bkoep Staff Lv 1
In an earlier blog post, I wrote about the challenges of designing a protein therapeutic for Alzheimer's disease. Such a molecule must be able to bind with both high affinity and specificity to the neurotoxic Aβ polypeptide that causes the disease. Furthermore, the binding must prevent Aβ from self-associating to form neurotoxic protein oligomers or aggregates. In addition, a successful protein therapeutic must be stable in the body for a long time, evading clearance by the immune system and by proteases. It must also be able to cross the blood-brain barrier. Ideally, we would also like to add some functionality that would allow one binder molecule to clear or break down many Aβ molecules, though this will be an additional challenge. All of these are difficult problems to solve, but by breaking the overall goal into its component parts, we can begin to address these one at a time – and Foldit players can help!
The first puzzle that we posted involved the redesign of the core and interface residues of an existing, homodimeric Aβ binder in order to break the symmetry of the binding interface and improve both the affinity and the specificity for the asymmetric Aβ molecule. I am currently examining the designs that players produced in Puzzle 801b (many of which look quite impressive), and we will be revisiting these designs in the near future with a new puzzle. This puzzle will involve linking the secondary structural elements with new loop regions (which Foldit players will design) in order to convert the homodimer into a single large, monomeric protein. As we prepare the follow-up puzzle, we also want to get players started on a parallel strategy that we'll be exploring: complete de novo design of an Aβ binder.
In the new de novo design puzzle, we will be giving you the Aβ polypeptide in a rigid backbone conformation that has been observed in the complex with the affibody binder in NMR studies. We will also be giving you eight short, separate peptides (two of 24 residues, two of 20 residues, and four of 10 residues). We would like you to pretend that these short peptides are secondary structural elements of a single-chain protein, in which these peptides would be linked by loops – but we'll worry about the lengths, conformations, and sequences of the loops in a subsequent puzzle. For now, we'd like you to assemble these components around the Aβ polypeptide in such a way as to favor high-affinity, high-specificity binding. We are starting half of these peptides out as helices, and the other half in extended, strand-like conformations, but you should feel free to change the secondary structure as you see fit in order to achieve excellent binding. While the Foldit score should guide you, keep in mind that there are features that we are looking for that are not always captured well by the score alone. A successful design will have excellent shape-complementarity between all of the components – i.e. the surface of each element should have bumps and grooves that pack tightly against the surface of the next element. In addition, good designs should have buried hydrophobic residues making the core (phenylalanine, methionine, isoleucine, leucine, tyrosine, valine, and tryptophan). The surface should be non-hydrophobic. Most of the Aβ polypeptide's hydrophobic surface should be buried by the binder, both for purposes of specific recognition and to prevent Aβ from engaging in hydrophobic interactions with other, unbound Aβ molecules. Voids in the core of the binder or in the Aβ-binder interface are a bad thing – they're rarely seen in natural protein structures, and are energetically very unfavorable, though it is difficult for us to capture this properly in the mathematics of the Foldit score.
I'm also interested in your feedback about how this type of puzzle feels – in part because, if this turns out to be an effective means of designing a protein to bind a target, I'd like to try to develop automated algorithms to do the same, emulating the strategies used by the best Foldit players. Do you like having the freedom to move secondary structural elements independently, or is this too open-ended and unconstrained a puzzle? Does this open up new strategies that you would not have if you were dealing with a single long chain? Can you think of new Foldit manipulation tools that would make this type of puzzle easier for you? Would you like to see more design puzzles of this type, with follow-up loop design puzzles, or do you prefer the classic, “fold-a-long-chain” type of puzzles?
Please leave your comments below!
