Frontiers in Multiscale Modeling of Photoreceptor Proteins

Maria Andrea Mroginski; Suliman Adam; Gil S. Amoyal; Avishai Barnoy; Ana Nicoleta Bondar; Veniamin A. Borin; Jonathan R. Church; Tatiana Domratcheva; Bernd Ensing; Francesca Fanelli; Nicolas Ferré; Ofer Filiba; Laura Pedraza-González; Ronald González; Cristina E. González-Espinoza; Rajiv K. Kar; Lukas Kemmler; Seung Soo Kim; Jacob Kongsted; Anna I. Krylov; Yigal Lahav; Michalis Lazaratos; Qays NasserEddin; Isabelle Navizet; Alexander Nemukhin; Massimo Olivucci; Jógvan Magnus Haugaard Olsen; Alberto Pérez de Alba Ortíz; Elisa Pieri; Aditya G. Rao; Young Min Rhee; Niccolò Ricardi; Saumik Sen; Ilia A. Solov'yov; Luca De Vico; Tomasz A. Wesolowski; Christian Wiebeler; Xuchun Yang; Igor Schapiro

doi:10.1111/php.13372

Frontiers in Multiscale Modeling of Photoreceptor Proteins

Maria Andrea Mroginski^*, Suliman Adam, Gil S. Amoyal, Avishai Barnoy, Ana Nicoleta Bondar, Veniamin A. Borin, Jonathan R. Church, Tatiana Domratcheva, Bernd Ensing, Francesca Fanelli, Nicolas Ferré, Ofer Filiba, Laura Pedraza-González, Ronald González, Cristina E. González-Espinoza, Rajiv K. Kar, Lukas Kemmler, Seung Soo Kim, Jacob Kongsted, Anna I. KrylovYigal Lahav, Michalis Lazaratos, Qays NasserEddin, Isabelle Navizet, Alexander Nemukhin, Massimo Olivucci, Jógvan Magnus Haugaard Olsen, Alberto Pérez de Alba Ortíz, Elisa Pieri, Aditya G. Rao, Young Min Rhee, Niccolò Ricardi, Saumik Sen, Ilia A. Solov'yov, Luca De Vico, Tomasz A. Wesolowski, Christian Wiebeler, Xuchun Yang, Igor Schapiro^*

^*Corresponding author for this work

Institute of Chemistry

Research output: Contribution to journal › Review article › peer-review

17 Scopus citations

Abstract

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

Original language	American English
Pages (from-to)	243-269
Number of pages	27
Journal	Photochemistry and Photobiology
Volume	97
Issue number	2
DOIs	https://doi.org/10.1111/php.13372
State	Published - 1 Mar 2021

Bibliographical note

Funding Information:
A. N. is thankful for discussion with Bella Grigorenko (Department of Chemistry, Lomonosov Moscow State University, Russia) and acknowledges funding from Russian Science Foundation (Grant Number 17‐13‐01051). A.P.A.O. received funding from the Mexican National Council for Science and Technology (CONACYT). Financial support was provided in part by the DFG Collaborative Research Center SFB 1078 Project C4 (to A.‐N.B.) and by the Freie Universität Berlin within the Excellence Initiative of the German Research Foundation. Computing time was provided to A.‐N.B. by the HLRN, the North‐German Supercomputing Alliance. A.‐N.B. thanks Jens Dreger (Physics Department, FU Berlin, Germany) for excellent technical support. Y.M.R. was financially supported by the Mid‐career Researcher Program of the National Research Foundation of Korea (Grant 2017R1A2B3004946). J. M. H. O. acknowledges financial support from the Research Council of Norway through its Centres of Excellence scheme (Project ID: 262695) and VILLUM FONDEN (Grant no. 29478). T.A.W. thanks the Swiss National Science Foundation (Grant No. 200020‐172532). N.F. thanks the French Agence Nationale de la Recherche for funding (grant ANR‐14‐CE35‐0015‐02, project FEMTO‐ASR). N.F. acknowledges Centre de Calcul Intensif d’Aix‐Marseille for granting access to its high‐performance computing resources. M.O. acknowledges funding NSF Grant No. CHE‐CLP‐1710191 and NIH Grant No. 1R15GM126627. M.O., L.P.‐G. and L.D.V. acknowledge a MIUR (Ministero dell’Istruzione, dell’Università e della Ricerca) Grant “Dipartimento di Eccellenza 2018−2022. A.I.K. was supported by the U.S. National Science Foundation (No. CHE‐1856342). A.I.K. is also a grateful recipient of the Simons Fellowship in Theoretical Physics and Mildred Dresselhaus Award from CFEL/DESY, which supported her sabbatical stay in Germany. I.A.S. acknowledges financial support by the Lundbeck Foundation, the Danish Councils for Independent Research, Volkswagen Stiftung (Lichtenberg professorship to IAS), and the DFG (GRK1885, SFB1372). J. K. acknowledges the Danish Council for Independent Research for financial support (Grant ID: DFF‐‐7014‐00050B) and the H2020‐MSCA‐ITN‐2017 COSINE Training network for Computational Spectroscopy In Natural sciences and Engineering (Project ID: 765739) for financial support. M.A.M. and R.G. acknowledge financial support by the DFG via the SFB 1078. I.S. thanks the SFB 1078 for support within the Mercator program. I.S. gratefully acknowledges funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 678169, “PhotoMutant”). R.K.K. acknowledges support from the Lady Davis Trust for the Arskin postdoctoral fellowship. S.A. acknowledges support by the Minerva Stiftung in the form of a postdoctoral fellowship. J.C. acknowledges the Zuckerman STEM leadership program. CW acknowledges funding by the Deutsche Forschungsgemeinschaft (WI 4853/2‐1 and 4853/1‐1). I. N. thanks the French Agence Nationale de la Recherche for funding (grant ANR‐16‐CE29‐0013‐02, project BIOLUM).

Publisher Copyright:
© 2021 American Society for Photobiology

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10.1111/php.13372

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Mroginski, M. A., Adam, S., Amoyal, G. S., Barnoy, A., Bondar, A. N., Borin, V. A., Church, J. R., Domratcheva, T., Ensing, B., Fanelli, F., Ferré, N., Filiba, O., Pedraza-González, L., González, R., González-Espinoza, C. E., Kar, R. K., Kemmler, L., Kim, S. S., Kongsted, J., ... Schapiro, I. (2021). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology, 97(2), 243-269. https://doi.org/10.1111/php.13372

@article{123b2075f7c04042991a7d61dbcf6724,

title = "Frontiers in Multiscale Modeling of Photoreceptor Proteins",

abstract = "This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.",

author = "Mroginski, {Maria Andrea} and Suliman Adam and Amoyal, {Gil S.} and Avishai Barnoy and Bondar, {Ana Nicoleta} and Borin, {Veniamin A.} and Church, {Jonathan R.} and Tatiana Domratcheva and Bernd Ensing and Francesca Fanelli and Nicolas Ferr{\'e} and Ofer Filiba and Laura Pedraza-Gonz{\'a}lez and Ronald Gonz{\'a}lez and Gonz{\'a}lez-Espinoza, {Cristina E.} and Kar, {Rajiv K.} and Lukas Kemmler and Kim, {Seung Soo} and Jacob Kongsted and Krylov, {Anna I.} and Yigal Lahav and Michalis Lazaratos and Qays NasserEddin and Isabelle Navizet and Alexander Nemukhin and Massimo Olivucci and Olsen, {J{\'o}gvan Magnus Haugaard} and {P{\'e}rez de Alba Ort{\'i}z}, Alberto and Elisa Pieri and Rao, {Aditya G.} and Rhee, {Young Min} and Niccol{\`o} Ricardi and Saumik Sen and Solov'yov, {Ilia A.} and {De Vico}, Luca and Wesolowski, {Tomasz A.} and Christian Wiebeler and Xuchun Yang and Igor Schapiro",

note = "Funding Information: A. N. is thankful for discussion with Bella Grigorenko (Department of Chemistry, Lomonosov Moscow State University, Russia) and acknowledges funding from Russian Science Foundation (Grant Number 17‐13‐01051). A.P.A.O. received funding from the Mexican National Council for Science and Technology (CONACYT). Financial support was provided in part by the DFG Collaborative Research Center SFB 1078 Project C4 (to A.‐N.B.) and by the Freie Universit{\"a}t Berlin within the Excellence Initiative of the German Research Foundation. Computing time was provided to A.‐N.B. by the HLRN, the North‐German Supercomputing Alliance. A.‐N.B. thanks Jens Dreger (Physics Department, FU Berlin, Germany) for excellent technical support. Y.M.R. was financially supported by the Mid‐career Researcher Program of the National Research Foundation of Korea (Grant 2017R1A2B3004946). J. M. H. O. acknowledges financial support from the Research Council of Norway through its Centres of Excellence scheme (Project ID: 262695) and VILLUM FONDEN (Grant no. 29478). T.A.W. thanks the Swiss National Science Foundation (Grant No. 200020‐172532). N.F. thanks the French Agence Nationale de la Recherche for funding (grant ANR‐14‐CE35‐0015‐02, project FEMTO‐ASR). N.F. acknowledges Centre de Calcul Intensif d{\textquoteright}Aix‐Marseille for granting access to its high‐performance computing resources. M.O. acknowledges funding NSF Grant No. CHE‐CLP‐1710191 and NIH Grant No. 1R15GM126627. M.O., L.P.‐G. and L.D.V. acknowledge a MIUR (Ministero dell{\textquoteright}Istruzione, dell{\textquoteright}Universit{\`a} e della Ricerca) Grant “Dipartimento di Eccellenza 2018−2022. A.I.K. was supported by the U.S. National Science Foundation (No. CHE‐1856342). A.I.K. is also a grateful recipient of the Simons Fellowship in Theoretical Physics and Mildred Dresselhaus Award from CFEL/DESY, which supported her sabbatical stay in Germany. I.A.S. acknowledges financial support by the Lundbeck Foundation, the Danish Councils for Independent Research, Volkswagen Stiftung (Lichtenberg professorship to IAS), and the DFG (GRK1885, SFB1372). J. K. acknowledges the Danish Council for Independent Research for financial support (Grant ID: DFF‐‐7014‐00050B) and the H2020‐MSCA‐ITN‐2017 COSINE Training network for Computational Spectroscopy In Natural sciences and Engineering (Project ID: 765739) for financial support. M.A.M. and R.G. acknowledge financial support by the DFG via the SFB 1078. I.S. thanks the SFB 1078 for support within the Mercator program. I.S. gratefully acknowledges funding by the European Research Council (ERC) under the European Union{\textquoteright}s Horizon 2020 research and innovation program (Grant No. 678169, “PhotoMutant”). R.K.K. acknowledges support from the Lady Davis Trust for the Arskin postdoctoral fellowship. S.A. acknowledges support by the Minerva Stiftung in the form of a postdoctoral fellowship. J.C. acknowledges the Zuckerman STEM leadership program. CW acknowledges funding by the Deutsche Forschungsgemeinschaft (WI 4853/2‐1 and 4853/1‐1). I. N. thanks the French Agence Nationale de la Recherche for funding (grant ANR‐16‐CE29‐0013‐02, project BIOLUM). Publisher Copyright: {\textcopyright} 2021 American Society for Photobiology",

year = "2021",

month = mar,

day = "1",

doi = "10.1111/php.13372",

language = "American English",

volume = "97",

pages = "243--269",

journal = "Photochemistry and Photobiology",

issn = "0031-8655",

publisher = "Wiley-Blackwell",

number = "2",

}

Mroginski, MA, Adam, S, Amoyal, GS, Barnoy, A, Bondar, AN, Borin, VA, Church, JR, Domratcheva, T, Ensing, B, Fanelli, F, Ferré, N, Filiba, O, Pedraza-González, L, González, R, González-Espinoza, CE, Kar, RK, Kemmler, L, Kim, SS, Kongsted, J, Krylov, AI, Lahav, Y, Lazaratos, M, NasserEddin, Q, Navizet, I, Nemukhin, A, Olivucci, M, Olsen, JMH, Pérez de Alba Ortíz, A, Pieri, E, Rao, AG, Rhee, YM, Ricardi, N, Sen, S, Solov'yov, IA, De Vico, L, Wesolowski, TA, Wiebeler, C, Yang, X & Schapiro, I 2021, 'Frontiers in Multiscale Modeling of Photoreceptor Proteins', Photochemistry and Photobiology, vol. 97, no. 2, pp. 243-269. https://doi.org/10.1111/php.13372

TY - JOUR

T1 - Frontiers in Multiscale Modeling of Photoreceptor Proteins

AU - Mroginski, Maria Andrea

AU - Adam, Suliman

AU - Amoyal, Gil S.

AU - Barnoy, Avishai

AU - Bondar, Ana Nicoleta

AU - Borin, Veniamin A.

AU - Church, Jonathan R.

AU - Domratcheva, Tatiana

AU - Ensing, Bernd

AU - Fanelli, Francesca

AU - Ferré, Nicolas

AU - Filiba, Ofer

AU - Pedraza-González, Laura

AU - González, Ronald

AU - González-Espinoza, Cristina E.

AU - Kar, Rajiv K.

AU - Kemmler, Lukas

AU - Kim, Seung Soo

AU - Kongsted, Jacob

AU - Krylov, Anna I.

AU - Lahav, Yigal

AU - Lazaratos, Michalis

AU - NasserEddin, Qays

AU - Navizet, Isabelle

AU - Nemukhin, Alexander

AU - Olivucci, Massimo

AU - Olsen, Jógvan Magnus Haugaard

AU - Pérez de Alba Ortíz, Alberto

AU - Pieri, Elisa

AU - Rao, Aditya G.

AU - Rhee, Young Min

AU - Ricardi, Niccolò

AU - Sen, Saumik

AU - Solov'yov, Ilia A.

AU - De Vico, Luca

AU - Wesolowski, Tomasz A.

AU - Wiebeler, Christian

AU - Yang, Xuchun

AU - Schapiro, Igor

N1 - Funding Information: A. N. is thankful for discussion with Bella Grigorenko (Department of Chemistry, Lomonosov Moscow State University, Russia) and acknowledges funding from Russian Science Foundation (Grant Number 17‐13‐01051). A.P.A.O. received funding from the Mexican National Council for Science and Technology (CONACYT). Financial support was provided in part by the DFG Collaborative Research Center SFB 1078 Project C4 (to A.‐N.B.) and by the Freie Universität Berlin within the Excellence Initiative of the German Research Foundation. Computing time was provided to A.‐N.B. by the HLRN, the North‐German Supercomputing Alliance. A.‐N.B. thanks Jens Dreger (Physics Department, FU Berlin, Germany) for excellent technical support. Y.M.R. was financially supported by the Mid‐career Researcher Program of the National Research Foundation of Korea (Grant 2017R1A2B3004946). J. M. H. O. acknowledges financial support from the Research Council of Norway through its Centres of Excellence scheme (Project ID: 262695) and VILLUM FONDEN (Grant no. 29478). T.A.W. thanks the Swiss National Science Foundation (Grant No. 200020‐172532). N.F. thanks the French Agence Nationale de la Recherche for funding (grant ANR‐14‐CE35‐0015‐02, project FEMTO‐ASR). N.F. acknowledges Centre de Calcul Intensif d’Aix‐Marseille for granting access to its high‐performance computing resources. M.O. acknowledges funding NSF Grant No. CHE‐CLP‐1710191 and NIH Grant No. 1R15GM126627. M.O., L.P.‐G. and L.D.V. acknowledge a MIUR (Ministero dell’Istruzione, dell’Università e della Ricerca) Grant “Dipartimento di Eccellenza 2018−2022. A.I.K. was supported by the U.S. National Science Foundation (No. CHE‐1856342). A.I.K. is also a grateful recipient of the Simons Fellowship in Theoretical Physics and Mildred Dresselhaus Award from CFEL/DESY, which supported her sabbatical stay in Germany. I.A.S. acknowledges financial support by the Lundbeck Foundation, the Danish Councils for Independent Research, Volkswagen Stiftung (Lichtenberg professorship to IAS), and the DFG (GRK1885, SFB1372). J. K. acknowledges the Danish Council for Independent Research for financial support (Grant ID: DFF‐‐7014‐00050B) and the H2020‐MSCA‐ITN‐2017 COSINE Training network for Computational Spectroscopy In Natural sciences and Engineering (Project ID: 765739) for financial support. M.A.M. and R.G. acknowledge financial support by the DFG via the SFB 1078. I.S. thanks the SFB 1078 for support within the Mercator program. I.S. gratefully acknowledges funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 678169, “PhotoMutant”). R.K.K. acknowledges support from the Lady Davis Trust for the Arskin postdoctoral fellowship. S.A. acknowledges support by the Minerva Stiftung in the form of a postdoctoral fellowship. J.C. acknowledges the Zuckerman STEM leadership program. CW acknowledges funding by the Deutsche Forschungsgemeinschaft (WI 4853/2‐1 and 4853/1‐1). I. N. thanks the French Agence Nationale de la Recherche for funding (grant ANR‐16‐CE29‐0013‐02, project BIOLUM). Publisher Copyright: © 2021 American Society for Photobiology

PY - 2021/3/1

Y1 - 2021/3/1

N2 - This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

AB - This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

UR - http://www.scopus.com/inward/record.url?scp=85100850859&partnerID=8YFLogxK

U2 - 10.1111/php.13372

DO - 10.1111/php.13372

M3 - Review article

C2 - 33369749

AN - SCOPUS:85100850859

SN - 0031-8655

VL - 97

SP - 243

EP - 269

JO - Photochemistry and Photobiology

JF - Photochemistry and Photobiology

IS - 2

ER -

Frontiers in Multiscale Modeling of Photoreceptor Proteins

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