The Sidechain Bonding Gallery shows which sidechain atoms can form hydrogen bonds.
The Foldit science team is particularly interested in hydrogen bond networks in symmetry puzzles, which involve a unit formed from two or more identical copies of a protein. Hydrogen bond networks between different copies of the protein can help to stabilize the entire structure.
In hydrogen bond network puzzles, a condition adds bonus points for hydrogen bond networks which meet certain criteria. The hydrogen bond network condition was introduced in a 2015 blog post. The details of how networks are rewarded have changed over time as the science team fine-tunes the condition.
Visualizing hydrogen bond networks
The view option "Show bonds (sidechain)" makes any existing hydrogen bond networks visible. This option also shows cases where a hydrogen bond has formed between a sidechain and the protein's backbone.
The "Show bondable atoms" option is also useful, since it highlights which atoms can form hydrogen bonds. An atom highlighted with red sphere can be hydrogen bond acceptor, and a blue sphere mmarks a hydrogen bond donor. A purple sphere means an atom can act either as a donor or acceptor.
The CPK coloring option and the closely related EnzDes coloring can be used to further clarify the places where hydrogen bonds can form. With these coloring options, oxygen is shown as a red "sleeve", and nitrogen is a blue sleeve.
In the 2015 blog post, Foldit scientist bkoep's clarified the use of CPK coloing:
- In Foldit, all CPK modes (including CPK, EnzDes, and variants such as Score/Hydro+CPK) color nitrogen atoms blue and oxygen atoms red. Imagining blue donors and red acceptors is a helpful simplification, but is not strictly correct. While nitrogen is usually a donor and oxygen is usually an acceptor, there are exceptions to this rule. For example, this image shows that one N of histidine can accept an H-bond, whereas the O of serine can also donate an H-bond. This picture in particular should be helpful for determining how many hydrogen bonds are required to completely satisfy each residue type. For example, note that the N of tryptophan can only make one H-bond, whereas the N of lysine can make three!
Th different behavior of the same atom is explained by the presence of hydrogen atoms, which are normally not visible in Foldit. There are several "+H" view options which reveal hydrogens. In particular, the "Stick+polarH" view, combined with CPK or EnzDes coloring, shows the hydrogens which are availalble for bonding as white sleeves.
- The key is to not only make a network, but to take care of the quality of network. Quality means several things:
- maintaining a balance between basic and acid polar aminos
- red links are as important as blue ones
- It gives much more score to have a red link that enhances the polarity of the entire network, that having a blue link that gets it worse. If the quality is too low, break it until to do sure the polarity is balanced.
- An example:
- Image 1: this net is ok on all its links, but polars=68%, netscore=685: it is too basic.
- If I break a basic bond then: Image 2 - 76%, netscore=766.
- Not all done by hand, but the balance in each net by hand.