An Electrostatic Funnel in the GABA-Binding Pathway

PLoS Comput Biol. 2016 Apr 27;12(4):e1004831. doi: 10.1371/journal.pcbi.1004831. eCollection 2016 Apr.

Abstract

The γ-aminobutyric acid type A receptor (GABAA-R) is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABAA-R is well characterized, and many of the binding site residues have been identified. However, most of these residues are obscured behind the C-loop that acts as a cover to the binding site. Thus, the mechanism by which the GABA molecule recognizes the binding site, and the pathway it takes to enter the binding site are both unclear. Through the completion and detailed analysis of 100 short, unbiased, independent molecular dynamics simulations, we have investigated this phenomenon of GABA entering the binding site. In each system, GABA was placed quasi-randomly near the binding site of a GABAA-R homology model, and atomistic simulations were carried out to observe the behavior of the GABA molecules. GABA fully entered the binding site in 19 of the 100 simulations. The pathway taken by these molecules was consistent and non-random; the GABA molecules approach the binding site from below, before passing up behind the C-loop and into the binding site. This binding pathway is driven by long-range electrostatic interactions, whereby the electrostatic field acts as a 'funnel' that sweeps the GABA molecules towards the binding site, at which point more specific atomic interactions take over. These findings define a nuanced mechanism whereby the GABAA-R uses the general zwitterionic features of the GABA molecule to identify a potential ligand some 2 nm away from the binding site.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • Computational Biology
  • Computer Simulation
  • Humans
  • Ion Channel Gating
  • Ligands
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Interaction Domains and Motifs
  • Protein Subunits
  • Receptors, GABA-A / chemistry*
  • Receptors, GABA-A / metabolism*
  • Static Electricity
  • gamma-Aminobutyric Acid / metabolism*

Substances

  • Ligands
  • Protein Subunits
  • Receptors, GABA-A
  • gamma-Aminobutyric Acid

Grants and funding

This project was internally funded. We thank the Livermore Institutional Grand Challenge for the computing time. We thank the Laboratory Directed Research and Development grant 13-LW-085 for funding. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-JRNL-674894.