Hydrogen Bond Network Filter

Started by jflat06

blivens Lv 1

Does resonance at the peptide bond account for it being a weak acceptor, since it has some N+ character?

sboyken Lv 1

Yes, that is a good point and is definitely part of it. Resonance is when covalent bonds, and the electrons that form them are in an equilibrium, alternating, between multiple states. Most bonds have some resonance, including peptide bonds (electrons are not static, far from it! we just draw them that way because it's easier):
Figure 2
http://www.open.edu/openlearn/science-maths-technology/science/biology/proteins/content-section-1.2

As blivens correctly pointed out, the resonance of peptide bonds gives the backbone N a partial positive character. The affect of this resonance will be largely dictated by how planar the C-N peptide bond is (the phi/psi angles), and proline has the interesting property that it can form cis omega angles, which affects the C(i-1)-N(i) bond where i is proline. These are good questions!

@jeff101, one cool case in nature where proline does form h-bonds as an acceptor is the polyproline helix: https://en.wikipedia.org/wiki/Polyproline_helix
It's a helix of all prolines. Because there are no h-bond donors, the hydrogen bonds are with water molecules and other protein atoms (that are not part of the proline helix).

Susume Lv 1

Would it be possible to get a list of how many donors and acceptors each aa has in foldit? The picture (jeff's 2nd link) shows 3 bonds possible for serine, but in foldit 2 bonds per serine in a triangle satisfies 100%, so foldit must count serine as having 2 possible. Similarly, the picture shows 4 bonds possible for asparagine, but 2 per asparagine in a triangle satisfies 66.67%, so foldit must count them as having 3 possible.

bkoep Staff Lv 1

In some more recent puzzles, we've emphasized that all buried polar atoms should be satisfied by forming hydrogen bonds. In reality, nearly all polar atoms in a protein will form at least one hydrogen bond. Polar atoms on the protein surface simply make hydrogen bonds with water; polar atoms in the protein core will need to make hydrogen bonds with other parts of the protein.

For those interested, this paper by Fleming and Rose discusses in more detail the importance of satisfying hydrogen bonds:
http://onlinelibrary.wiley.com/doi/10.1110/ps.051454805/full