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1150: 60 Residue Symmetric Dimer Design: Limited HBonds

Closed since over 10 years ago

Intermediate Overall Design Symmetry

Summary

Created
October 19, 2015
Expires
Max points
100
Description

In this puzzle, the bonus for Hbond networks has been increased, but only Hbond networks that are at least 75% satisfied will be rewarded. Furthermore, no more than three inter-molecular Hbonds may contribute to the filter! There are several other filters in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

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Comments

bkoep Staff Lv 1

Actually, interface H-bonds will ideally be buried at the interface. The problem is that massive, nonpolar interfaces are nonspecific—they will bind to any other decoys with a nonpolar surface.

Ideal interface H-bonds confer specificity because they are extremely difficult to satisfy. Decoy binding partners will not satisfy all the interface H-bonds and will not bind; only the designed target will satisfy these H-bonds when it binds the interface.

If you place your H-bond network on the "outer interface," it can probably be satisfied with surrounding water, regardless of the binding partner. This is not ideal, because other nonpolar decoys can still bind just as well as the target.

martin.szew Lv 1

More clear every time…specially with:

"…Actually, interface H-bonds will ideally be buried at the interface…"
and "…If you place your H-bond network on the "outer interface," it can probably be satisfied with surrounding water, regardless of the binding partner…"

Most of the high scoring pieces do have the H-bonds on the "outer interface", if I have to guess, I said it is because you do have more room to maneuver the polar AAs in order to make the h-bonds…

Will it be possible to assign more filter bonus to "inner interfase" H-bonds like for example serine or threonine? Or even better not considering the H-bond network on the "outer interface".