Millisecond molecular dynamics simulation of the mu Opioid Receptor

Type of resource
software, multimedia
Date created
2015 - 2017

Digital content

Context

Item belongs to a collection

Folding@home Collection

Metadata associated with publications derived from data generated on the Folding@home distributed computing network. Includes trajectory and Markov state model (MSM) data.
Digital collection
12 digital items

Description

Abstract/Contents

Abstract
The μ Opioid Receptor (μOR) is a G-Protein Coupled Receptor (GPCR) that mediates pain and is a key target for clinically administered analgesics. The current generation of prescribed opiates -- drugs that bind to μOR -- engender dangerous side effects such as respiratory depression and addiction in part by stabilizing off-target conformations of the receptor. To determine both the key conformations of μOR to atomic resolution as well as the transitions between them, long timescale molecular dynamics (MD) simulations were conducted and analyzed. These simulations predict new and potentially druggable metastable states that have not been observed by crystallography. We applied cutting edge algorithms (e.g., tICA and Transfer Entropy) to guide our analysis and distill the key events and conformations from simulation, presenting a transferrable and systematic analysis scheme. Our approach provides a complete, predictive model of the dynamics, structure of states, and structure-ligand relationships of μOR with broad applicability to GPCR biophysics and medicinal chemistry.

Bibliographic information

Preferred Citation
Feinberg, Evan N and Barati Farimani, Amir and Pande, Vijay S. (2015-2017). Millisecond molecular dynamics simulation of the mu Opioid Receptor. Stanford Digital Repository. Available at: https://purl.stanford.edu/rj473gf5751
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Location
https://arxiv.org/abs/1803.04479
Location
https://purl.stanford.edu/rj473gf5751

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License
This work is licensed under a Creative Commons Attribution Share Alike 3.0 Unported license (CC BY-SA).
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