Optogenetics is genetically encoded, optically induced, control of cells through transgenic expression of microbial opsins in mammalian neurons. When these opsins are expressed in a cell-type specific manner and light activated, they provide temporally and spatially separated stimulation of independent hyperpolarizing and depolarizing channels in neurons in living animals. Channelrhodopsins (ChRs) are the microbial opsins used in optogenetics to trigger light induced depolarization. ChRs are light-gated ion channels that operate on the order of milliseconds, a time scale relevant for neuronal activation, and can be expressed in the membrane of distinct cell types with high temporal precision in well-defined brain regions. This contrasts with the poor temporal dynamics or lack of specificity of chemical or electrical stimulation methods. However, the optogenetics tools currently available for neuronal circuit interrogation are limited based on expression, light-wavelength activation, kinetics and ion specificity. Our proposed project addresses these limitations through protein engineering. Protein engineering through directed evolution and structure-guided recombination are well-established methods for modifying and optimizing proteins for desired functions. Current literature and preliminary collaborative work between the Gradinaru and Arnold labs at Caltech indicate that channelrhodopsins are amenable to functionally useful laboratory evolution and manipulation. This work will be focused toward engineering improved channelrhodopsins for use as biological tools in optogenetics.
The aim i s to engineer channelrhodopsins for optimal ion selectivity, kinetics, reversibility, and shifted light excitatio wavelengths. These new channel proteins will have applications in probing the brain's circuitry to better understand and model healthy and non-healthy brain function as a foundation for controlling and diagnosing neurological disorders such as addiction, depression and Parkinson's disease.
Optogenetics allows for excellent spatial and temporal control of neuronal activity with the orthogonal stimulus, light. This technique has successfully enabled interrogation of brain circuitry in normal brain function compared with circuitry resulting from neurological disorders, such as Parkinson's. Our goal is to develop novel protein-tools to facilitate progress in optogenetics through collaboration between protein engineering and neurobiology.
| Yang, Kevin K; Wu, Zachary; Bedbrook, Claire N et al. (2018) Learned protein embeddings for machine learning. Bioinformatics 34:2642-2648 |
| Yang, Kevin K; Wu, Zachary; Bedbrook, Claire N et al. (2018) Learned protein embeddings for machine learning. Bioinformatics 34:4138 |
| Bedbrook, Claire N; Yang, Kevin K; Rice, Austin J et al. (2017) Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization. PLoS Comput Biol 13:e1005786 |
| Herwig, Lukas; Rice, Austin J; Bedbrook, Claire N et al. (2017) Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore. Cell Chem Biol 24:415-425 |
| Nath, Ravi D; Bedbrook, Claire N; Abrams, Michael J et al. (2017) The Jellyfish Cassiopea Exhibits a Sleep-like State. Curr Biol 27:2984-2990.e3 |
| Bedbrook, Claire N; Rice, Austin J; Yang, Kevin K et al. (2017) Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins. Proc Natl Acad Sci U S A 114:E2624-E2633 |
| McIsaac, R Scott; Bedbrook, Claire N; Arnold, Frances H (2015) Recent advances in engineering microbial rhodopsins for optogenetics. Curr Opin Struct Biol 33:8-15 |
| Bedbrook, Claire N; Kato, Mihoko; Ravindra Kumar, Sripriya et al. (2015) Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo. Chem Biol 22:1108-21 |
