1 reply [Last post]
Joined: 05/09/2008
Groups: None

This thread is where we can follow-up to questions that were asked at Office Hours:

We'll start with the 9/25/20 chat:

[9:27 AM] jeff101:
For h-bonding to a particular atom, is there a limit on how many h-bonds can form?
Like a on a bent O acceptor, is the most h-bonds 2 ? Do they sort of form a tetrahedron around the O atom?

It is possible to have one atom forming more than one hydrogen bond. Sometimes in crystal structures, we’ll see situations where it looks like an atom is forming more hydrogen bonds at once than would be useful, but it’s likely that it dynamically switches between hydrogen bonding partners close by.

Unfortunately Rosetta/Foldit does not limit the number of H-bonds to an atom. In Foldit it is possible to make 5+ good-scoring H-bonds to a single acceptor, even though this is physically unrealistic.

[9:27 AM] jeff101:
Also, for a carbonyl (C=O) oxygen atom, is the most h-bonds to the O acceptor 2? Do they come in 120 degrees apart?

“Most” is actually kind of hard to define here, but it would be rare to see more than 2 at a time. The 120 degrees is probably close to optimal, but carbonyl groups are actually really open to having wider angles so long as it’s in the plane of the carbonyl bond.

For the Rosetta/Foldit H-bond potential, see Figure 3 (Fig, 3B for carbonyl): https://pubmed.ncbi.nlm.nih.gov/28430426/

[9:33 AM] jeff101:A harder question is what is the max # of h-bonds to a nitrogen that is an acceptor atom.
Can nitrogens even be acceptor atoms? Perhaps N's on rings like C=N-C can be acceptors? Would the hydrogen bond be in a plane with the C=N-C atoms, so that all 3 angles are 120 degrees?

Nitrogens can definitely be acceptors. The key is it needs to have a lone pair of electrons. I haven’t looked specifically at this case, but I think it probably would be strongest in plane.

In Rosetta/Foldit, only the HIS nitrogen can accept H-bonds.

jeff101's picture
User offline. Last seen 28 min 52 sec ago. Offline
Joined: 04/20/2012
Groups: Go Science
H-Bond Quotas for H-Bond Networks in Foldit?
https://fold.it/portal/node/2010483#comment-43043 asks more 
questions like the above.

I think that for Foldit to decide if a Hydrogen Bond Network is 
complete, it must have certain H-Bond quotas that each donor and 
acceptor must satisfy. Is it possible to satisfy these quotas
using physically unrealistic H-Bonds?

https://fold.it/portal/files/images/newsletter_hbond_angles.gif
and https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111238
list maximum numbers of H-Bonds for each donor and acceptor. Do
these maximum numbers match Foldit's H-Bond Network Quotas?

One suggestion is to make Foldit display each H-Bond as if it 
comes from a hydrogen atom rather than a donor atom like nitrogen. 
I think right now if 2 H-Bonds go from the nitrogen on a glutamine 
sidechain to the oxygen on an asparagine sidechain, Foldit will 
show them as if they were just one H-Bond going from the nitrogen 
atom to the oxygen atom. This makes it hard to count H-Bonds and
hard to tell why certain H-Bond Networks are not fully satisfied.
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons