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Deconstructing activation events in rhodopsin.

Elena N Laricheva1, Karunesh Arora, Jennifer L Knight

  • 1Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

Journal of the American Chemical Society
|July 12, 2013
PubMed
Summary
This summary is machine-generated.

The protonation of E134 in rhodopsin (Rh) is linked to the movement of helix H6 during activation. This pH-dependent process reveals E134

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biophysics

Background:

  • Class-A G-protein-coupled receptors (GPCRs) undergo significant structural changes during activation, involving interhelical network reorganization.
  • In rhodopsin (Rh), activation is coupled to the protonation state of glutamate 134 (E134), but its precise role remains unclear.
  • Studying millisecond, pH-dependent processes like E134 protonation presents experimental challenges.

Purpose of the Study:

  • To elucidate the structural mechanisms underlying E134 protonation during rhodopsin activation.
  • To investigate the interplay between E134 protonation state and helix H6 movement.
  • To refine existing models of rhodopsin activation at an atomic level.

Main Methods:

  • Development of a computational scheme combining harmonic Fourier beads (HFB) and constant-pH molecular dynamics with pH-based replica exchange (pH-REX).
  • Simulation of structural changes along the activation pathway as a function of E134 protonation.
  • Analysis of interhelical network rearrangements and salt bridge dynamics.

Main Results:

  • E134 protonation is triggered by a ~4.0° tilt and ~23° rotation of helix H6.
  • H6 movement disrupts salt bridges (E247-R135, R135-E134), releasing E134 and increasing its pKa above physiological pH.
  • Increased local hydrophobicity further promotes H6 motion and E134 pKa upshift, indicating a coupled mechanism.

Conclusions:

  • The E134 protonation switch is both a cause and consequence of H6 motion during rhodopsin activation.
  • This study provides atomic-level insights into a pH-dependent activation mechanism not easily accessible experimentally.
  • Findings refine the sequential model of rhodopsin activation, highlighting the dynamic interplay of structural elements.