Computational Simulation of the Activation Cycle of Gα Subunit in the G Protein Cycle Using an Elastic Network Model

PLoS One. 2016 Aug 2;11(8):e0159528. doi: 10.1371/journal.pone.0159528. eCollection 2016.

Abstract

Agonist-activated G protein-coupled receptors (GPCRs) interact with GDP-bound G protein heterotrimers (Gαβγ) promoting GDP/GTP exchange, which results in dissociation of Gα from the receptor and Gβγ. The GTPase activity of Gα hydrolyzes GTP to GDP, and the GDP-bound Gα interacts with Gβγ, forming a GDP-bound G protein heterotrimer. The G protein cycle is allosterically modulated by conformational changes of the Gα subunit. Although biochemical and biophysical methods have elucidated the structure and dynamics of Gα, the precise conformational mechanisms underlying the G protein cycle are not fully understood yet. Simulation methods could help to provide additional details to gain further insight into G protein signal transduction mechanisms. In this study, using the available X-ray crystal structures of Gα, we simulated the entire G protein cycle and described not only the steric features of the Gα structure, but also conformational changes at each step. Each reference structure in the G protein cycle was modeled as an elastic network model and subjected to normal mode analysis. Our simulation data suggests that activated receptors trigger conformational changes of the Gα subunit that are thermodynamically favorable for opening of the nucleotide-binding pocket and GDP release. Furthermore, the effects of GTP binding and hydrolysis on mobility changes of the C and N termini and switch regions are elucidated. In summary, our simulation results enabled us to provide detailed descriptions of the structural and dynamic features of the G protein cycle.

MeSH terms

  • Animals
  • Cattle
  • Computer Simulation
  • Databases, Protein
  • GTP-Binding Protein alpha Subunits, Gs / chemistry
  • GTP-Binding Protein alpha Subunits, Gs / metabolism*
  • GTP-Binding Proteins / chemistry
  • GTP-Binding Proteins / metabolism*
  • Guanosine Diphosphate / metabolism
  • Guanosine Triphosphate / metabolism
  • Humans
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Rats
  • Receptors, Adrenergic, beta-2 / metabolism
  • Thermodynamics
  • Wolves

Substances

  • Receptors, Adrenergic, beta-2
  • Guanosine Diphosphate
  • Guanosine Triphosphate
  • GTP-Binding Proteins
  • GTP-Binding Protein alpha Subunits, Gs

Grants and funding

This research was supported by Pioneer Research Center Program (2012-0009579) and Basic Science Research Program (2015R1D1A1A01057280) through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning and by the Ministry of Education. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.