Literature DB >> 27151871

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.

Kanupriya Pande1, Christopher D M Hutchison2, Gerrit Groenhof3, Andy Aquila4, Josef S Robinson4, Jason Tenboer5, Shibom Basu6, Sébastien Boutet4, Daniel P DePonte4, Mengning Liang4, Thomas A White7, Nadia A Zatsepin8, Oleksandr Yefanov7, Dmitry Morozov3, Dominik Oberthuer7, Cornelius Gati7, Ganesh Subramanian8, Daniel James8, Yun Zhao8, Jake Koralek4, Jennifer Brayshaw5, Christopher Kupitz5, Chelsie Conrad6, Shatabdi Roy-Chowdhury6, Jesse D Coe6, Markus Metz7, Paulraj Lourdu Xavier9, Thomas D Grant10, Jason E Koglin4, Gihan Ketawala6, Raimund Fromme6, Vukica Šrajer11, Robert Henning11, John C H Spence8, Abbas Ourmazd5, Peter Schwander5, Uwe Weierstall8, Matthias Frank12, Petra Fromme6, Anton Barty7, Henry N Chapman13, Keith Moffat14, Jasper J van Thor2, Marius Schmidt5.   

Abstract

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
Copyright © 2016, American Association for the Advancement of Science.

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Year:  2016        PMID: 27151871      PMCID: PMC5291079          DOI: 10.1126/science.aad5081

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  64 in total

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Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

2.  Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: protein versus solvent environments.

Authors:  Mikas Vengris; Michael A van der Horst; Goran Zgrablic; Ivo H M van Stokkum; Stefan Haacke; Majed Chergui; Klaas J Hellingwerf; Rienk van Grondelle; Delmar S Larsen
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

3.  Bicycle-pedal model for the first step in the vision process.

Authors:  A Warshel
Journal:  Nature       Date:  1976-04-22       Impact factor: 49.962

4.  Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein.

Authors:  Karsten Heyne; Omar F Mohammed; Anwar Usman; Jens Dreyer; Erik T J Nibbering; Michael A Cusanovich
Journal:  J Am Chem Soc       Date:  2005-12-28       Impact factor: 15.419

5.  Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein.

Authors:  L J G W van Wilderen; M A van der Horst; I H M van Stokkum; K J Hellingwerf; R van Grondelle; M L Groot
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-02       Impact factor: 11.205

6.  3V: cavity, channel and cleft volume calculator and extractor.

Authors:  Neil R Voss; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2010-05-16       Impact factor: 16.971

7.  Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser.

Authors:  David Arnlund; Linda C Johansson; Cecilia Wickstrand; Anton Barty; Garth J Williams; Erik Malmerberg; Jan Davidsson; Despina Milathianaki; Daniel P DePonte; Robert L Shoeman; Dingjie Wang; Daniel James; Gergely Katona; Sebastian Westenhoff; Thomas A White; Andrew Aquila; Sadia Bari; Peter Berntsen; Mike Bogan; Tim Brandt van Driel; R Bruce Doak; Kasper Skov Kjær; Matthias Frank; Raimund Fromme; Ingo Grotjohann; Robert Henning; Mark S Hunter; Richard A Kirian; Irina Kosheleva; Christopher Kupitz; Mengning Liang; Andrew V Martin; Martin Meedom Nielsen; Marc Messerschmidt; M Marvin Seibert; Jennie Sjöhamn; Francesco Stellato; Uwe Weierstall; Nadia A Zatsepin; John C H Spence; Petra Fromme; Ilme Schlichting; Sébastien Boutet; Gerrit Groenhof; Henry N Chapman; Richard Neutze
Journal:  Nat Methods       Date:  2014-08-10       Impact factor: 28.547

8.  Low-barrier hydrogen bond in photoactive yellow protein.

Authors:  Shigeo Yamaguchi; Hironari Kamikubo; Kazuo Kurihara; Ryota Kuroki; Nobuo Niimura; Nobutaka Shimizu; Yoichi Yamazaki; Mikio Kataoka
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-02       Impact factor: 11.205

9.  Short hydrogen bonds in photoactive yellow protein.

Authors:  Spencer Anderson; Sean Crosson; Keith Moffat
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-05-21

10.  The Coherent X-ray Imaging instrument at the Linac Coherent Light Source.

Authors:  Mengning Liang; Garth J Williams; Marc Messerschmidt; M Marvin Seibert; Paul A Montanez; Matt Hayes; Despina Milathianaki; Andrew Aquila; Mark S Hunter; Jason E Koglin; Donald W Schafer; Serge Guillet; Armin Busse; Robert Bergan; William Olson; Kay Fox; Nathaniel Stewart; Robin Curtis; Alireza Alan Miahnahri; Sébastien Boutet
Journal:  J Synchrotron Radiat       Date:  2015-04-15       Impact factor: 2.616

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  110 in total

Review 1.  A Bright Future for Serial Femtosecond Crystallography with XFELs.

Authors:  Linda C Johansson; Benjamin Stauch; Andrii Ishchenko; Vadim Cherezov
Journal:  Trends Biochem Sci       Date:  2017-07-18       Impact factor: 13.807

2.  Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography.

Authors:  Christopher D M Hutchison; Jasper J van Thor
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2019-05-20       Impact factor: 4.226

3.  Laue diffraction and time-resolved crystallography: a personal history.

Authors:  Keith Moffat
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2019-06-17       Impact factor: 4.226

4.  The next big hit in molecule Hollywood.

Authors:  Mark Peplow
Journal:  Nature       Date:  2017-04-26       Impact factor: 49.962

5.  Probing the early stages of photoreception in photoactive yellow protein with ultrafast time-domain Raman spectroscopy.

Authors:  Hikaru Kuramochi; Satoshi Takeuchi; Kento Yonezawa; Hironari Kamikubo; Mikio Kataoka; Tahei Tahara
Journal:  Nat Chem       Date:  2017-02-06       Impact factor: 24.427

6.  Bacteriophytochrome Photoisomerization Proceeds Homogeneously Despite Heterogeneity in Ground State.

Authors:  Cheng Wang; Moira L Flanagan; Ryan D McGillicuddy; Haibin Zheng; Alan Ruvim Ginzburg; Xiaojing Yang; Keith Moffat; Gregory S Engel
Journal:  Biophys J       Date:  2016-11-15       Impact factor: 4.033

7.  Experimental evaluation of the generalized vibrational theory of G protein-coupled receptor activation.

Authors:  Ross D Hoehn; David E Nichols; John D McCorvy; Hartmut Neven; Sabre Kais
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-12       Impact factor: 11.205

8.  Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography.

Authors:  Nadine L Samara; Yang Gao; Jinjun Wu; Wei Yang
Journal:  Methods Enzymol       Date:  2017-05-03       Impact factor: 1.600

Review 9.  Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM.

Authors:  Andrii Ishchenko; Cornelius Gati; Vadim Cherezov
Journal:  Curr Opin Struct Biol       Date:  2018-03-16       Impact factor: 6.809

Review 10.  Serial Femtosecond Crystallography of G Protein-Coupled Receptors.

Authors:  Benjamin Stauch; Vadim Cherezov
Journal:  Annu Rev Biophys       Date:  2018-03-15       Impact factor: 12.981

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