The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Chavdar Slavov; Tobias Fischer; Avishai Barnoy; Heewhan Shin; Aditya G. Rao; Christian Wiebeler; Xiaoli Zeng; Yafang Sun; Qianzhao Xu; Alexander Gutt; Kai Hong Zhao; Wolfgang Gärtner; Xiaojing Yang; Igor Schapiro; Josef Wachtveitl

doi:10.1073/pnas.1921706117

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Chavdar Slavov^*, Tobias Fischer, Avishai Barnoy, Heewhan Shin, Aditya G. Rao, Christian Wiebeler, Xiaoli Zeng, Yafang Sun, Qianzhao Xu, Alexander Gutt, Kai Hong Zhao, Wolfgang Gärtner, Xiaojing Yang^*, Igor Schapiro^*, Josef Wachtveitl^*

^*Corresponding author for this work

Institute of Chemistry

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

Abstract

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z = E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (P_r) and far red-absorbing (P_fr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the P_r form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ∼300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

Original language	American English
Pages (from-to)	16356-16362
Number of pages	7
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	117
Issue number	28
DOIs	https://doi.org/10.1073/pnas.1921706117
State	Published - 14 Jul 2020

Bibliographical note

Funding Information:
C.S. and J.W. acknowledge the Deutsche Forschungsgemeinschaft (WA 1850/4-2). A.G. and W.G. are grateful to the Max Planck Society. K.-H.Z. acknowledges the National Natural Science Foundation of China (NSFC: 31861143029; 44131770822). A.B. is thankful to the Moscona Foundation and the Center for Nanoscience and Nanotechnology at the Hebrew University. I.S. acknowledges the European Research Council (Horizon 2020, Grant 678169 “PhotoMutant”) and the SFB 1078 “Protonation Dynamics in Protein Function” (Mercator fellowship). C.W. is thankful for funding by the Deutsche Forschungsgemeinschaft (WI 4853/1-1 and WI 4853/2-1). We thank the Life Science Consortium Access Team staff at the advanced Photon Source for support in X-ray diffraction data collection. X.Y. acknowledges the NIH (NIH R01EY024363), Chicago Biomedical Consortium (CBC C-086), and the University of Illinois at Chicago. We thank J. Clark Lagarias for insightful discussions.

Funding Information:
Society. K.-H.Z. acknowledges the National Natural Science Foundation of China (NSFC: 31861143029; 44131770822). A.B. is thankful to the Moscona Foundation and the Center for Nanoscience and Nanotechnology at the Hebrew University. I.S. acknowledges the European Research Council (Horizon 2020, Grant 678169 “PhotoMutant”) and the SFB 1078 “Protonation Dynamics in Protein Function” (Mercator fellowship). C.W. is thankful for funding by the Deutsche Forschungsgemeinschaft (WI 4853/1-1 and WI 4853/2-1). We thank the Life Science Consortium Access Team staff at the advanced Photon Source for support in X-ray diffraction data collection. X.Y. acknowledges the NIH (NIH R01EY024363), Chicago Biomedical Consortium (CBC C-086), and the University of Illinois at Chicago. We thank J. Clark Lagarias for insightful discussions.

Publisher Copyright:
© 2020 National Academy of Sciences. All rights reserved.

Keywords

Knotless phytochrome
Photoisomerization
QM/MM
Ultrafast spectroscopy
X-ray structure

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10.1073/pnas.1921706117

Cite this

Slavov, C., Fischer, T., Barnoy, A., Shin, H., Rao, A. G., Wiebeler, C., Zeng, X., Sun, Y., Xu, Q., Gutt, A., Zhao, K. H., Gärtner, W., Yang, X., Schapiro, I., & Wachtveitl, J. (2020). The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome. Proceedings of the National Academy of Sciences of the United States of America, 117(28), 16356-16362. https://doi.org/10.1073/pnas.1921706117

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title = "The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome",

abstract = "Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z = E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (Pr) and far red-absorbing (Pfr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the Pr form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ∼300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.",

keywords = "Knotless phytochrome, Photoisomerization, QM/MM, Ultrafast spectroscopy, X-ray structure",

author = "Chavdar Slavov and Tobias Fischer and Avishai Barnoy and Heewhan Shin and Rao, {Aditya G.} and Christian Wiebeler and Xiaoli Zeng and Yafang Sun and Qianzhao Xu and Alexander Gutt and Zhao, {Kai Hong} and Wolfgang G{\"a}rtner and Xiaojing Yang and Igor Schapiro and Josef Wachtveitl",

note = "Funding Information: C.S. and J.W. acknowledge the Deutsche Forschungsgemeinschaft (WA 1850/4-2). A.G. and W.G. are grateful to the Max Planck Society. K.-H.Z. acknowledges the National Natural Science Foundation of China (NSFC: 31861143029; 44131770822). A.B. is thankful to the Moscona Foundation and the Center for Nanoscience and Nanotechnology at the Hebrew University. I.S. acknowledges the European Research Council (Horizon 2020, Grant 678169 “PhotoMutant”) and the SFB 1078 “Protonation Dynamics in Protein Function” (Mercator fellowship). C.W. is thankful for funding by the Deutsche Forschungsgemeinschaft (WI 4853/1-1 and WI 4853/2-1). We thank the Life Science Consortium Access Team staff at the advanced Photon Source for support in X-ray diffraction data collection. X.Y. acknowledges the NIH (NIH R01EY024363), Chicago Biomedical Consortium (CBC C-086), and the University of Illinois at Chicago. We thank J. Clark Lagarias for insightful discussions. Funding Information: Society. K.-H.Z. acknowledges the National Natural Science Foundation of China (NSFC: 31861143029; 44131770822). A.B. is thankful to the Moscona Foundation and the Center for Nanoscience and Nanotechnology at the Hebrew University. I.S. acknowledges the European Research Council (Horizon 2020, Grant 678169 “PhotoMutant”) and the SFB 1078 “Protonation Dynamics in Protein Function” (Mercator fellowship). C.W. is thankful for funding by the Deutsche Forschungsgemeinschaft (WI 4853/1-1 and WI 4853/2-1). We thank the Life Science Consortium Access Team staff at the advanced Photon Source for support in X-ray diffraction data collection. X.Y. acknowledges the NIH (NIH R01EY024363), Chicago Biomedical Consortium (CBC C-086), and the University of Illinois at Chicago. We thank J. Clark Lagarias for insightful discussions. Publisher Copyright: {\textcopyright} 2020 National Academy of Sciences. All rights reserved.",

year = "2020",

month = jul,

day = "14",

doi = "10.1073/pnas.1921706117",

language = "American English",

volume = "117",

pages = "16356--16362",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

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Slavov, C, Fischer, T, Barnoy, A, Shin, H, Rao, AG, Wiebeler, C, Zeng, X, Sun, Y, Xu, Q, Gutt, A, Zhao, KH, Gärtner, W, Yang, X, Schapiro, I & Wachtveitl, J 2020, 'The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 28, pp. 16356-16362. https://doi.org/10.1073/pnas.1921706117

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome. / Slavov, Chavdar; Fischer, Tobias; Barnoy, Avishai et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, No. 28, 14.07.2020, p. 16356-16362.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

AU - Slavov, Chavdar

AU - Fischer, Tobias

AU - Barnoy, Avishai

AU - Shin, Heewhan

AU - Rao, Aditya G.

AU - Wiebeler, Christian

AU - Zeng, Xiaoli

AU - Sun, Yafang

AU - Xu, Qianzhao

AU - Gutt, Alexander

AU - Zhao, Kai Hong

AU - Gärtner, Wolfgang

AU - Yang, Xiaojing

AU - Schapiro, Igor

AU - Wachtveitl, Josef

N1 - Funding Information: C.S. and J.W. acknowledge the Deutsche Forschungsgemeinschaft (WA 1850/4-2). A.G. and W.G. are grateful to the Max Planck Society. K.-H.Z. acknowledges the National Natural Science Foundation of China (NSFC: 31861143029; 44131770822). A.B. is thankful to the Moscona Foundation and the Center for Nanoscience and Nanotechnology at the Hebrew University. I.S. acknowledges the European Research Council (Horizon 2020, Grant 678169 “PhotoMutant”) and the SFB 1078 “Protonation Dynamics in Protein Function” (Mercator fellowship). C.W. is thankful for funding by the Deutsche Forschungsgemeinschaft (WI 4853/1-1 and WI 4853/2-1). We thank the Life Science Consortium Access Team staff at the advanced Photon Source for support in X-ray diffraction data collection. X.Y. acknowledges the NIH (NIH R01EY024363), Chicago Biomedical Consortium (CBC C-086), and the University of Illinois at Chicago. We thank J. Clark Lagarias for insightful discussions. Funding Information: Society. K.-H.Z. acknowledges the National Natural Science Foundation of China (NSFC: 31861143029; 44131770822). A.B. is thankful to the Moscona Foundation and the Center for Nanoscience and Nanotechnology at the Hebrew University. I.S. acknowledges the European Research Council (Horizon 2020, Grant 678169 “PhotoMutant”) and the SFB 1078 “Protonation Dynamics in Protein Function” (Mercator fellowship). C.W. is thankful for funding by the Deutsche Forschungsgemeinschaft (WI 4853/1-1 and WI 4853/2-1). We thank the Life Science Consortium Access Team staff at the advanced Photon Source for support in X-ray diffraction data collection. X.Y. acknowledges the NIH (NIH R01EY024363), Chicago Biomedical Consortium (CBC C-086), and the University of Illinois at Chicago. We thank J. Clark Lagarias for insightful discussions. Publisher Copyright: © 2020 National Academy of Sciences. All rights reserved.

PY - 2020/7/14

Y1 - 2020/7/14

N2 - Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z = E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (Pr) and far red-absorbing (Pfr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the Pr form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ∼300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

AB - Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z = E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (Pr) and far red-absorbing (Pfr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the Pr form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ∼300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

KW - Knotless phytochrome

KW - Photoisomerization

KW - QM/MM

KW - Ultrafast spectroscopy

KW - X-ray structure

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DO - 10.1073/pnas.1921706117

M3 - Article

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AN - SCOPUS:85088176666

SN - 0027-8424

VL - 117

SP - 16356

EP - 16362

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 28

ER -

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Abstract

Bibliographical note

Keywords

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