2
$\begingroup$

I was wondering if, say, glutamic acid and arginine can form H-bonds at physiological pH?

amino acids, their protonated and deprotonated forms and pKa-values

According to the figure arginine has a $\ce{NH3+}$ group and glutamic acid a $\ce{COO-}$ group at physiological pH. I know hydrogen bonding is possible amongst $\ce{NH2}$, $\ce{HF}$ and $\ce{OH}$. But $\ce{-NH2}$ is in the protonated form and the $\ce{-COOH}$ in the deprotonated form.

What will happen:

  • Will $\ce{-NH3+}$ donate its $\ce{H+}$ to $\ce{-COO^-}$ to form $\ce{-NH2}$ and $\ce{-COOH}$ and then form hydrogen bonds?
  • Will they attract each other because of the opposite charge, with resulting H-bonding
  • No H-bonding will occur.

(maybe the first and second option are combined, I didn't really know how to formulate it)

UPDATE
How is the H-bond possible in the following figure (I would think this is just an electrostatic interaction, this figure suggest it would a combination of both):

Hydrogen bonding between lysine and glutamate
source of picture: Wikipedia

$\endgroup$

migrated from biology.stackexchange.com Sep 17 '16 at 8:31

This question came from our site for biology researchers, academics, and students.

  • $\begingroup$ See this: The distributing basics of the moderate structure found in geometry, charge distribution, and ability to form multiple H-bonds make arginine ideal for binding negatively charged groups. For this reason, arginine prefers to be on the outside of the proteins, where it can interact with the polar environment. So, it can form H-bond or, preferably, dipole-dipole interaction. $\endgroup$ – another 'Homo sapien' Sep 16 '16 at 14:08
0
$\begingroup$

As none of the chemists have picked up on this one, I will venture an answer.

First, I am answering on the assumption that this question relates to proteins as it was originally posted on Biology SE and you have previously asked chemical questions about proteins.

Second, I would have thought that you would be aware that weak interactions in proteins are usually categorized in three different types. The section on non-covalent bonds in Berg et al. states:

The three fundamental noncovalent bonds are electrostatic interactions, hydrogen bonds, and van der Waals interactions. They differ in geometry, strength, and specificity. Furthermore, these bonds are greatly affected in different ways by the presence of water.

So I find it strange that you wish to make an electrostatic interaction (aka an ionic bond) involving integral positive and negative charges into a hydrogen bond which can be regarded as a sort of poor man’s ionic bond as it involves only partial positive and negative charges. To quote Berg et al. again:

The relatively electronegative atom to which the hydrogen atom is covalently bonded pulls electron density away from the hydrogen atom so that it develops a partial positive charge (δ+). Thus, it can interact with an atom having a partial negative charge (δ-) through an electrostatic interaction.

The glutamic acid and arginine side-chains will be ionized at physiological pH because of the values of their ionization constants — the position of the equilibrium between the ionized and unionized forms. One extra hydrogen ion in the sea of hydrogen ions in the aqueous environment is not going to affect this one iota.

You should also be aware that the aqueous environment (in this case the surface of a globular soluble protein) is most unfavourable to the formation of hydrogen bonds between residues because of the competition of polar water molecules. To quote once more:

A hydrogen atom of water can replace the amide hydrogen atom as a hydrogen-bond donor, whereas the oxygen atom of water can replace the carbonyl oxygen atom as a hydrogen-bond acceptor. Hence, a strong hydrogen bond between a CO group and an NH group forms only if water is excluded.

You should read the whole of this section (which also applies to ionic bonds) to appreciate how these bonds are most important in the hydrophobic interior of proteins.

In summary, the answer to your question is “No hydrogen bonding will occur — if anything there will be ionic bonding, but in an aqueous environment this will be disrupted.”

You clearly have a reason for wanting glu and arg to form hydrogen bonds. Perhaps you could explain why.

$\endgroup$
  • $\begingroup$ You have described hydrogen bond using an "electrostatic" dipole-dipole interaction model. However, I would like to add that it has some features of "covalent bonding"-- it is directional and strong, produces interatomic distances shorter than the sum of the van der Waals radii, involves a limited no. of interaction partners, etc. $\endgroup$ – getafix Sep 22 '16 at 0:49
  • $\begingroup$ Thankyou @David, I'm a little bit confused because one of my books (fundamentals of general ,organic and biological Chemistry; McMurry) says this: "A peptide rich in Asp and Lys is more soluble, because it's SIDE CHAINS are more polar and can form hydrogen bonds with water?? (Sorry for the late reply) $\endgroup$ – KingBoomie Sep 26 '16 at 18:50
  • $\begingroup$ The book says that those amino acids: Arg, Asp, Asn, Glu, Gln, His, Lys, Ser, Thr, Tyr can form hydrogen bonds using there side chains @David $\endgroup$ – KingBoomie Sep 26 '16 at 19:30
  • $\begingroup$ @RickBeeloo — Indeed. Draw out the structures and you will see that in addition to the changed oxygen there is also a =O in the acidic residues. That is what can form a hydrogen bond. I leave you to work it out for the basics. I'm on holiday in Italy with only a phone for Internet connection. Ciao! $\endgroup$ – David Sep 26 '16 at 20:29
  • $\begingroup$ Enjoy your holiday! @David $\endgroup$ – KingBoomie Sep 26 '16 at 20:31
2
$\begingroup$

Yes, glutamate and arginine can form a hydrogen bond at physiological pH. Remember of course, that as soon as you enter aquaeous media, everything will be saturated by hydrogen bonds from the surrounding water molecules. But inside a protein an arginine—glutamate hydrogen bond is perfectly viable. Arginine will donate the hydrogen bond using an $\ce{N-H}$ bond and glutamate will receive towards a carboxylate.

Note, by the way, that your picture gives a wrong structure of protonated arginine. The correct protonation of the guanidine group is given in the image below (taken from Wikipedia).

Resonance forms of Arginine

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.