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Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency.

ABSTRACT: The activation of rhodopsin, the light-sensitive G-protein-coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. In this study we used hundreds of quantum-classical trajectories to show that, 15 fs after light absorption, a degeneracy between the reactive excited state and a neighbouring state causes the splitting of the rhodopsin population into subpopulations. These subpopulations propagate with different velocities and lead to distinct contributions to the quantum efficiency. We also show here that such splitting is modulated by protein electrostatics, thus linking amino acid sequence variations to quantum efficiency modulation. Finally, we discuss how such a linkage that in principle could be exploited to achieve higher quantum efficiencies would simultaneously increase the receptor thermal noise leading to a trade-off that may have played a role in rhodopsin evolution.

SUBMITTER: Yang X

PROVIDER: S-EPMC8983576 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency.

Yang Xuchun X Manathunga Madushanka M Gozem Samer S Léonard Jérémie J Andruniów Tadeusz T Olivucci Massimo M

Nature chemistry 20220303 4

The activation of rhodopsin, the light-sensitive G-protein-coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. In this study we used hundreds of quantum-classical trajectories to show that, 15 fs after light absorption, a degenerac ...[more]

PMID: 35241801

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Project description:Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer-fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer-fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer-fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.

Dataset Information

Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency.

Publications

Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency.

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