Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

Elife. 2018 Oct 5;7:e38465. doi: 10.7554/eLife.38465.

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.

Keywords: G proteins; Markov state models; allostery; computational biology; molecular biophysics; molecular dynamics; none; structural biology; systems biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Allosteric Regulation
  • Binding Sites
  • GTP-Binding Protein alpha Subunits, Gq-G11 / chemistry
  • GTP-Binding Protein alpha Subunits, Gq-G11 / metabolism
  • GTP-Binding Proteins / chemistry
  • GTP-Binding Proteins / metabolism*
  • Guanosine Diphosphate / chemistry
  • Guanosine Diphosphate / metabolism*
  • Markov Chains
  • Molecular Dynamics Simulation*
  • Probability
  • Protein Structure, Secondary
  • Receptors, G-Protein-Coupled / chemistry
  • Receptors, G-Protein-Coupled / metabolism
  • Thermodynamics

Substances

  • Receptors, G-Protein-Coupled
  • Guanosine Diphosphate
  • GTP-Binding Proteins
  • GTP-Binding Protein alpha Subunits, Gq-G11