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2249: Revisiting Puzzle 62: Halorhodopsin

Closed since about 3 years ago

Novice Overall Prediction

Summary

Created
January 06, 2023
Expires
Max points
100
Description

This is a throwback puzzle to the early days of Foldit. This protein is able to absorb light and use the energy to transfer chloride ions across the cell membrane. We are revisiting old Foldit puzzles so we can see how useful the recent additions to the game have been.

Sequence
RENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGATSWAYSVLDVFAKYVFAFILLRWVANNERTVAV

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Comments

spmm Lv 1

https://www.rcsb.org/3d-view/1E12/1 - is the 'official' view although I note that iMOL lite for the iPad has a slightly different secondary structure. Use NtoC colour if available to match a rainbow in foldlit.
So for these revisiting puzzles - copy the sequence - list of letters into rcsb- and select advanced search, sequence. Once you have your choice of the four letter solution it can be used as a reference in other systems.
Unfortunately neither of these apps shows the detailed alignment of the side chains - especially the 'tennis racquets' (sic) and that is what you really need to get the rapid high scores on these revisiting and other puzzles. You can click to see the detailed side chain for specific areas which does work, slowly. The view on the foldit page shows the side chains with the 'disturbed' chain.
Hydrophobic bonds are not visible in foldit but can massively affect the score.
My 2010 version of MacPymol is way out of date and does not open but it is perhaps still possible to get an educational version.
Have fun :)