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Revista de Chimie (Rev. Chim.), Year 2008, Volume 59, Issue 11,

https://doi.org/10.37358/RC.08.11.2015

Ana-Nicoleta Bondar, Minoru Sugihara

Theoretical Analysis of Hydrogen Bonding in the Active Site of Bovine Rhodopsin

Abstract:

The retinal binding pocket of bovine rhodopsin contains an extended hydrogen-bonded network that involves protein amino acids and water molecules. The protonation state and the role of Glu181, which is part of the hydrogen-bonded network, have been debated. According to the counterion switch model, Glu181 is protonated in the rhodopsin state and it becomes negatively charged (and a counterion for the protonated retinal Schiff base) in Meta II, upon proton transfer to Glu113[24, 25]. In contrast, in the complex counterion model Glu181 is negatively charged in rhodopsin, and the role of counterion is gradually shifted from Glu113 to Glu181 during activation [13]. Here we perform computer simulations to examine the energetics of a putative proton transfer path from Glu181 to the counterion of the retinal Schiff base, Glu113, in the rhodopsin and bathorhodopsin intermediates. The calculated energy barriers and reaction energies are significant. This suggests that proton transfer from Glu181 to Glu113 is very unlikely in the rhodopsin and bathorohodopsin protein structures.

Keywords:
rhodopsin; hydrogen bonding; QM/MM; proton transfer

Issue: 2008, Volume 59, Issue 11
Pages:
Publication date: 2008/10/9
https://doi.org/10.37358/RC.08.11.2015
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