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Rhodopsin Overview Structure and mechanics Main classes of rhodopsin Recent developments Eukaryotes Bacteria Material Science Rhodopsin Overview Membrane protein that binds retinal to form a light absorbing pigment (AKA: retinylidene proteins) Over 300 versions of rhodopsin found so far Diverse functions: Light sensitive protein found in all animal eyes Light driven proton pump Light driven chloride pump Phototaxis receptors Close relatives: a heat shock protein, a translocase in mitochondria Structure and Mechanics All have the same physical structure and mechanics Seven trans-membrane alpha helices Retinal attached by Schiff base linkage to a lysine residue in the seventh helix in all known cases Structural changes induced by binding retinal are similar Two distinct rhodopsin families: Type 1 and Type 2 Look and act the same but the gene sequence is quite different http://www.prism.gatech.edu/~gt7966a/research.html Bacteriorhodopsin http://anx12.bio.uci.edu/~hudel/br/index.html Bacteriorhodopsin Ground state on left, bleached state on right http://anx12.bio.uci.edu/~hudel/br/index.html Main classes of rhodopsin Type 1 Rhodopsins First observed in 1971 in the archaea Halobacterium Salinarum Note: archaea were classed with bacteria in '71 Type 2 Rhodopsins Photosensitive receptor proteins in animal eyes Receptor proteins in other tissues in early branching vertebrates Receptor proteins found in human and mouse brains Type 1 Rhodopsins Bacteriorhodopsin: Halorhodopsin: Each photocycle pumps one proton out of the cytoplasm Increases proton gradient to drive ATPsynthase Change in pH converts to chloride pump Each photocycle pumps one chloride ion out of the cytoplasm Change in pH converts to proton pump Sensory Rhodopsin 1: Works with bound accessory protein to initiate motility cascade Removal of accessory protein converts to proton pump Recent developments Type 1 Rhodopsins have been found in eukaryotes Several filamentous fungi Several algae A yeast Fungus zoospores Proteorhodopsin, a bacteriorhodopsin like protein, recently discovered in marine bacteria Discovery of Proteorhodopsin Sequenced large gene fragment from uncultivated marine bacteria group (SAR 86) Gene fragment included 16s rRNA gene and ORF for bacteriorhodopsin No other archaeal ORFs found in fragment Proteorhodopsin verified Study 1: Protein expressed in E. coli E. coli turned reddish Absorbed same frequency of light as bacteriorhodopsin Light induced acidification Proteorhodopsin verified Study 2: Membranes from native marine bacteria used Showed same absorbance peaks Same light induced acidification Bacteria from different areas had different absorbance peaks Proteorhodopsin is an important source of energy for SAR68 bacteria Proteorhodopsin is highly expressed Proteorhodopsin tuned for each environment Many genetic variants have been found Carbon Flow in the Ocean SAR86 bacteria are abundant and widespread Can live where food is scarce Become food for others SAR86 bacteria are related to chemolithoautotrophs Photoheterotrophic lifestyle? New form of photoautotrophy? Uses of Bacteriorhodopsin Discovery of bacteriorhodopsin has opened a whole new field in materials science optically addressed spatial light modulators real-time interferometry holographic pattern recognition optical data storage all-optical logic gates (light driven computers) Dieter Oesterhelt discovered bacteriorhodopsin in 1971 and was still publishing research on it as late as 1994. References 7/16/2015 Spudich, J.L., Yang, C.S. Jung, K. H., & Spudich, E. N. Retinylidene proteins: Structures and functions from archaea to humans. Annu. Rev. Cell Dev. Biol. 16, 365-392 (2000). Oesterhelt D., & Stoeckenius, W. Rhodopsin like protein from the purple membrane of Halobacterium halobium Nature 233, 149-152 (1971) Beja, O., Aravind, L., Koonin, V., Suzuki, M., Hadd, A., Nguyen, L., Jovanovich, S., Gates, C., Feldman, R., Spudich, J., Spudich, E. & DeLong, E. Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea Science 289, 1902-1906 (2000) Beja, O., DeLong, E., Spudich, J., Leclerc, M. & DeLong, E. Proteorhodopsin phototrophy in the ocean Nature 411, 786-789 (2001) Hampp, N., Thoma, R. & Bräuchle, Kreuzer, C.F.-H., Maurer, R., & Oesterhelt, D. Bacteriorhodopsin variants for optical information processing: A new approach in material science AIP Conference Proceedings -- July 20, 1992 -- Volume 262, Issue 1, pp. 181-190 Zhang, T., Zhang, C., Fu, G., Li, Y., Gu, L., Zhang, G., Song, Q. W., Parsons, B., Birge, R. All-optical logic gates using bacteriorhodopsin films Optical Engineering -- February 2000 -- Volume 39, Issue 2, pp. 527-534 23