10 20 30 40 50 60
70 80 90 100 110 120
since i really like the psipred data, i decided to spend some time playing with it and figuring out what it can do and what the confidence actually means (0 is low, not 10), I am a visual person when it comes to data, so am sharing these for others that may find them useful.
In this protein's sequence are 7 cysteines.
These could form up to 3 disulfide bonds.
says there are 105 different ways to make
3 disulfide bonds from 7 cysteines.
It also says there are 21 different
ways to make 1 disulfide bond from
7 cysteines. I think there are also
105 different ways to make 2 disulfide
bonds from 7 cysteines. This all begs
the question, should any disulfide bonds
form in this protein, and if so, how many?
We don't expect any disulfide bonds to form in this protein.
know that ? (if you have time to explain, just curious)
It's thought that this protein's function is intracellular. The interior of the cell has a reduction potential that favors free cysteines instead of disulfides, so disulfide bonds rarely form in proteins that remain within the cell.
Is the cysteine bridge 'strength' reduced in terms of Foldit? How much?
Not sure what "stress" means. Should these cysteines be outward facing as part of their function? Does this stress trigger involve competing for and breaking disulfide bonds on the counterpart protein, causing the stress response? Does this protein live in a highly reducing environment, and so, we should consider cysteine to be just a small-sidechain AA?
I have 3 cysteine bridges design that looks pretty nice.
IMHO 1 extra cysteine could be used to move the long helix, switching between 2 protein conformations.
But there is the important note: I know that it may sound a bit stupid but sheet markup by PSIPRED looks wrong. I used different beta-sheets layout.
Here is the structures i've got from my script of 1820 SS prediction:
(helices are red, sheets are green)
Some idea for design for that structures:
But it has a lot of exposed hydrophobic segments. So if it is not a membrane protein (but it could be because of the long helix), it doesn't hit the good score.
I do work at this puzzle two, i was able to fold it, but i have no biology science background was kind off thrown away by the complexity of it.