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Journal Articles Journal of Chemical Theory and Computation Year : 2016

Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores

Madushanka Manathunga
Xuchun Yang
  • Function : Author
Samer Gozem
Nicolas Ferré
Massimo Olivucci

Abstract

While the light-induced population dynamics of different photoresponsive proteins has been investigated spectroscopically, systematic computational studies have not yet been possible due to the phenomenally high cost of suitable high level quantum chemical methods and the need of propagating hundreds, if not thousands, of nonadiabatic trajectories. Here we explore the possibility of studying the photodynamics of rhodopsins by constructing and investigating quantum mechanics/molecular mechanics (QM/MM) models featuring reduced retinal chromophores. In order to do so we use the sensory rhodopsin found in the cyanobacterium Anabaena PCC7120 (ASR) as a benchmark system. We find that the basic mechanistic features associated with the excited state dynamics of ASR QM/MM models are reproduced using models incorporating a minimal (i.e., three double-bond) chromophore. Furthermore, we show that ensembles of nonadiabatic ASR trajectories computed using the same abridged models replicate, at both the CASPT2 and CASSCF levels of theory, the trends in spectroscopy and lifetimes estimated using unabridged models and observed experimentally at room temperature. We conclude that a further expansion of these studies may lead to low-cost QM/MM rhodopsin models that may be used as effective tools in high-throughput in silico mutant screening.
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Dates and versions

hal-01409056 , version 1 (10-01-2024)

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Madushanka Manathunga, Xuchun Yang, Hoi Ling Luk, Samer Gozem, Luis Manuel Frutos, et al.. Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores. Journal of Chemical Theory and Computation, 2016, 12 (2), pp.839 - 850. ⟨10.1021/acs.jctc.5b00945⟩. ⟨hal-01409056⟩
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