The phosphate tail of ATP binds the p-loop motif, evolutionary conserved, going back to since forever. In the dominant model, the deprotonated hydroxyl groups are complexed with Mg2+, at least two of them.

I was wondering about a hypothetical model (could consider it "fantasy" or just thought experiment, without disclosing if there is any actual credible reason to think about it. )

If the three deprotonated hydroxyl groups were actually protonated, is there still a fit in the p-loop? This would remove the Mg2+, since it is substituted by H+, charge-wise.

That ATP does not actually get protonated like that in the dominant models, is neglected in the question. I am just wondering about fit in the p-loop. To have a way to think of that, imagine the ATP might be slightly modified, or some other input altered, but the p-loop itself is the same, and the phosphate tail except here it is fully protonated.

  • $\begingroup$ I’m voting to close this question because it assumes a chemical impossibility, and therefore, as well as having no relevance to biology, it is impossible to answer. $\endgroup$
    – David
    Commented Apr 26 at 14:53

1 Answer 1


A really simple answer is that hydrogen bonds are stronger when the hydroxyl groups on the phosphates are deprotonated, because hydrogen bonds are like a competition for a proton, but, hydrogen bonds form between hydroxyl groups even when one is not deprotonated.

This gets a bit more interesting if a few facts are considered. The deprotonated group has, relatively speaking, less negative charge. Otherwise, it would be able to hold onto the proton just as well. And since the hydrogen bond acceptor is the group with most negative charge, the deprotonated one would only be favoured because it lacks the proton, not because is has less negative charge in itself. This is a fact but it does not in itself say much. But consider the following.

In a "lock and key" setting with a specific type of fit, the deprotonated group might actually be the hydrogen bond donor. This is very counter-intuitive, but, it relies on the groups being forced close to each other to start with. Then, the combined negative charge of the groups, will actually protonate the deprotonated group, and it will be the donor to the more negatively charged other group. It is a fact that, with added negative charge, the ability to attract a proton increases. And hydrogen bonds rely on physical closeness.

So, the p-loop/ATP complex is acting like a base, using a lock-in-key fit for... protons.


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