Publications

2026

20. Reversing the Electronic Character of 7-Azaindole Upon Functionalization with Different Donor and Acceptor Groups

María del Carmen Marín†, Javier Álvarez-Conde†, Israel Callejas-Vidoy, David Sanchez-Torres, Marcos de Lucas, Amparo Navarro*, Juan Cabanillas-González*, Eva M García-Frutos* (2026) Dyes & Pigmets, 254, 113987. (†: Equally contributed)

DOI: https://doi.org/10.1016/j.dyepig.2026.113987

19. Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria

María del Carmen Marín*, Masae Konno, Andrey Rozenberg, Oded Béjà, Keiichi Inoue* (2026) Biophysical Journal, 125, 2391-2404.

DOI: https://doi.org/10.1016/j.bpj.2026.02.022

2025

18. Light-harvesting by antenna-containing xanthorhodopsin from an Antarctic Pseudanabaenaceae cyanobacterium

María del Carmen Marín*†, Shunya Murakoshi†, Andrey Rozenberg, Tatsuki Tanaka, Masae Konno, Wataru Shihoya*, Osamu Nureki*, Oded Béjà*, Keiichi Inoue* (2025) Communications Biology, 9, 28. (†: Equally contributed)

DOI: https://doi.org/10.1038/s42003-025-09294-z

17. Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea

Gali Tzlil†, María del Carmen Marín†, Yuma Matsuzaki†, Probal Nag†, Shota Itakura, Yosuke Mizuno, Shunya Murakoshi, Tatsuki Tanaka, Shirley Larom, Masae Konno, Rei Abe-Yoshizumi, Ana Molina-Márquez, Daniela Bárcenas-Pérez, José Cheel, Michal Koblížek, Rosa León, Kota Katayama, Hideki Kandori, Igor Schapiro, Wataru Shihoya*, Osamu Nureki*, Keiichi Inoue*, Andrey Rozenberg*, Ariel Chazan*, Oded Béjà* (2025) Nature Microbiology, 10, 1484-1500. (†: Equally contributed)

DOI: https://doi.org/10.1038/s41564-025-02016-5

2024

16. Hydrogen-bonding and hydrophobic interaction networks as structural determinants of microbial rhodopsin function

Éva Bertalan†, Masae Konno†, María del Carmen Marín, Reza Bagherzadeh, Takashi Nagata, Leonid Brown, Keiichi Inoue*, Ana-Nicoleta Bondar* (2024) The Journal of Physical Chemistry B, 128, 7407-7426. (†: Equally contributed)

DOI: https://doi.org/10.1021/acs.jpcb.4c02946

15. Multiple roles of a conserved glutamate residue for unique biophysical properties in a new group of microbial rhodopsins homologous to TAT rhodopsin

Kentaro Mannen, Takashi Nagata, Andrey Rozenberg, Masae Konno, María del Carmen Marín, Reza Bagherzadeh, Oded Béjà, Takayuki Uchihashi, Keiichi Inoue* (2024) Journal of Molecular Biology, 436, 168331.

DOI: https://doi.org/10.1016/j.jmb.2023.168331

2023

14. Converting a natural-light-driven outward proton pump rhodopsin into an artificial inward proton pump

María del Carmen Marín, Masae Konno, Hiromu Yawo, Keiichi Inoue* (2023) Journal of the American Chemical Society, 145, 10938-10942.

DOI: https://doi.org/10.1021/jacs.2c12602

13. Biophysical characterization of microbial rhodopsins with DSE motif

María del Carmen Marín†, Alexander L. Jaffe†, Patrick T. West, Masae Konno, Jillian F. Banfield, Keiichi Inoue* (2023) Biophysics and Physicobiology, 20, e201023. (†: Equally contributed)

DOI: https://doi.org/10.2142/biophysico.bppb-v20.s023

2022

12. Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography

Kano Suzuki†, María del Carmen Marín†, Masae Konno†, Reza Bagherzadeh, Takeshi Murata, Keiichi Inoue (2022) Journal of Biological Chemistry, 298, 101722. (†: Equally contributed)

DOI: https://doi.org/10.1016/j.jbc.2022.101722

2021

11. Sub-picosecond CC bond photo-isomerization: evidence for the role of excited state mixing

Damianos Agathangelou, Partha Pratim Roy, María del Carmen Marín, Nicolas Ferré, Massimo Olivucci, Tiago Buckup, Jérémie Léonard, Stefan Haacke* (2021) Comptes Rendus. Physique, 22, 111-138.

DOI: https://doi.org/10.5802/crphys.41

2020

10. Web-ARM: a web-based interface for the automatic construction of QM/MM models of rhodopsins

Laura Pedraza-González, María del Carmen Marín, Alejandro N. Jorge, Tyler D. Ruck, Xuchun Yang, Alessio Valentini, Massimo Olivucci*, Luca De Vico* (2020) Journal of Chemical Information and Modeling, 60, 1481-1493.

DOI: https://doi.org/10.1021/acs.jcim.9b00615

BOOK CHAPTER. On the Automatic Construction of QM/MM Models for Biological Photoreceptors: Rhodopsins as Model Systems

Laura Pedraza-González†, María del Carmen Marín†, Luca De Vico, Xuchun Yang, Massimo Olivucci* (2020) QM/MM Studies of Light-responsive Biological Systems, 1-75, Springer. (†: Equally contributed)

DOI: https://doi.org/10.1007/9

2019

9. Red-shifting mutation of light-driven sodium-pump rhodopsin

Keiichi Inoue, María del Carmen Marín, Sahoko Tomida, Ryoko Nakamura, Yuta Nakajima, Massimo Olivucci, Hideki Kandori* (2019) Nature Communications, 10, 1993.

DOI: https://doi.org/10.1038/s41467-019-10000-x

8. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement

Laura Pedraza-González, Luca De Vico, Marı́a del Carmen Marı́n, Francesca Fanelli, Massimo Olivucci* (2019) Journal of Chemical Theory and Computation, 15, 3134-3152.

DOI: https://doi.org/10.1021/acs.jctc.9b00061

7. Assessment of MC-PDFT excitation energies for a set of QM/MM models of rhodopsins

María del Carmen Marín, Luca De Vico, Sijia S Dong, Laura Gagliardi*, Donald G. Truhlar*, Massimo Olivucci* (2019) Journal of Chemical Theory and Computation, 15, 1915-1923.

DOI: https://doi.org/10.1021/acs.jctc.8b01069

DOCTORAL THESIS. Benchmarking and applications of a computational photobiology tool for design of novel and highly fluorescent rhodopsin proteins

María del Carmen Marín (2019) Università degli Studi di Siena. Advisor: Prof. Massimo Olivucci; Co-advisors: Dr. Alessio Valentini and Luca De Vico

DOI: https://usiena-air.unisi.it/handle/11365/1070289

2018

6. Fluorescence enhancement of a microbial rhodopsin via electronic reprogramming

María del Carmen Marín†, Damianos Agathangelou†, Yoelvis Orozco-Gonzalez, Alessio Valentini, Yoshitaka Kato, Rei Abe-Yoshizumi, Hideki Kandori, Ahreum Choi, Kwang-Hwan Jung, Stefan Haacke*, Massimo Olivucci* (2018) Journal of the American Chemical Society, 141, 262-271. (†: Equally contributed)

DOI: https://doi.org/10.1021/jacs.8b09311

5. Systematic excited state studies of reversibly switchable fluorescent proteins

Daryna Smyrnova*, María del Carmen Marin, Massimo Olivucci, Arnout Ceulemans* (2018) Journal of Chemical Theory and Computation, 14, 3163-3172.

DOI: https://doi.org/10.1021/acs.jctc.8b00050

4. Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin

Damianos Agathangelou, Yoelvis Orozco-Gonzalez, María del Carmen Marin, Partha Pratim Roy, Johanna Brazard, Hideki Kandori, Kwang-Hwan Jung, Jérémie Léonard, Tiago Buckup, Nicolas Ferré, Massimo Olivucci, Stefan Haacke* (2018) Faraday discussions, 207, 55-75.

DOI: https://doi.org/10.1039/c7fd00200a

2017

3. An average solvent electrostatic configuration protocol for QM/MM free energy optimization: Implementation and application to rhodopsin systems

Yoelvis Orozco-Gonzalez*, Madushanka Manathunga, María del Carmen Marín, Damianos Agathangelou, Kwang-Hwan Jung, Federico Melaccio, Nicolas Ferré, Stefan Haacke, Kaline Coutinho, Sylvio Canuto*, Massimo Olivucci* (2017) Journal of Chemical Theory and Computation, 13, 6391-6404.

DOI: https://doi.org/10.1021/acs.jctc.7b00860

2. Toward automatic rhodopsin modeling as a tool for high-throughput computational photobiology

Federico Melaccio*, María del Carmen Marín, Alessio Valentini, Fabio Montisci, Silvia Rinaldi, Marco Cherubini, Xuchun Yang, Yoshitaka Kato, Michael Stenrup, Yoelvis Orozco-Gonzalez, Nicolas Ferré, Hoi Ling Luk, Hideki Kandori, Massimo Olivucci* (2017) Journal of Chemical Theory and Computation, 12, 6020-6034.

DOI: https://doi.org/10.1021/acs.jctc.6b00367

2016

1. Electrochemical behavior of hybrid carbon nanomaterials: the chemistry behind electrochemistry

María Moreno-Guzman, Aída Martín, María del Carmen Marín, Tania Sierra, Alejandro Ansón-Casaos, María Teresa Martínez*, Alberto Escarpa* (2016) Electrochimica Acta, 214, 286-294.

DOI: https://doi.org/10.1016/j.electacta.2016.08.056

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