Let's take a look at D-glucose. It exists as a mixture of anomers and the authors of the featured article suggest that the alpha form binds to glycogen phosphorylase about 3-fold more strongly than the more abundant beta form. You'll also notice some hydroxyl groups. Quite a few hydroxyl groups in fact and we'll try to explore the significance of this observation in the next post.
The Ki values for the two anomeric forms of glucose provide the reference and all we need to do now is measure Ki values for close analogs of the reference and we'll know what the hydrogen bonds contribute to binding. The authors of the featured study removed hydroxyl groups and replaced them with fluorine atoms. Fluorine is thought to be a slightly weaker hydrogen bond acceptor than hydroxyl oxygen but cannot function as a donor. The authors suggest using the 1mM Ki measured for the alpha anomer to make comparisions with and this appears to be a sensible suggestion.
Let's see what happens for the hydroxyl at C1. Removal of the hydroxyl (1-deoxy-D-glucose) results in a Ki of 11mM while replacement of hydroxyl with fluorine is slightly favorable (Ki = 0.6mM) for binding. The crystal structure of the complex of glycogen phosphorylase with glucose suggested that the 1-hydroxyl did not function as a hydrogen bond donor. The C2 hydroxyl shows a broadly similar profile although the Ki for the deoxy analog is 27mM and the fluoro analog is not anomerically pure. Removal of the hydroxyl groups at C3, C4 or C6 all lead to Ki values that are quoted as >> 100mM and the fluoro analogs all show weaker (25-200) binding than their parents.
So what are we to make of all this? According to Table II in the featured article, the hydroxyl at C1 accepts a hydrogen bond from Leu136 so the 11-fold decrease in affinity resulting from deletion of this hydroxyl can be linked to that hydrogen bond. The real question however is whether this hydrogen bond represents the upper limit of what a neutral-neutral hydrogen bond can contribute.
The oxygen of the C1 hydroxyl is linked to the ring oxygen by a single carbon and to the C2 hydroxyl by two carbons. These structural features weaken the C1 hydroxyl as a hydrogen bond acceptor. But there is another problem. In bulk water both the oxygen and hydrogen atoms of the C1 hydroxyl form hydrogen bonds with water and in doing so strengthen each other's interaction an a synergistic (or cooperative) manner. So the next question is whether accepting a hydrogen bond from Leu136 compromises the ability of the C1 hydroxyl to donate hydrogen bonds to water. If so, this represents a thermodynamic penality that must be paid (like income tax) in order for the hydrogen bond to form. You have to be absolutely certain that this is not happening if you are going top present this as an upper limit for the contribution of a neutral-neutral hydrogen bond to binding affinity.
The interactions of the other hydroxyls with the protein are more complicated. Each forms more than one hydrogen bond with the protein and the deoxy analogs are not anomerically pure. The effect of deleting these hydroxyl groups is clearly catastrophic but we need to know how catastrophic if we are to set establish upper limits for the contributions of hydrogen bonds. Also two (C3 & C6) of the hydroxyl groups appear to be interacting with charged amino acid side chains.
We like this paper and recommend it to anybody with an interest in molecular recognition of carbohydrates. However the real question here is whether the contributions to binding of the hydroxyl groups at C1, C2 and C4 support the statement that a neutral-neutral hydrogen bond contributes no more than 15-fold to binding affinity. We are simple folk and leave that to you, the reader, to decide.
But there is another issue which we've not yet touched on and you'll need to wait until the next post to find out about Molecules for Simpletons. We hope your day has been enriched by this Crapshoot and that you'll drop by again real soon.
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SMILES for indexing
O1[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
O1[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
O1[C@@H][C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
O1[C@@H](F)[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
O1[C@H](F)[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
O1[C@@H](O)C[C@@H](O)[C@H](O)[C@H]1CO
O1[C@@H](O)[C@H](O)C[C@H](O)[C@H]1CO
O1[C@@H](O)[C@H](O)[C@@H](O)[C@H][C@H]1CO
4 comments:
Intramolecular Hydrogen Bonding and Cooperative Interactions in Carbohydrates via the Molecular Tailoring Approach
Deshmukh, M. M.; Bartolotti, L. J.; Gadre, S. R.
J. Phys. Chem. A.; (Article); 2008; 112(2); 312-321. DOI: 10.1021/jp076316b
The ∆H for H-bonding may be 1-2 kcal/mol. But the ∆G could be more if waters are displaced from a hydrophobic site by the bind, wouldn't it? In their study, Friesner had calculated a ∆G of 4.5 kcal/mol for a hydrogen bond in streptavidin-biotin.
Also, F is usually a very poor H-bond acceptor if at all as you probably know.
I still need to take a look at the JPC paper. The main point that I'm exploring in this series of Crapshoots is whether the articles cited in support of the assertion that neutral-neutral hydrogen bonds contribute <1.5kcal/mol really do support that assertion. That assertion was made in terms of ∆G so considerations of ∆H do not really apply.
The fluorine is indeed a weaker acceptor although the relevance of that to this study is not clear. I am more concerned that the hydroxyl groups don't get to deploy their donor and acceptor potential in an optimal manner.
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