Designing Proteins With Sequences Like Text Messages:

Started by jeff101

jeff101 Lv 1 

The other night, I was talking with some of my teammates
about a new type of Design Puzzle that might be fun around 
the Holidays, like past Snowflake Design Puzzles:
https://fold.it/portal/node/996492 Puzzle 825
https://fold.it/portal/node/996573 Puzzle 825
https://fold.it/portal/node/2001693 Puzzle 1174
https://fold.it/portal/node/2001765 Puzzle 1174
https://fold.it/portal/node/2001775 Puzzle 1174

The goal is to design a protein with a single-letter-code 
amino acid sequence that is meaningful, like a Tweet or
short text message. This means the text message can only
use the 20 letters for the 20 different amino acids
(all letters from a-z except b j o u x and z). Some 
examples are below:

catchascatchcanastitchintimesavesnine
thisgameisverytrickychallenginghardandaddictive
ihaveaflamingheartcantgetmyfill
anappleadaykeepsamanhealthywealthyandwise
apennysavedisapennyearned
thecatsinthecradle
theladyinredisdancingwithme
myfairladytheraininspainfallsmainlyintheplains
thisgamehasmanysmartandniceplayersandadmins
etcetceteraandtherestandetalallmeanthesamething

It would be interesting to see how the above examples 
would fold. Which parts would form helices, sheets,
and loops? Which would have good cores or hydrogen
bond networks? Which could form dimers?

jeff101 Lv 1 

Below is another, much longer, example
for fans of the TV show "Frasier":

cheerspsychiatristfrasiercraneliveswithhis
fathermartininahighrisenearthespaceneedle
inseattletheylikeplayingadrinkinggamewhile
watchingtvtheydrinkwhenevertheyheartheterm
vernierandsaykachingwhenanitemisappraised
highlymarriedpsychiatristnilescranereally
likesmartinsliveinphysicaltherapistnamed
daphneeddieisaterrierlivingwithfrasierand
martinattimeseddietriessittinginmartins
chairperigilpinplaysfrasierscallscreener
andmanagerhercharacterisfriendswithmartin
anddaphnewhileshethinksnilesisveryeffete
frasierscatchphraseisimlisteningkelsey
grammerplaysfrasierwhiledavidhydepierce
playsniles

jeff101 Lv 1

If writing without j o u is too hard,
perhaps one could substitute i q v
for them, because Q looks a lot like O,
and the Romans sometimes used i and v
in place of j and u (like ivlivs caesar
in place of julius caesar).

Susume Lv 1

Fun!! One could write a little program that would pull out of a standard dictionary all the words whose letters match canonical protein snippets (using foldit colors, blue-orange-blue-orange… for sheets, blue-blue-orange-blue-blue-orange-orange… for helices, plus some ideal loop sequences from the Koga papers). Then these words could be assembled like legos into the little alpha/beta proteins that foldit likes.