We're very curious to hear what you think about this new type of puzzle. Please read the recent blog post by Baker Lab scientist Vikram Mulligan, and leave your comments on the blog page here:
First, can we place the "pieces" anywhere around the locked segment? or are place we should not have them?
Second, how bad is having 2,3, or 6 Low Scoring Residues??
>First, can we place the "pieces" anywhere
>around the locked segment? or are place
>we should not have them?
Yes, you can place them anywhere. Remember, though, that the goal is to come up with a plausible design for a folded protein that has bound to the Abeta peptide. This means that designs that fail to bury hydrophobic residues well (e.g. ones that leave a bunch of Abeta's hydrophobic residues exposed) won't be very good designs. Isolated secondary structure elements that don't contact or support one another at all (especially isolated beta-strands) are probably also not terrific designs. Beyond those vague, qualitative guidelines, though, you've got a lot of leeway. We don't want to restrict you too much. Be creative!
>Second, how bad is having 2,3, or 6 Low
It's hard to say for certain. The score should be used as a guide (and a VERY low-scoring residue is almost certainly "bad"), but real proteins do sometimes have a residue or two that are in somewhat non-ideal or unusual configurations (and which would be scored somewhat poorly by Foldit).
Good questions, by the way!
If the conserved portion is buried within our fragments, how will it perform its function?
That's a very good question, brow42. First, to clarify: by "the conserved portion", do you mean the part with a fixed backbone shape? That's the ABeta molecule, which we want to bind up in order to block its toxic effects.
It is counter-intuitive, but real proteins sometimes bury the molecules that they bind pretty deeply -- which seems strange, since how the heck would the bound molecule get into or out of the binding site? The reality is that proteins aren't the static, rigid structures that we think of when we look at a Foldit model. Proteins -- and the water molecules that surround them -- are constantly jiggling and jittering around. On average, there is one state (the "native state", which is what we ask Foldit players to design or predict) that they tend to occupy, but they can deviate from that for short periods of time. Here's a short Youtube video of a molecular dynamics simulation of the sorts of motions that a folded protein might undergo. (Keep in mind that this is a simulation, and that actual protein motions are very difficult to study experimentally.) Although this simulation seems to show a pretty leisurely wobbling motion, the entire 34-second movie represents two billionths of a second of simulated time. Over longer periods of time -- milliseconds or seconds, for example -- a protein can, for brief instants, sample conformations that are farther from the folded state, including fairly open conformations in which a deeply-bound molecule could get in or out.
Even more counter-intuitively, a very buried binding site might result in slower binding or release (meaning that binding could take milliseconds or seconds instead of microseconds) as compared to a more exposed binding site, but since burial slows both binding and release, it will not necessarily reduce the fraction of protein molecules that have successfully bound the target molecule once the system reaches its equilibrium between bound and unbound states. On the contrary, greater burial can result in more favourable interactions between the binding protein and the molecule that it binds, meaning that at equilibrium, more of the target molecule will be bound.
Does this make sense?
This explanation was very helpful. I thought the small peptide itself disrupted Abeta sheets. I understand now that it is the target of our design.