Molecular bases for the selection of the chromophore of animal rhodopsins

Luk, Hoi Ling; Melaccio, Federico; Rinaldi, Silvia; Gozem, Samer; Olivucci, Massimo

doi:10.1073/pnas.1510262112

Cited by 45 publications

(82 citation statements)

References 63 publications

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“…In Rh, this torsion is accompanied by torsional motion along the adjacent C9=C10 bond. 20,21 Such a mechanism, termed the bicycle-pedal coordinate, was first proposed by Warshel 22 and confirmed for rhodopsins from different organisms 23,24 after the development of CASSCF-based quantum mechanics/molecular mechanics models (i.e. full protein models).…”

Section: Computational Studies: Rh Isomerizes Via a Two-state Three-mentioning

confidence: 93%

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Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores

et al. 2017

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Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.

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Section: Computational Studies: Rh Isomerizes Via a Two-state Three-mentioning

confidence: 93%

“…the C6-C7 double bond in rPSB11). The magnitude of such effect has been calculated 23 and the corresponding values are displayed in Fig. 3.2B bot-…”

Section: Scheme 32mentioning

confidence: 99%

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores

et al. 2017

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“…929 The CASSCF method has been used in the QM part of the QM/MM protocol to compare the photodynamics of isorhodopsin containing 9-cis instead of 11-cis retinal of rhodopsin. 709 926 to explain the evolutionary scenario of a common ancestor to retynilidene proteins supported by an experimental study of Devine et al 930 As stated above, the character of the emission spectrum of Trp is widely used to monitor changes in proteins reflecting the local structure and dynamics. 931 932 Similarly, the CASPT2 level has provided benchmark data for the TDDFT calculations on the effect of substitution and local environment of different Trp residues on the UV-B absorption spectra in the photoreceptor Arabidopsis thaliana UV RESISTANCE LOCUS8 (UVR8) protein.…”

Section: Proteinsmentioning

confidence: 99%

Multireference Approaches for Excited States of Molecules

et al. 2018

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Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications.

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“…This system has become a benchmark system for advanced electronic structure methods in recent years (see, for instance, Refs. [103][104][105][106][107][108][109][110][111][112][113][114][115][116][117]. For the channelrhodopsin protein, we employ the M2P2 potential constructed in Ref.…”

Section: Computational Methodologymentioning

confidence: 99%

Polarizable Embedding Density Matrix Renormalization Group

Hedegård

Reiher

2016

J. Chem. Theory Comput.

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The polarizable embedding (PE) approach is a flexible embedding model where a pre-selected region out of a larger system is described quantum mechanically while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG).This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces.Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment.

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Molecular bases for the selection of the chromophore of animal rhodopsins

Cited by 45 publications

References 63 publications

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores

Multireference Approaches for Excited States of Molecules

Polarizable Embedding Density Matrix Renormalization Group

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