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Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct

Author

Listed:
  • Partha Malakar

    (The Hebrew University of Jerusalem)

  • Samira Gholami

    (Università di Bologna)

  • Mohammad Aarabi

    (Università di Bologna)

  • Ivan Rivalta

    (Università di Bologna
    Laboratoire de Chimie UMR 5182)

  • Mordechai Sheves

    (The Weizmann Institute of Science)

  • Marco Garavelli

    (Università di Bologna)

  • Sanford Ruhman

    (The Hebrew University of Jerusalem)

Abstract

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as “K”. We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Suggested Citation

  • Partha Malakar & Samira Gholami & Mohammad Aarabi & Ivan Rivalta & Mordechai Sheves & Marco Garavelli & Sanford Ruhman, 2024. "Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46061-w
    DOI: 10.1038/s41467-024-46061-w
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    References listed on IDEAS

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    1. Dario Polli & Piero Altoè & Oliver Weingart & Katelyn M. Spillane & Cristian Manzoni & Daniele Brida & Gaia Tomasello & Giorgio Orlandi & Philipp Kukura & Richard A. Mathies & Marco Garavelli & Giulio, 2010. "Conical intersection dynamics of the primary photoisomerization event in vision," Nature, Nature, vol. 467(7314), pages 440-443, September.
    2. Karl Edman & Peter Nollert & Antoine Royant & Hassan Belrhali & Eva Pebay-Peyroula & Janos Hajdu & Richard Neutze & Ehud M. Landau, 1999. "High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle," Nature, Nature, vol. 401(6755), pages 822-826, October.
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