Hydrogen bonds

In the unfolded form all hydrogen bonds that the protein can make are actually there (with water). In the folded form, however, not all hydrogen bond donors/acceptors are at all times involved in a hydrogen bond. So, in a way, hydrogen bonds are energetically favouring the unfolded form of the protein.

What is a hydrogen bond

The best explanation of a hydrogen bond (that is still somewhat readable) that I could find is in Physics News Reviews. If that one is unavailable, take a look at the local copy.

Figure 29. 'Artist rendering' of a hydrogen bond

But for those of you who want it at a lower level, here we go (be aware that this explanation is a bit,as we say in Dutch, popie-jopie):

Except for pure hydrogen, protons are always bound to some heavy atom. In bio-macromolecules this heavy atom is most of the time carbon, but oxygen, nitrogen and sulphur (in un-bridged cysteine) can also carry a proton(s). Carbon is a mentally well balanced atom. It likes just as much to pick up some electrons as that it likes to get rid of them. Therefore, there is little shift of electrons from the one atom to the other in most C-H bonds.

Figure 30. Example of hydrogen bond between two waters. Charges shown are partial charges of course.

Nitrogen and oxygen on the other hand like to get electrons around them, so they pull at the shared electrons in the N-H or O-H bond. This puts the hydrogen in the situation that it is short of electrons, and when the hydrogen sees some nice lone pairs around, it starts pulling at those. If the relative orientation of the atoms is OK, this electronic imbalance leads to overlap of orbitals so that an extra almost-bond comes to exist.

Figure 31. The one heavy atom has so much orbital overlap with the proton that we call it a bond. The other has less overlap and we call it a hydrogen bond.

Hydrogen bond statistics

The hydrogenbond atlas, unfortunately, has died. And equally unfortunately,
the owners didn't allow me to make a local copy. So... Skip this exercise.

Figure 32. Take a look at Ian McDonald's hydrogen bond atlas. This atlas is more than 10 years old, but don't worry, the numbers did not change dramatically over the years. If an atom with the potential to be the proton donor in a hydrogen bond is not not involved in a hydrogen bond, we commonly call that an unsatisfied donor (and similarly we can speak of an unsatisfied acceptor).

Question 22:

• Which donor is most often unsatisfied when buried?
• Which side chain can form most hydrogen bonds?
• Serine can be involved in very many hydrogen bonds at once. What is wrong here?
• Try to come up with an explanation for the dramatic Asp/Glu differences (obviously the word 'entropy' will be part of your answer).
• Analyze the hydrogen bonds of Arg 10 in crambin (1crn).
• In general, which are more abundant in proteins, backbone - backbone, backbone - side chain, or side chain - side chain hydrogen bonds? And why?

Hydrogen bonds in crambin.

We will see in the cysteine bridges section that the three cysteine bridges in crambin form some kind of cable running along the long axis of the molecule.

We will now see that hydrogen bonds (and a saltbridge) do something similar. Get crambin up on the screen. Look for the hydrogenbonding pattern of the side chain of Arg-10. Draw this in 2D (that means on a piece of paper...).

Now it is time to ask the teacher to explain how we guestimate the strength of hydrogen bonds.

With the qualitative explanation of hydrogen bond strength at hand, describe the strength of the hydrogen bonds made by the side chain of Arg-10.

Feel free to use the YASARA-scene ′cramhbo.sce′ that is available from the Exercise Files section.