Title:    In silico studies of the interactions between propofol and fentanyl using gaussian accelerated molecular dynamics - data

Citation
Faulkner C, de Leeuw NH (2020). In silico studies of the interactions between propofol and fentanyl using gaussian accelerated molecular dynamics - data. Cardiff University. https://doi.org/10.17035/d.2020.0106797733

Dataset Details

Publisher: Cardiff University

Date (year) of data becoming publicly available: 2020

Data format: .dat .py .in

Software Required: No specialist software required

Estimated total storage size of dataset: Less than 1 gigabyte

DOI : 10.17035/d.2020.0106797733

DOI URL: http://doi.org/10.17035/d.2020.0106797733

Description

The data presented here provides the basis for the results reported in the manuscript entitled "In silico studies of the interactions between propofol and fentanyl using gaussian accelerated molecular dynamics". This study utilises sophisticated GPU accelerated gaussian accelerated molecular dynamics simulations to study the interactions between the general anesthetic propofol, and the opioid anesthetic fentanyl, with the Gloeobacter violaceus ion channel (GLIC). Our results show a detailed pathway by which propofol physically blocks the ion conducting channel pore which has been predicited previously, but no pathway has previously been suggested. We also observe for the first time a direct interaction between propofol and fentanyl in which a fentanyl molecule stabilises propofol in an extracellular binding site. The structural results of propofol and fentanyl interacting at GLIC present a compelling case for the allosteric action of anesthetics and opioids at pentameric ligand-gated ion channels. 

The data here consists of Amber input files for the gaussian accelerated simulations, raw data for hydrogen-bonding and RMSD calculations, and scripts used to construct the 2D PMF plots from the re-weighted simulations.

Research results based upon these data are published at http://doi.org/10.1080/07391102.2020.1814415