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WIREs Comput Mol Sci
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Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations

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Abstract The photoisomerization of retinal is a unifying primary event in the rhodopsin protein family. In vertebrate rhodopsins it is the first step in the vision process, while in the microbial rhodopsins it activates the transport of ions across the cell‐membrane. This reaction is highly optimized in the protein, which is ultrafast, selective, and efficient. A great effort was directed to elucidate the mechanism due to the overall complexity of the process inside the protein. The classical one‐bond‐flip is too demanding in space for the confined protein cavity. Therefore, various space saving mechanisms based on the rotation of multiple double bonds have been proposed. The hybrid quantum mechanics/molecular mechanics (QM/MM) method played an important role in the elucidation of the mechanism inside the tight protein environment. It allows to take the entire protein into account while describing the ground and excited states of retinal. The predicted mechanisms include full isomerization of two or three double bonds, a simultaneous isomerization of a single and a double bond as well as the partial rotation of bonds adjacent to the central isomerization. This review summarizes mechanistic studies in the literature and compares them. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Software > Molecular Modeling
Wring‐a‐wet‐towel motion for the twists of the active and associate dihedral angles in the retinal protonated Schiff base isomerization
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Crankshaft torsional values observed in retinal protonated Schiff base at 110 fs delay49
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Hula‐twist (HT) isomerization mechanism of the retinal protonated Schiff base (rpSb) involves a volume‐conserving isomerization of neighboring single and double bonds. The observed final photoproduct is the 10‐s‐cis rpSb
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Bicycle‐pedal isomerization mechanism of the retinal protonated Schiff base shows simultaneous twisting of two double bonds
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One‐bond‐flip mechanism of the 11‐cis retinal protonated Schiff base involves a rotation around the central double bond
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Multiscale partitioning of the visual rhodopsin structure. The quantum mechanics (QM) region consists of the retinal protonated Schiff base whereas the rest of the protein composes the molecular mechanics (MM) region. The inset shows the chromophore cavity with 11‐cis retinal linked to the lysine sidechain
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Schematic representation of the photoisomerization process of retinal protonated Schiff base (rpSb). Electrostatic potentials (in units of kT/e) in ground and excited state mapped onto the molecular surface of rpSb for rhodopsin
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(a) Photoisomerization of retinal from 11‐cis to all‐trans. Purple and gray highlighted regions show the β‐ionone ring and protonated Schiff base, respectively. (b) Various isomerization mechanisms: One‐bond‐flip (OBF), bicycle‐pedal (BP), hula‐twist (HT), and folding‐table (FT)
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Software > Molecular Modeling
Electronic Structure Theory > Combined QM/MM Methods
Structure and Mechanism > Computational Biochemistry and Biophysics

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