Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein.

Proceedings of the National Academy of Sciences of the United States of America
Jocelyne VreedePeter G Bolhuis

Abstract

Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the alpha-helical region 43-51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge that is part of the N-terminal domain. Additional molecular dynamics simulations indicate that the exposure of the chromophore does not result in a productive pathway. We discuss several possibilities for experimental validation of these predictions. Our results open the way for studying millisecond conformational changes in other medium-sized (signaling) proteins.

References

May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J L PellequerE D Getzoff
Jan 28, 2003·Biophysical Journal·Johnny HendriksKlaas J Hellingwerf
Feb 22, 2005·Biophysical Journal·Jocelyne VreedePeter G Bolhuis
Apr 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Robert B Best, Gerhard Hummer
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Christopher D SnowVijay S Pande
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hyotcherl IheeKeith Moffat
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Jul 21, 2006·The Journal of Physical Chemistry. B·Ao Ma, Aaron R Dinner
Sep 1, 2006·The Journal of Chemical Physics·Baron Peters, Bernhardt L Trout
Mar 29, 2007·The Journal of Physical Chemistry. B·Elske J M LeendersEvert Jan Meijer
Jul 28, 2007·The Journal of Chemical Physics·Baron PetersBernhardt L Trout
Aug 5, 2008·Biophysical Journal·Jarek Juraszek, Peter G Bolhuis
May 27, 2009·The Journal of Chemical Physics·Eric Vanden-Eijnden, Maddalena Venturoli
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Xuhui HuangVijay S Pande

❮ Previous
Next ❯

Citations

Sep 29, 2011·Biochemistry·Sabyashachi Mishra, Amedeo Caflisch
Oct 28, 2011·The Journal of Physical Chemistry. B·Dimitri Antoniou, Steven D Schwartz
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Gerhard Hummer
Apr 5, 2011·The Journal of Chemical Physics·Kazuhito Itoh, Masaki Sasai
Nov 9, 2010·The Journal of Chemical Physics·Wolfgang LechnerPeter G Bolhuis
Nov 26, 2015·The Journal of Physical Chemistry. B·Koichi Tamura, Shigehiko Hayashi
Dec 21, 2010·Current Opinion in Biotechnology·Gregg T BeckhamMichael F Crowley
Jul 3, 2015·The Journal of Physical Chemistry. B·Sanjib Paul, Srabani Taraphder
Mar 23, 2011·Journal of Molecular Graphics & Modelling·Martin Raunest, Christian Kandt
Sep 10, 2014·Molecular Simulation·Wenjin Li, Ao Ma
Oct 31, 2014·PLoS Computational Biology·Mary A RohrdanzCecilia Clementi
Oct 12, 2010·Current Opinion in Pharmacology·Matthew C Zwier, Lillian T Chong
Jul 12, 2017·The Journal of Physical Chemistry. B·Ioanna ZoiSteven D Schwartz
Jul 14, 2017·Physical Chemistry Chemical Physics : PCCP·Z Faidon BrotzakisPeter G Bolhuis
Aug 1, 2015·Physical Chemistry Chemical Physics : PCCP·Wojciech PlazinskiMateusz Drach
Jun 16, 2015·Nature Communications·F PontiggiaD Kern
Jun 13, 2012·Chemistry : a European Journal·Jeung-Hoi Ha, Stewart N Loh
Apr 25, 2020·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Tanmoy Kumar Paul, Srabani Taraphder
Apr 28, 2012·Journal of Computational Chemistry·Wojciech Plazinski, Mateusz Drach
Apr 17, 2019·Nature Communications·Kei-Ichi OkazakiGerhard Hummer
Aug 11, 2020·The Journal of Chemical Physics·Yusuke MoriNobuyuki Matubayasi
Aug 23, 2011·Physical Chemistry Chemical Physics : PCCP·Jan-Hendrik PrinzFrank Noé
Nov 11, 2019·The Journal of Chemical Physics·Z Faidon Brotzakis, Peter G Bolhuis
Dec 29, 2020·Photochemistry and Photobiology·Maria-Andrea MroginskiIgor Schapiro
Dec 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Xuewei JiangYi Xiao
Apr 18, 2021·Nature Communications·Maithili Krishnan-SchmiedenAnjali Pandit
May 19, 2011·The Journal of Physical Chemistry Letters·Gregg T Beckham, Baron Peters
Feb 22, 2011·The Journal of Physical Chemistry. B·Dimitri Antoniou, Steven D Schwartz
Jul 26, 2014·Journal of Chemical Theory and Computation·Anthony HazelJames C Gumbart
Feb 5, 2019·The Journal of Physical Chemistry. B·Z F Brotzakis, P G Bolhuis
Mar 13, 2013·The Journal of Physical Chemistry. B·Li XiBernhardt L Trout
Jul 27, 2011·The Journal of Physical Chemistry. B·Manas ShahBernhardt L Trout
Oct 20, 2018·Journal of Chemical Theory and Computation·David W H SwensonPeter G Bolhuis
Apr 30, 2015·The Journal of Physical Chemistry. B·Baron Peters
Jun 2, 2011·Journal of the American Chemical Society·Pradeep L RamachandranJasper J van Thor
Feb 22, 2018·The Journal of Physical Chemistry. B·Sanjib PaulSrabani Taraphder

❮ 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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Gerhard Hummer
Proceedings of the National Academy of Sciences of the United States of America
Jarek Juraszek, Peter G Bolhuis
Journal of Physics. Condensed Matter : an Institute of Physics Journal
Fernando A EscobedoJuan C Araque
© 2021 Meta ULC. All rights reserved