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Overview Structure and mechanics Main classes of rhodopsin Recent developments Eukaryotes Bacteria Material Science

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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)

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Presentation Transcript
slide1

Rhodopsin

  • Overview
  • Structure and mechanics
  • Main classes of rhodopsin
  • Recent developments
    • Eukaryotes
    • Bacteria
    • Material Science
rhodopsin overview
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
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
slide5

Bacteriorhodopsin

http://anx12.bio.uci.edu/~hudel/br/index.html

slide6

Bacteriorhodopsin

Ground state on left, bleached state on right

http://anx12.bio.uci.edu/~hudel/br/index.html

main classes of rhodopsin
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
Type 1 Rhodopsins
  • Bacteriorhodopsin:
    • Each photocycle pumps one proton out of the cytoplasm
    • Increases proton gradient to drive ATPsynthase
    • Change in pH converts to chloride pump
  • Halorhodopsin:
    • 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
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
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
Proteorhodopsin verified
  • Study 1:
    • Protein expressed in E. coli
    • E. coli turned reddish
    • Absorbed same frequency of light as bacteriorhodopsin
    • Light induced acidification
proteorhodopsin verified14
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
slide17
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
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
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
References
  • 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
  • Nature233, 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
  • Science289, 1902-1906 (2000)
  • Beja, O., DeLong, E., Spudich, J., Leclerc, M. & DeLong, E.
  • Proteorhodopsin phototrophy in the ocean
  • Nature411, 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
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