Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides

Biochemistry
Josh V VermaasEmad Tajkhorshid

Abstract

Ubiquinone forms an integral part of the electron transport chain in cellular respiration and photosynthesis across a vast number of organisms. Prior experimental results have shown that the photosynthetic reaction center (RC) from Rhodobacter sphaeroides is only fully functional with a limited set of methoxy-bearing quinones, suggesting that specific interactions with this substituent are required to drive electron transport and the formation of quinol. The nature of these interactions has yet to be determined. Through parameterization of a CHARMM-compatible quinone force field and subsequent molecular dynamics simulations of the quinone-bound RC, we have investigated and characterized the interactions of the protein with the quinones in the Q(A) and Q(B) sites using both equilibrium simulation and thermodynamic integration. In particular, we identify a specific interaction between the 2-methoxy group of ubiquinone in the Q(B) site and the amide nitrogen of GlyL225 that we implicate in locking the orientation of the 2-methoxy group, thereby tuning the redox potential difference between the quinones occupying the Q(A) and Q(B) sites. Disruption of this interaction leads to weaker binding in a ubiquinone analogue that lacks a 2-...Continue Reading

References

Sep 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·M Y OkamuraG Feher
Aug 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J P AllenD C Rees
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Mar 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·H L AxelrodG Feher
May 17, 2000·Biochimica Et Biophysica Acta·M Y OkamuraG Feher
Mar 23, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ana DamjanovićKlaus Schulten
Dec 24, 2002·Journal of Computational Chemistry·Matteo CeccarelliMassimo Marchi
Jun 24, 2004·Journal of the American Chemical Society·Hiroshi Ishikita, Ernst-Walter Knapp
Jul 21, 2004·Journal of Computational Chemistry·Alexander D Mackerell
Jul 21, 2004·Journal of Computational Chemistry·Felix AutenriethZaida Luthey-Schulten
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Jan 17, 2009·The Journal of Physical Chemistry. B·Yuqing Deng, Benoît Roux
May 26, 2010·The Journal of Physical Chemistry. B·Jeffery B KlaudaRichard W Pastor
Aug 3, 2010·Journal of the American Chemical Society·Erik MartinSergei A Dikanov
Feb 1, 2011·Protein Science : a Publication of the Protein Society·Alexander D Scouras, Valerie Daggett
Sep 29, 2011·Journal of Computational Chemistry·Thomas SteinbrecherDavid A Case
Aug 21, 2012·Journal of Chemical Theory and Computation·Elio A CinoMikko Karttunen
Sep 4, 2013·Journal of Computational Chemistry·Christopher G MayneJames C Gumbart
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Aug 14, 2012·Journal of Chemical Theory and Computation·Peng LiuChristophe Chipot

❮ Previous
Next ❯

Citations

Jul 24, 2015·Photosynthesis Research· GovindjeeDonald R Ort
Aug 10, 2015·Biochimica Et Biophysica Acta·Vanesa Viviana Galassi, Guilherme Menegon Arantes
Mar 5, 2016·Biochimica Et Biophysica Acta·Javier L BaylonEmad Tajkhorshid

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bacterial Transport Proteins

Bacterial transport proteins facilitate active and passive transport of small molecules and solutes across the bacterial membrane. Here is the latest research.

Bacterial Transport Proteins (ASM)

Bacterial transport proteins facilitate active and passive transport of small molecules and solutes across the bacterial membrane. Here is the latest research.