em>in-vitro</em> experiments and making use of a homologous series of 5HT analogues, we decoded the essential coupling mechanism between the substrate and the transporter which triggers uptake. The free energy calculations showed that only scaffold-bound substrates can correctly close the extracellular gate by pulling on the bundle domain through long-range electrostatic interactions. The associated spatial and physico-chemical requirements define substrate and inhibitor properties, opening new possibilities for rational drug design approaches.</p>
G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations
<p>Data and Python scripts used for generation and analysis of RAMD dissociation trajectories for several GPCR complexes (including example showing generation of the Protein-Ligand Interaction Fingerprints, IFP, for several representative RAMD trajectories),</p> <p>reported in the manuscript</p> <p>"G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tRAMD Simulations" "G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations"</p> <p>by Daria B. Kokh, Rebecca C. Wade</p> <p>submitted to the Journal of Chemical Theory and Computation</p> <p> </p> <p>1. <strong>README.txt </strong>- instruction for script usage</p> <p>2. <strong>PDBs.zip</strong> - PDB structures of complexes in water box used in the analysis, ligand PDB and mol2 structures</p> <p>3. <strong>tauRAMD_v2.py </strong>- Python sctipt for estimation relative residence times from Gromacs-RAMD output </p> <p>4. <strong>IFP_preprocess_Gromacs.py</strong> and <strong>IFP_SL-B2AR-WB-EX.py - </strong>Python scripts for preprocessing of RAMD trajectories and generation of IFPs</p> <p>5. <strong>Scripts.zip</strong> - additional python functions </p> <p>6. <strong>IXO-CHL.zip, IXO-ALO-CHL.zip, ACh-CHL.zip, b2AR.zip</strong> - Protein-Ligand Interaction Fingerprints (PL IFPs) generated from RAMD trajectories for <em>mAChR M2 with iperoxo</em>, <em>mAChR M2 </em><em> with iperoxo and PAM, mAChR M2 with ACh, and </em>β<em>2AR with alprenolol </em><em>.</em> </p> <p>7. <strong>Topology.zip</strong> - Gromacs topology, index.ndx, and coordinate gro files for all four systems</p> <p>8. <strong>Example_b2AR-alprenolol.zip </strong>- a set of data for a test example showing how IFP can be generated from RAMD trajectories (including several representative trajectories)</p> <p>9. <strong>Example_b2AR-alprenolol.tar </strong>- almost the same set of data as above (compressed in Windows) but for Linux users. The only difference between tar and zip archive: a short equilibration trajectory that is missing in the zip set but is included in the tar archive.</p> <p>10.<strong> Gromacs-IFP-GPCR.ipynb</strong> - Jupyter Notebook for analysis of trajectories using generated IFP data</p> <p>11. <strong>Auxi-Plots-GPCR.ipynb - </strong>Jupyter Notebook for generation additional plots from the paper</p> <p>12. <strong>Waters.zip</strong> - number of water molecules in the binding pocket in dissociation trajectories of the <em> </em>β<em>2AR - alprenolol system</em></p> <p>13. <strong>GPCR.yml</strong> - JN environment file</p> <p> </p>
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