How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations

Angewandte Chemie
Shu-Hua XiaWalter Thiel

Abstract

Photoswitchable azobenzene cross-linkers can control the folding and unfolding of peptides by photoisomerization and can thus regulate peptide affinities and enzyme activities. Using quantum mechanics/molecular mechanics (QM/MM) methods and classical MM force fields, we report the first molecular dynamics simulations of the photoinduced folding and unfolding processes in the azobenzene cross-linked FK-11 peptide. We find that the interactions between the peptide and the azobenzene cross-linker are crucial for controlling the evolution of the secondary structure of the peptide and responsible for accelerating the folding and unfolding events. They also modify the photoisomerization mechanism of the azobenzene cross-linker compared with the situation in vacuo or in solution.

References

Jul 2, 1998·Biophysical Journal·C N Pace, J M Scholtz
Jul 3, 2003·Journal of the American Chemical Society·Thomas SchultzAlbert Stolow
Mar 12, 2004·Journal of the American Chemical Society·Alessandro CembranGiorgio Orlandi
Apr 28, 2004·Chemistry : a European Journal·Cosimo CiminelliMaurizio Persico
Feb 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jens BredenbeckPeter Hamm
Jun 22, 2005·Accounts of Chemical Research·G Andrew Woolley
Dec 27, 2005·The Journal of Chemical Physics·Cosimo CiminelliMaurizio Persico
Mar 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Janne A IhalainenPeter Hamm
Oct 27, 2007·Journal of the American Chemical Society·Fuzhong ZhangG Andrew Woolley
Apr 18, 2008·The Journal of Biological Chemistry·Shibani BhattacharyaDavid Cowburn
Jul 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Janne A IhalainenPeter Hamm
Sep 17, 2008·Current Opinion in Chemical Biology·Laura K HencheyParamjit S Arora
Oct 18, 2008·Science·Pau Gorostiza, Ehud Y Isacoff
Dec 31, 2008·The Journal of Physical Chemistry. B·Vincent PradinesReinhard Miller
Jan 28, 2009·Journal of the American Chemical Society·Fuzhong ZhangG Andrew Woolley
Mar 20, 2009·Nature·Raag D AiranKarl Deisseroth
Oct 27, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Robert TuranskýDominik Marx
Nov 13, 2009·Nature·Raymond E MoelleringJames E Bradner
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Benno SchierlingAlfred Pingoud
Jan 22, 2010·The Journal of Physical Chemistry. B·B PaoliA Caflisch
Jan 28, 2010·Journal of the American Chemical Society·Harald NieberNikos L Doltsinis
Apr 27, 2010·Angewandte Chemie·Fuzhong ZhangG Andrew Woolley
Sep 17, 2010·Physical Chemistry Chemical Physics : PCCP·Robert TuranskýDominik Marx
Mar 16, 2011·Journal of the American Chemical Society·Teresa CusatiMaurizio Persico
Apr 13, 2011·Chemical Society Reviews·Andrew A Beharry, G Andrew Woolley
Jun 22, 2011·The Journal of Physical Chemistry. a·Marek PederzoliHans Lischka
Jun 24, 2011·Chembiochem : a European Journal of Chemical Biology·Subhas Samanta, G Andrew Woolley
Sep 24, 2011·The Journal of Physical Chemistry. B·Phuong H NguyenGerhard Stock
Oct 20, 2011·Chemical Society Reviews·H M Dhammika Bandara, Shawn C Burdette
May 31, 2012·Angewandte Chemie·Subhas SamantaG Andrew Woolley
Jun 14, 2013·Physical Chemistry Chemical Physics : PCCP·José A GámezWalter Thiel
Apr 15, 2014·Angewandte Chemie·Volker GatterdamRobert Tampé
Jun 24, 2014·The Journal of Physical Chemistry. B·Dominique RastädterIrene Burghardt
Aug 21, 2014·Biophysical Journal·Mithun Biswas, Irene Burghardt
Oct 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·S Walter Englander, Leland Mayne
Jul 10, 2012·Journal of Chemical Theory and Computation·José A GámezWalter Thiel
Sep 1, 2007·Journal of Chemical Theory and Computation·Marcus BöckmannDominik Marx

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Citations

Mar 21, 2017·The Journal of Physical Chemistry. a·Yuan-Jun GaoWalter Thiel
Aug 20, 2016·Chemical Communications : Chem Comm·Robert J Mart, Rudolf K Allemann
Oct 27, 2018·Organic & Biomolecular Chemistry·Alexander V StrizhakDavid R Spring
Nov 9, 2019·Structural Dynamics·François AuvrayMatthieu Réfrégiers
Nov 23, 2017·The Journal of Chemical Physics·Xiang-Yang LiuGanglong Cui
Jun 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Dong-Hui XuGanglong Cui
Feb 6, 2018·The Journal of Physical Chemistry Letters·Ziye WuJun Jiang
Jan 25, 2019·The Journal of Physical Chemistry Letters·Jing QiuLinjun Wang
Mar 19, 2020·The Journal of Physical Chemistry. a·Ya-Hui ZhangGanglong Cui
Sep 22, 2021·Physical Chemistry Chemical Physics : PCCP·Juanjuan ZhangZhenggang Lan

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