QM/MM Study of the NMR Spectroscopy of the Retinyl Chromophore in Visual Rhodopsin

Gascón, José A.; Sproviero, Eduardo M.; Batista, Víctor S.

doi:10.1021/ct0500850

Cited by 47 publications

(84 citation statements)

References 103 publications

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“…49 In contrast, QM/MM studies found that the most significant upfield shift on C5 is due to Trp-265, with an upfield effect of -2.0 ppm. 2 This upfield effect, however, is almost completely canceled by the 1.8 ppm downfield shift due to . Therefore, it is concluded that the net upfield shift of σ C at C5 is not determined by the nearby residue with the largest upfield contribution but rather by the overall polarization of the π-system, predominantly modulated by the counterion Glu-113.…”

Section: Orientation Of the -Ionone Ringmentioning

confidence: 98%

“…32 An objective of recent DFT QM/MM studies has been to resolve such a contradictory picture by providing a detailed first principles description of the electronic density of the chromophore as influenced by the protein environment. 1,2 To analyze the extent of positive charge delocalization along the polyene chain, Figure 8 (upper panel) shows the distribution of electronic density difference after and before protonation of the retinyl chromophore in the rhodopsin binding site. It is shown that protonation of the Schiff base linkage induces electronic charge redistribution, driving electronic density from the polyene chain toward the NH+ bond (see violet isosurface).…”

Section: Charge Distributionmentioning

confidence: 99%

“…In fact, a very similar alternation pattern is found in computational models of the chromophore in solution. 2 …”

Section: Charge Distributionmentioning

confidence: 99%

“…1,2,[5][6][7][20][21][22] In particular, recent DFT QM/MM studies 1,2 have addressed the elucidation of chromophoreopsin interactions responsible for phototransduction and energy storage through 11-cis/all-trans isomerization, a problem that has been largely elusive to first-principles examinations. Some of the fundamental questions are as follows: What are the molecular rearrangements responsible for 11-cis/all-trans isomerization in the rhodopsin binding pocket?…”

Section: Introductionmentioning

confidence: 99%

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Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

2006

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This Account addresses recent advances in the elucidation of the detailed molecular rearrangements due to the primary photochemical event in rhodopsin, a prototypical G-protein-coupled receptor (GPCR) responsible for the signal transmission cascade in the vertebrate vision process. The reviewed studies provide fundamental insight on long-standing problems regarding the assembly and function of the individual residues and bound water molecules that form the rhodopsin active site, a center that catalyzes the 11-cis/all-trans isomerization of the retinyl chromophore in the primary step of the phototransduction mechanism. Emphasis is placed on the authors' recent computational studies, based on state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, addressing the structural refinement of the retinyl chromophore binding site in high-resolution X-ray structures of bovine visual rhodopsin, the energy storage mechanism, and the molecular origin of spectroscopic changes due to the primary photochemical event.

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Section: Orientation Of the -Ionone Ringmentioning

confidence: 98%

Section: Charge Distributionmentioning

confidence: 99%

“…In fact, a very similar alternation pattern is found in computational models of the chromophore in solution. 2 …”

Section: Charge Distributionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

2006

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“…2 The lower panel of Figure 9 compares theoretical and experimental values of changes in the chromophore 1 …”

Section: Primary Phototransduction Event In Visual Rhodopsinmentioning

confidence: 99%

Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

2006

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QM/MM‐Methoden für biomolekulare Systeme

2009

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Quantenmechanische/molekülmechanische (QM/MM‐)Verfahren sind die Methode der Wahl für die theoretische Behandlung reaktiver oder anderer elektronischer Prozesse in Biomolekülen. Der Aufsatz diskutiert methodische Aspekte des QM/MM‐Ansatzes, seine Verwendung in Optimierungs‐ und Simulationsstudien sowie verschiedene Anwendungsfelder, immer im Hinblick auf biomolekulare Systeme. Kombinierte quantenmechanische/molekülmechanische (QM/MM‐) Ansätze sind zur Methode der Wahl bei der Modellierung von Reaktionen in biomolekularen Systemen geworden. Einerseits braucht man quantenmechanische Methoden, um chemische Reaktionen und andere elektronische Prozesse wie Ladungstransfer oder elektronische Anregungen zu beschreiben; allerdings bleibt deren Anwendbarkeit auf Systeme mit bis zu einigen hundert Atomen beschränkt. Andererseits fordert die Größe und konformative Komplexität von Biopolymeren Methoden, mit denen man Systeme mit 100 000 oder mehr Atomen behandeln und über eine Zeitskala von einigen Nanosekunden simulieren kann. Dies ist mit effizienten kraftfeldbasierten molekularmechanischen Verfahren möglich. Zur Beschreibung großer Biomoleküle bietet es sich daher an, quantenmechanische Methoden für die chemisch aktive Region (z. B. Substrate und Cofaktoren in einer enzymatischen Reaktion) zu nutzen und mit einer molekularmechanischen Behandlung der Umgebung (z. B. Protein und Solvens) zu kombinieren. Die resultierenden Ansätze werden gemeinhin als kombinierte oder Hybrid‐QM/MM‐Methoden bezeichnet. Sie ermöglichen die Modellierung reaktiver biomolekularer Systeme mit vertretbarem Rechenaufwand und der nötigen Genauigkeit.

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QM/MM Study of the NMR Spectroscopy of the Retinyl Chromophore in Visual Rhodopsin

Cited by 47 publications

References 103 publications

Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

QM/MM‐Methoden für biomolekulare Systeme

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