QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2

Kai Welke, Hiroshi Watanabe, Tino Wolter, Michael Gaus, Marcus Elstner

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Channelrhodopsin-2 is a light-gated ion channel, which has been studied intensively over the last decade. Vibrational spectroscopic experiments started to shed light on the structural changes, that occur during the photocycle, especially in the hydrogen-bonded network surrounding the protonated D156 and C128-the DC gate. However, the interpretation of these experiments was only based on homology models. Since then, an X-ray structure and better computational models became available. In this article, we show that in combination with a recent reparametrization, the approximate DFT method, DFTB, is able to describe the effects of hydrogen bonding on the CO stretch vibration in carboxylic acids reliably and agrees well with full DFT results. We apply DFTB in a QM/MM framework to perform vibrational analysis of buried aspartic acids in bacteriorhodopsin and channelrhodopsin-2. Using this approach, we can simulate the FTIR spectral difference between D115 in the dark-adapted and K states of bacteriorhodopsin. The FTIR experiments on the DC gate in channelrhodopsin-2 are well described using an indirect model, where D156 and C128 are bridged via a water molecule.

Original languageEnglish
Pages (from-to)6651-6659
Number of pages9
JournalPhysical Chemistry Chemical Physics
Volume15
Issue number18
DOIs
Publication statusPublished - 2013 May 14
Externally publishedYes

Fingerprint

Bacteriorhodopsins
Vibrational spectra
vibrational spectra
Discrete Fourier transforms
direct current
aspartic acid
simulation
light ions
Experiments
homology
hydrogen
Carbon Monoxide
Carboxylic Acids
Ion Channels
Aspartic Acid
carboxylic acids
Hydrogen
Hydrogen bonds
X rays
vibration

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2. / Welke, Kai; Watanabe, Hiroshi; Wolter, Tino; Gaus, Michael; Elstner, Marcus.

In: Physical Chemistry Chemical Physics, Vol. 15, No. 18, 14.05.2013, p. 6651-6659.

Research output: Contribution to journalArticle

Welke, Kai ; Watanabe, Hiroshi ; Wolter, Tino ; Gaus, Michael ; Elstner, Marcus. / QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2. In: Physical Chemistry Chemical Physics. 2013 ; Vol. 15, No. 18. pp. 6651-6659.
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