An interesting way to study the hydrophobic effect between protein surfaces

Protein interaction domains haven’t been studied to nearly the extent they need to be, and we know far less about them than we should. All the large molecular machines of the cell (ribosome, mediator, spliceosome, mitochondrial respiratory chain) involve large numbers of proteins interacting with each other not by the covalent bonds beloved by organic chemists, but by much weaker forces (van der Waals,charge attraction, hydrophobic entropic forces etc. etc.).

Designing drugs to interfere (or promote) such interactions will be tricky, yet they should have profound effects on cellular and organismal physiology. Off target effects are almost certain to occur (particularly since we know so little about the partners of a given motif). Showing how potentially useful such a drug can be, a small molecule inhibitor of the interaction of the AIDs virus capsid protein with two cellular proteins (CPSF6, TNPO3) the capsid protein must interact with to get into the nucleus has been developed. (Unfortunately I’ve lost the reference). For more about the host of new protein interaction domains (and potential durable targets) just discovered please see

Hydrophobic ‘forces’ are certain to be important in protein protein interactions. A very interesting paper figured out a way to measure them using atomic force microscopy (AFM). [ Nature vol. 517 pp. 277 – 279, 347 – 350 ’15 ]. This is particularly interesting to me because entropy has nothing to do with the force as measured. I’ve always assumed that the the hydrophobic force was entropic, similar to the force exerted by rubber when you stretch it. It’s what pushes hydrophobic side chains into the interior of proteins (e.g water doesn’t have to decrease its entropy by organizing itself to solvate hydrophobic side chains). Not so in this case.

The authors prepared self-assembled monolayers using dodecyl thiol (CH3 (CH2) 10 CH2 SH) bound to gold. Every now and then an amino group or a guanido group was placed at the other end of the thiol. This allowed them to produce a mixture of hydrophobic groups (60%) and ionic species (NH4+ or guanidinium ions) within nanoMeters of the hydrophobic regions. The amine and the guanidino groups were the same distance as the hydrocarbon ends from the gold surface. A gold atomic force microscope (AFM) with a hydrophobic tip (the same C(12) moiety), was then used to measure the adhesive force between the tip and the surface in aqueous solution.

This is important because it is a measurement not a theoretical calculation (apologies Ashutosh). This is particularly useful since water is so complex that we don’t have a good understanding (potential function) for it.

Methanol was added (which eliminated most of the hydrophobic interactions). Sensitivity to methanol was taken as a signature of the hydrophobic component of the force. The pH could be manipulated, so the R – NH2 could be charged to R -NH3+, ditto for guanidinium to the uncharged species.

So guess what the effect of amino and guanidine groups were on the hydrophobic interaction. I was rather surprised.

The strength of hydrophobic interactions between the mixed monolayers and the tip doubled when neutral amino groups found within nanoMeters of hydrophobic regions are charged to form R -NH3+ ions by lowering the pH. A similarly placed guanidinium ion eliminates the hydrophobic interactions at all pHs. So the effect of the two side chains (NH2 for lysine, guanidinium for arginine) is opposite.

They note that the ammonium ion is well hydrated, but guanidinium is hydrated only at the edges of the plane (where the electrons are) but not above it. This allows guanidinium an amphipathic behavior, which is why it can be a denaturant (did you know this? I didn’t).

I’m sure that the effect of negative ions (e.g. carboxyl groups) and every other conceivable side chain will be studied in the future.

Thus hydrophobicity is not an intrinsic property of any given nonPolar domain. It can be changed by functional groups within 10 Angstroms.. So placing a charged group near a hydrophobic domain, should allow tuning of the hydrophobic driving force. I’d be amazed if this isn’t found to be the case evolutionarily.

They also studied some wierd looking stuff resembling proteins (beta peptides { e.g. the amino and carboxyl groups on adjacent carbons rather than the same one as with alpha amino acids) with weird side chains which are known to adopt an amphipathic helical conformation. THe nonpolar side chains were trans 2 aminocyclohexanecarboxylic acid (ACHC), and the cationic side chains were beta3 homolysine. Why didn’t they use something more natural. The peptide forms an ACHC rich nonPolar square domain 10 Angstroms on a side with a polar patch on the other side of the helix.

So it’s a fascinating piece of work with large implications for the design of drugs attacking protein protein interfaces.

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