Computational design of environmental sensors for the potent opioid fentanyl
- University of Washington, United States
- Colorado State University, United States
- Lawrence Berkeley National Laboratory, United States
- Institute of Chemical Sciences and Engineering (ISIC), Switzerland
Abstract
We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.
Article and author information
Author details
Funding
National Cancer Institute (F32CA171572)
- Matthew J Bick
Howard Hughes Medical Institute
- Matthew J Bick
- Per J Greisen
- David La
- David Baker
Defense Threat Reduction Agency (HDTRA1-13-1-0054)
- Matthew J Bick
- Per J Greisen
- Kevin J Morey
- Mauricio S Antunes
- June I Medford
- David Baker
European Molecular Biology Organization (EMBO ALTF 1605-2011)
- Per J Greisen
Carlsbergfondet
- Per J Greisen
National Institutes of Health
- Banumathi Sankaran
National Institute of General Medical Sciences
- Banumathi Sankaran
U.S. Department of Energy (DE-AC02-05CH11231)
- Banumathi Sankaran
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Benjamin F Cravatt, The Scripps Research Institute, United States
Version history
- Received: May 23, 2017
- Accepted: September 18, 2017
- Accepted Manuscript published: September 19, 2017 (version 1)
- Version of Record published: October 24, 2017 (version 2)
Copyright
© 2017, Bick et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 7,785
- views
-
- 1,087
- downloads
-
- 78
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Computational design of environmental sensors for the potent opioid fentanyl
eLife 6:e28909.
https://doi.org/10.7554/eLife.28909
Further reading
-
- Biochemistry and Chemical Biology
Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventional in vitro and cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.
-
- Biochemistry and Chemical Biology
- Chromosomes and Gene Expression
Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
