Computational Biology
Structural Model of Channelrhodopsin*

https://doi.org/10.1074/jbc.M111.320309Get rights and content
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Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs are now widely used for the analysis of neural networks in tissues and living animals with light (optogenetics). For elucidation of functional mechanisms at the atomic level, as well as for further engineering and application, a detailed structure is urgently needed. In the absence of an experimental structure, here we develop a structural ChR model based on several molecular computational approaches, capitalizing on characteristic patterns in amino acid sequences of ChR1, ChR2, Volvox ChRs, Mesostigma ChR, and the recently identified ChR of the halophilic alga Dunaliella salina. In the present model, we identify remarkable structural motifs that may explain fundamental electrophysiological properties of ChR2, ChR1, and their mutants, and in a crucial validation of the model, we successfully reproduce the excitation energy predicted by absorption spectra.

Chlamydomonas
Electrophysiology
Homology Modeling
Optogenetics
Photoreceptors
Potassium Channels
Quantum Chemistry
Rhodopsin
Sodium Channels
Molecular Dynamics Simulation

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*

This work was supported by Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (to H. C. W.).

This article contains supplemental text, references, Tables S1–S4, and Figs. S1–S10.

1

Supported by Deutsche Forschungsgemeinschaft Grant FOR1279, “Protein Based Photoswitches.”