Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding
- Washington University School of Medicine, United States
Abstract
Activation of heterotrimeric G proteins is a key step in many signaling cascades. However, a complete mechanism for this process, which requires allosteric communication between binding sites that are ~30 Å apart, remains elusive. We construct an atomically-detailed model of G protein activation by combining three powerful computational methods: metadynamics, Markov state models (MSMs), and CARDS analysis of correlated motions. We uncover a mechanism that is consistent with a wide variety of structural and biochemical data. Surprisingly, the rate-limiting step for GDP release correlates with tilting rather than translation of the GPCR-binding helix 5. β-Strands 1-3 and helix 1 emerge as hubs in the allosteric network that links conformational changes in the GPCR-binding site to disordering of the distal nucleotide-binding site and consequent GDP release. Our approach and insights provide foundations for understanding disease-implicated G protein mutants, illuminating slow events in allosteric networks, and examining unbinding processes with slow off-rates.
Data availability
Summary data for all figures are made available with this manuscript. Specifically, MSM data, CARDS data, and numerical data for histograms are each provided as zipped archives. Simulation data are available upon request as there is no standard repository for such data, especially given the size of our dataset (3847 GB). The algorithms employed for calculating geometric features of protein conformations are available through MDTraj (https://github.com/mdtraj/mdtraj) and methods for building and analyzing MSMs are available through MSMBuilder (https://github.com/msmbuilder/msmbuilder) and Enspara (https://github.com/bowman-lab/enspara). The CARDS algorithm is also available through Enspara.
Article and author information
Author details
Funding
National Institutes of Health (Grant R01GM12400701)
- Gregory R Bowman
National Science Foundation (CAREER Award MCB-1552471)
- Gregory R Bowman
Burroughs Wellcome Fund (Career Award at the Scientific Interface)
- Gregory R Bowman
David and Lucile Packard Foundation (Packard Fellowship for Science and Engineering)
- Gregory R Bowman
National Institutes of Health (Grant R01GM044592)
- Kendall Blumer
- Gregory R Bowman
National Institutes of Health (Grant R01GM12409301)
- Kendall Blumer
- Gregory R Bowman
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2018, Sun 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
-
- 4,206
- views
-
- 624
- downloads
-
- 57
- 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)
Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding
eLife 7:e38465.
https://doi.org/10.7554/eLife.38465
