Hydrogen bonds help stabilize proteins. In Foldit, hydrogen bonds appears as blue-and-white spirals (or "candy canes") when the "Show bonds" is selected in the View Options menu. The strength of hydrogen bonds varies; the thicker the blue-and-white spiral, the stronger the bond.
Hydrogen bonds are a relatively weak type of chemical bond. They're much weaker than the peptide bonds that hold together the protein's backbone or the covalent bond found in a disulfide bridge. But hydrogen bonds are numerous, and they help determine both the secondary structure -- helixes and sheets -- of a protein and its overall shape (or "tertiary structure").
The shape of a helix is determined by the regular pattern of hydrogen bonds between the backbone atoms in the amino acids (or segments in the helix. Similarly, the "flat" structure of sheets occurs when hydrogen bonds form between the backbone atoms of two or more groups of segments.
Hydrogen bonds can also form between the sidechain of one segment and the sidechains of other segments. Often, the sidechains of three or more segments are bonded together to form a "hydrogen bond network". This type of bonding helps to stabilize the protein, especially when it occurs on the surface of the protein. In some design puzzles, hydrogen bond networks receive a special bonus.
Hydrogen bonds can also occur between sidechains and the backbone atoms of helixes, sheets, and loops.
Visualizing hydrogen bondsEdit
The familiar blue-and-white spirals appear whenever "Show bonds" is selected in View Options. In the basic GUI, there's just a single "Show bonds" option, which shows a spiral for each hydrogen bond in the protein. This can lead to information overload. In the advanced GUI, there are separate options such as "Show bonds (helix)" and "Show bonds (sheet)", which can help to reduce the visual clutter. For example, with "Show bonds (helix)" selected by itself, only hydrogen bonds which have one or both ends on the backbone of a helix are shown.
There's also a "Show bondable atoms" view option. This option shows a red sphere for an atom which can act as a hydrogen bond acceptor, and a blue sphere for an atom which can act as a hydrogen bond donor. Hydrogen bonds can form between the red spheres and the blue spheres. In the advanced GUI, the bondable atoms are shown only for the corresponding "Show bonds" selection. For example, if "Show bonds (sheet)" is not checked, no bondable atom markers will appear on sheets.
For three specific sidechains, there is also a third bonding option revealed with "Show bondable atoms". The bondable sidechain atoms for serine, tyrosine, and threonine are highlighted in purple, indicating that they can act as either a hydrogen bond donor or as a hydrogen bond acceptor. The bondable atoms in these cases are oxygen plus an attached hydrogen. The oxygen acts as a hydrogen bond acceptor, and the hydrogen acts as a hydrogen bond donor. (The oxygen wants one or two more hydrogens to bond with, in addition to the one that's already there.)
Since hydrogen bonds require hydrogen atoms, looking at the hydrogen atoms in a protein can be helpful in understanding why a particular atom has red, blue, or purple "bondable atom" color.
Normally, hydrogen atoms aren't shown in Foldit. Several "View protein" options available in the View Options menu of the advanced GUI reveal the normally hidden hydrogen atoms which can form hydrogen bonds. For example, the "Stick + H" protein view option represents hydrogens as white caps. There are also corresponding "polar" options, such as "Stick + polarH", which show only the hydrogens which are available to form hydrogen bonds.
Particularly for sidechains, the hydrogens help to illustrate how many hydrogen bonds can form. For example, arginine has three nitrogen atoms in its sidechain that can act as hydrogen bond donors. The two nitrogens at the tip of the sidechain both have two hydrogen atoms available for hydrogen bonds, but the nitrogen in the middle of the sidechain has only one hydrogen available for a hydrogen bond.
Note: this section is a work-in-progress.
Hydrogen possesses no inner electron shell isolating its nucleus from bonding electrons. The hydrogen kernel is a proton. When bonded to electronegative atoms like nitrogen, oxygen or sulfur the electrons of the O-H, N-H or S-H bond are drawn strongly to the electronegative atom, leaving the hydrogen proton as a relatively bare positive charge at the outer end of the covalent bond. As such it is peculiarly capable of attracting closely an external negatively charged center, such as another amino acid segment containing an unshared electron pair, in other words, a localized site of negative charge such as a nitrogen or oxygen atom in a protein chain (the red and blue “stubs” on the backbone and some sidechains. The attraction between a hydrogen covalently bonded to a heteroatom and another atom with its unshared electrons is called a hydrogen bond. In proteins it is essentially electrostatic in character and relatively weak, but it is of enormous importance in ordering the arrangements of amino acid sequences of a protein chain in space. In the hydrogen bond are two electronegative atoms with a proton between them. The hydrogen bond is stronger the more electronegative the two atoms and most stable when it is possible to be linear (hydrogen bond shown dotted below):
- O-H····: O: - O-H····: N - N-H····: O: - N-H····: N - S-H····: S: - S-H····: N - S-H····: O:
Other similar interactions are also present and contribute to protein stability. The current Foldit algorithms do not appear to place a high level of importance to them except for: - O-H····: N - N-H····: O: and
(-S-H····: S-H) --> -S- S- a covalent bond (oxidized to form cysteine bridge).