Closed since over 8 years ago
Intermediate PilotHow chaperones help proteins to fold is still a matter of great debate in the scientific literature. This Classroom puzzle will help students explore different possible ways that a chaperone can interact with its client proteins. The puzzle includes a frozen chaperone protein—a miniaturized version of GroEL that can perform some of the functions of the full GroEL chaperone. The folding client is barnase, an well-behaved bacterial protein that is a popular model in protein folding studies. Players can choose to start with barnase in either the folded or unfolded state. To switch between the folded and unfolded starts, reset the puzzle (see the Actions menu in Original Interface; or the Undo menu in Selection Interface). It will be up to you to determine what provides the optimal balance between folding and interaction with the chaperone!
University of Denver students will be asked to read two articles alongside this Foldit puzzle. The first is a 1996 paper by Zahn et al., which reports chaperone activity in this small subdomain of the larger GroEL complex. The second is a 2008 study by Tang et al., in which the authors investigate GroEL function by testing the chaperone activity of GroEL mutants with different properties. See the blog for more information about the Classroom puzzle series.
When this puzzle starts, you may see only the locked part, segments 109 to 301, on-screen. For me, the designable part, 1 to 108 was off-screen on the top right.
The "q" shortcut or the home key on windows centers the protein in the window. Shift-drag on the background and zoom the protein in or out.
Even though a lot of them are locked, 301 segments is on the ginnormous size for a Foldit puzzle.
I'm able to play this puzzle on my old laptop, with two logical processors ("cores") and 2 GB memory. Unlike most puzzles, this one uses significantly more than one logical processor when running a recipe with the window minimized. On the two-processor system, just one Foldit client is using 70% or more of CPU, using up most of one processor and much of the other one.
See also: http://fold.it/portal/node/990207
Snarky PowerPoint presentation framerate comments aside I really wish I could have my GPU pick up some of the slack for this big boy puzzle.
Personally, I don't understand what we are suppose to look for, and what the students are suppose to learn from the papers.
As I understand, we have a freezed (part of) solved protein and another (solved) one that is supposed to glue to the first one (with sidechain bonds or so). We could try to make as much bonds as possible, or not to glue but to try to optimize the proteins separately.
Is that correct?
The papers then confused me. If I understand well, the freezed one is supposed to change the ideal shape of the second one. I don't know if a part of the second one has to go inside of a tunel in the first one.
Any recipe with bands will attempt to bind the foldable protein to the frozen one. Is this useless or intentional?
Would it be feasible to wrap the foldable protein around the frozen protein in order to create bonds?
