Mar 132009
ResearchBlogging.orgI’ve mentioned urea and guanidinium (Gdm) before on this blog, usually with reference to questions about their mechanism of action. These small molecules cause proteins to denature, or lose their higher levels of structure and become unfolded chains. The complete unfolding of a protein typically requires a fairly high concentration of denaturant, almost always more than 1M, and the explanation for this is that the denaturant molecules preferentially associate with the polypeptide chain with low affinity. In a recent issue of PNAS, a paper from Walter Englander argues that urea, but not guanidinium, associates with the backbone of the protein via hydrogen-bonding interactions.

Lim et al. reached this conclusion using hydrogen-exchange experiments. Amide nitrogens in proteins freely exchange their covalently-bound hydrogens (protons) with the surrounding water. The rate of this process can be measured (among other ways), by placing a protonated amide group into a deuterated solvent and tracking the decline in proton signal by NMR; this is called an HX experiment. In the case of a folded protein chain the observed rate will depend on the intrinsic chemistry of the particular amide and the stability of the protein structure, because this structure excludes water from the backbone and makes hydrogen bonds that lock the protons in place. Rather than deal with all of that, the authors used a small peptide mimic that (probably) has no complex structure. This had the additional advantage that the simple spectrum could be tracked by 1-D NMR, substantially increasing the time-resolution of the measurements. The authors measured the rates as they varied the pH — because we’re talking about D2O, it’s called the pD instead — and added various cosolutes that are known to denature or stabilize protein folds.

As expected, the dialanine itself had a V-shaped rate profile in these HX experiments, with a minimum at a pD of 4. The hydrogen exchange reaction can be catalyzed by acid or base, so the rate increases as you go up or down in pD from this minimum. When urea was added to the solution, the authors found that acid-catalyzed HX accelerated while base-catalyzed HX decelerated. The most reasonable explanation for the latter result is that a hydrogen bond between the carbonyl of urea and the amide proton protects it from water attack. The authors do some mathematical modeling to establish that the effect on rate reflects a bonding association between the peptide and urea, not just random collisions or thermodynamically neutral associations.

The acid-catalyzed result is interesting, because in theory one would expect that urea would accelerate acid-catalyzed HX more than it actually does, because under acidic conditions it can accept a hydrogen from the amide nitrogen. While there are some confounding factors, the most likely explanation for this result is that the NH2 groups of urea form hydrogen bonds to the carbonyl of the peptide. Because acid catalysis of HX hinges on the favorability of protonating this carbonyl, a hydrogen bond would be expected to reduce the HX rate. The authors argue that the ability of urea to serve as an acid catalyst is therefore mitigated by its propensity to bind to the carbonyl.

The formation of hydrogen bonds between urea and the peptide group meshes well with evidence that it denatures proteins through interactions with the backbone, some of which I have mentioned before. From HX experiments under native conditions we know that even a folded protein chain regularly undergoes excursions from its water-excluded, hydrogen-bonded state. Urea may bind to the backbone during these fluctuations, preventing or slowing a return to the folded structure.

Lim et al. also tested a number of other cosolutes, and found that none of them had a similar effect on the HX rate. In the case of the stabilizing molecules (glycerol, sorbitol) this is entirely expected, as their action cannot be explained in terms of a preferential association with the backbone anyway. The surprise concerns guanidinium, which is a more powerful denaturant than urea. The authors noted that Gdm has a small effect on the rate, but not in a pD-dependent way, and one that was little different from an equivalent concentration of NaCl (ordinary table salt). Gdm has no groups that can hydrogen bond to the amide, so the absence of an effect on base-catalyzed HX is expected. However, it should be possible for guanidinium to hydrogen-bond to the carbonyl, so it should seemingly have an effect on acid catalysis. This is not in fact the case.

The authors note that existing evidence does not support the idea that Gdm forms hydrogen bonds with water (although urea is known to do so). Lim et al. suggest instead that the planar Gdm molecule forms favorable stacking interactions with other planar groups. These include the peptide bond and several side chains. They argue that the stacking of Gdm with these groups pries the protein apart without requiring hydrogen bonds.

As a means to investigate diseases that result from protein misfolding, many groups are now trying to structurally characterize the unfolded state of protein molecules. Many of these experiments model the in vivo denatured state by using chemical denaturants such as urea or Gdm. The possibility that direct interactions between the denaturant and the protein will give rise to experimental artifacts should be taken seriously. Urea’s promiscuous formation of hydrogen bonds with the backbone, itself, and water, may give rise to loose networks of hydrogen-bonded molecules that act to condense the chain. By contrast, Gdm’s stacking effect will likely act to artificially extend the chain by steric obstruction. Because of the difference in these mechanisms, it may be of value to cross-validate findings from structural studies on unfolded states by repeating experiments with alternative denaturants.

Lim, W., Rosgen, J., & Englander, S. (2009). Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group Proceedings of the National Academy of Sciences, 106 (8), 2595-2600 DOI: 10.1073/pnas.0812588106

  One Response to “Urea binds to the peptide group”

  1. Michael – read your blog on our paper about urea to peptide group interaction. That is one very smart commentary. Think you described it better than we did.

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