Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping
TLDR
Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spectra, the dipole moment changes, and the energy stored in the photocycle intermediate K.Abstract:
Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spectra, the dipole moment changes, and the energy stored in the photocycle intermediate K. The computed reaction coordinate indicates that the isomerization of the retinal chromophore occurs via a complex motion accounting for three distinct regimes: (i) production of the excited state intermediate I, (ii) evolution of I toward a conical intersection between the excited state and the ground state, and (iii) formation of K. We show that, during stage ii, a space-saving mechanism dominated by an asynchronous double bicycle-pedal deformation of the C10═C11─C12═C13─C14═N moiety of the chromophore dominates the isomerization. On this same stage a N─H/water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.read more
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Journal ArticleDOI
Conical intersection dynamics of the primary photoisomerization event in vision
Dario Polli,Piero Altoè,Oliver Weingart,Katelyn M. Spillane,Cristian Manzoni,Daniele Brida,Gaia Tomasello,G. Orlandi,Philipp Kukura,Richard A. Mathies,Marco Garavelli,Giulio Cerullo +11 more
TL;DR: Ultrafast optical spectroscopy with sub-20-fs time resolution and spectral coverage from the visible to the near-infrared allows us to follow the dynamics leading to the conical intersection in rhodopsin isomerization and finds excellent agreement between the experimental observations and molecular dynamics calculations that involve a true electronic state crossing.
Journal ArticleDOI
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
TL;DR: By using feature selection algorithms to identify the most appropriate subset of relevant variables that describe a certain phenomenon, the high-dimensionality of QM/MM data can be reduced and used for further analysis with causal inference algorithms to establish unique cause-effect relationships.
Journal ArticleDOI
Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser
Przemyslaw Nogly,Tobias Weinert,Daniel James,Sergio Carbajo,Dmitry Ozerov,Antonia Furrer,Dardan Gashi,Veniamin Borin,Petr Skopintsev,Kathrin Jaeger,Karol Nass,Petra Båth,Robert Bosman,Jason E. Koglin,Matthew Seaberg,Thomas J. Lane,Demet Kekilli,Steffen Brünle,Tomoyuki Tanaka,Wenting Wu,Christopher J. Milne,Thomas P. White,Anton Barty,Uwe Weierstall,Valerie Panneels,Eriko Nango,So Iwata,Mark S. Hunter,Igor Schapiro,Gebhard F. X. Schertler,Gebhard F. X. Schertler,Richard Neutze,Jörg Standfuss +32 more
TL;DR: The principal mechanism of isomerization in this prototypical retinal-binding protein has direct relevance for all other members of this important family of membrane proteins, and it provides insight into how protein environments catalyze photochemical reactions in general.
Journal ArticleDOI
Functions, Therapeutic Applications, and Synthesis of Retinoids and Carotenoids
TL;DR: Carotenoids Rosana Álvarez,† Beleń Vaz,† Hinrich Gronemeyer,‡ and Ángel R. de Lera are reported on.
Journal ArticleDOI
Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores.
TL;DR: 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 is presented.
References
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Book
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