Rhodopsin

Rhodopsin is the protein component of the light receptor in the retinal rods of the vertebrate eye.  Similar molecules are found in the light-sensing structures of all animals.  A bacterial form of rhodopsin is used as a light absorbing molecule for photosynthesis.  The protein is associated with cis-retinal, a derivative of Vitamin A.  Rhodopsin is responsible for vision under low light conditions.  Duplication and modification of the rhodopsin gene seems to be the origin of the three receptor pigments responsible for color vision. See Bluecone.  Rhodopsin is a membrane protein with seven transmembrane domains.  The protein winds in and out of the membrane with extracellular and cytoplasmic domains alternating with the transmembrane domains.

The primary sequence of rhodopsin is given below, with the sequence of the blue cone photoprotein for comparison.  The extracellular, transmembrane and cytoplasmic regions are aligned to make the similarities between the two amino acid sequences more evident.

More information on rhodopsin from Access Excellence.

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Rhodopsin ( )= extracellular domain [ ]= transmembrane domain { } = cytoplasmic domain	Blue Cone Photoprotein ( )= extracellular domain [ ]= transmembrane domain { } = cytoplasmic domain
(MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQ) [FSMLAAYMFLLIVLGFPINFLTLYV] {TVQHKKLRTPLN} [YILLNLAVADLFMVLGGFTSTLYTS] (LHGYFVFGPTGCNLE) [GFFATLGGEIALWSLVVLAI] {ERYVVVCKPMSNFRFGENH} [AIMGVAFTWVMALACAAPPLAGWS] (RYIPEGLQCSCGIDYYTLKPEVNNES) [FVIYMFVVHFTIPMIIIFFCYGQLVFTV] {KEAAAQQQESATTQKAEKEVTR} [MVIIMVIAFLICWVPYAS VAFYIF] (THQGSNFG) [PIFMTIPAFFAKSAAIYNPVIYIMM] {NKQFRNCMLTTICCGKNPLGDDEASATVSKT ETSQVAPA}	(MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWA)  [FYLQAAFMGTVFLIGFPLNAMVLVA]  {TLRYKKLRQPLN}  [YILVNVSFGGFLLCIFSVFPVFVASC]  (NGYFVFGRHVCALE)  [GFLGTVAGLVTGWSLAFLAF]  {ERYIVICKPFGNFRFSSKH}  [ALTVVLATWTIGIGVSIPPFFGWS]  (RFIPEGLQCSCGPDWYTVGTKYRSES)  [YTWFLFIFCFIVPLSLICFSYTQLLRAL]  {KAVAAQQQESATTQKAEREVSR}  [MVVVMVGSFCVCYVPYAAFAMYMV]  (NNRNHGLD)  [LRLVTIPSFFSKSACIYNPIIYCFM]  {NKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTV  SSTQVGPN}
Link to the Music: Rhodopsin

Notes on the Music:

In the music based on this protein, the transmembrane domains are emphasized at the beginning and end of the piece.  You can hear the overall similarity of these domains, even though this similarity is not obvious from the primary structure.  In the first section, the transmembrane musical sections, played by oboe and voices, are linked by very spare scoring (vibraphone) that represents the nonpolar amino acid residues ILVFM as they occur in the sequence.  As you might expect, these nonpolar residues occur more frequently in the transmembrane regions.  In the middle section, the extracellular, transmembrane and cytoplasmic domains of the protein are all represented by different voices: the two "exterior" voices are both plucked strings, with the transmembrane domains sounding as two reedy voices playing in parallel.  In the last section, the transmembrane domains are sandwiched between two lightly scored voices the represent polar residues.  The high "ping" that you hear periodically in this section is the lysine (K) that appears one or more times in each of the cytoplasmic domains.