Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181

Journal of Molecular Biology
Katherine F HallMichael J Bearpark

Abstract

A computational three-layer ONIOM(QM-high:QM-low:MM) hybrid scheme has been applied to analyze the protonation state of the Glu181 amino acid residue in rhodopsin, which is vital to determining the rhodopsin photoactivation mechanism. Due to conflicting evidence from previous studies, it has yet to be conclusively resolved. In this study, we fully optimize dark-state rhodopsin model structures differing only at the 181-residue site-protonated and unprotonated Glu181-and calculate several experimentally observable properties. Comparison of calculated structures, excitation energies, and NMR chemical shifts for the two models with values from the literature allows a reevaluation of previously reported conclusions. A key finding is that the S(1)-->S(2) energy level splitting, previously used as evidence for a neutral Glu181, is found to be almost identical for the two protonation states. We highlight a need for caution when interpreting experimental data. Small differences in the properties of the two model structures are also identified, which may be useful targets for future high-resolution experimental approaches.

References

Aug 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·K PetersP M Rentzepis
Jun 13, 1978·Biochemistry·A G DoukasT G Ebrey
Nov 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·T P SakmarH G Khorana
Jun 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·C LongstaffR R Rando
Jan 1, 1983·Biophysics of Structure and Mechanism·K Yamamoto, H Shichi
Jan 23, 1996·Proceedings of the National Academy of Sciences of the United States of America·D Baylor
Mar 17, 2000·Science·J Drews
Aug 5, 2000·Science·K PalczewskiM Miyano
Apr 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Tetsuji OkadaYoshinori Shichida
Apr 1, 2003·Journal of Computational Chemistry·Thom VrevenMichael J Frisch
Jul 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·Elsa C Y YanRichard A Mathies
Mar 25, 2004·Journal of the American Chemical Society·Marina CarravettaMalcolm H Levitt
Oct 20, 2004·Journal of Molecular Biology·Jade LiGebhard F X Schertler
Dec 9, 2004·Journal of the American Chemical Society·Alessandro CembranMarco Garavelli
Dec 18, 2004·Proceedings of the National Academy of Sciences of the United States of America·Tadeusz AndruniówMassimo Olivucci
Mar 17, 2005·Journal of Molecular Biology·Ashish B PatelSteven O Smith
Sep 20, 2005·Journal of Molecular Biology·Steffen LüdekeReiner Vogel
Feb 21, 2006·Physical Review Letters·I B NielsenL H Andersen
Mar 22, 2006·Accounts of Chemical Research·José A GascónVictor S Batista
Jul 21, 2006·The Journal of Physical Chemistry. B·M WankoM Elstner
Aug 11, 2006·Journal of Computational Chemistry·Azuma MatsuuraMinoru Sakurai
Oct 18, 2006·Journal of Computer-aided Molecular Design·Marius WankoMarcus Elstner
Nov 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·Pedro B CotoMassimo Olivucci
Nov 23, 2006·Angewandte Chemie·Sivakumar SekharanVolker Buss
Dec 21, 2006·Journal of the American Chemical Society·Karina Martínez-MayorgaMichael F Brown
Jul 1, 2005·Journal of Chemical Theory and Computation·José A GascónVictor S Batista

❮ Previous
Next ❯

Citations

Feb 16, 2011·Journal of the American Chemical Society·Megan N SandbergRobert R Birge
Oct 3, 2009·Journal of the American Chemical Society·Shivani AhujaSteven O Smith
Jun 7, 2012·The Journal of Chemical Physics·Benjamin P FingerhutRegina de Vivie-Riedle
Oct 26, 2016·Journal of Chemical Theory and Computation·Federico MelaccioMassimo Olivucci
Dec 18, 2016·The Journal of Chemical Physics·Alessandro BiancardiMarco Caricato
Feb 15, 2017·Journal of Chemical Theory and Computation·K V Jovan Jose, Krishnan Raghavachari
Mar 1, 2018·Annual Review of Physical Chemistry·Juan J Nogueira, Leticia González
Oct 13, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Jun-ya HasegawaHiroshi Nakatsuji
Nov 17, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Johannes Neugebauer
Mar 27, 2010·Journal of Computational Chemistry·Peng Tao, H Bernhard Schlegel
Sep 16, 2010·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Kei Tsutsui, Yoshinori Shichida
Oct 2, 2019·The Journal of Membrane Biology·Mikhail N RyazantsevMichael F Brown
Apr 16, 2013·Physical Chemistry Chemical Physics : PCCP·Hwee-Jia Tan, Ryan P A Bettens
Sep 23, 2009·Chemical Society Reviews·Jasper J van Thor
Jun 16, 2012·Physical Chemistry Chemical Physics : PCCP·Federico MelaccioMassimo Olivucci
Nov 11, 2016·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Daniele VarsanoEmanuele Coccia
Nov 10, 2009·Journal of Chemical Theory and Computation·Tadeusz Andruniów, Massimo Olivucci
Jun 23, 2009·The Journal of Physical Chemistry. a·Jean-Christophe PoullyJean-Pierre Schermann
Jan 11, 2011·Journal of Chemical Theory and Computation·Marco CaricatoMichael J Frisch
Apr 7, 2015·Chemical Reviews·Michael A Collins, Ryan P A Bettens
Apr 9, 2015·Chemical Reviews·Lung Wa ChungKeiji Morokuma
Dec 11, 2012·Journal of Chemical Theory and Computation·Thom VrevenMichael J Bearpark

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.