The Smallest Allosteric System

Allostery is still a badly understood but very general mechanism in the protein world. In principle, an allosteric event occurs when a ligand (small or big) binds to a certain site of a protein and something (activity or function) changes at a different, distant site. A well-known example would be G-protein-coupled receptors that transport such an allosteric signal even across a membrane. But it does not have to be that far apart. As part of the Protein Folding and Dynamics series, I have recently watched a talk by Peter Hamm (Zurich) who presented work on an allosteric system that I thought was very interesting because it was small and most importantly, controllable.

PDZ domains are peptide-binding domains, often part of multi-domain proteins. For the work presented the researchers used the PDZ3 domain which is a bit special and has an additional (third) C-terminal α-helix (α3-helix) which is packing to the other side of the binding pocket. Previous work (Petit et al. 2009) had shown that removal of the α3-helix had changed ligand affinity but not PDZ structure, major changes were of an entropic nature instead. Peter Hamm’s group linked an azobenzene-derived photoswitch to that α3-helix; in its cis configuration stabilizing the α3-helix and destabilising in trans (see Figure 1).

Figure 1: PDZ3 domain (purple) and photoswitch (red) have different affinities for the peptide ligand (green), depending on the photoswitch’s isomerisation state (and temperature). From Bozovic, O., Jankovic, B. & Hamm, P. Sensing the allosteric force. Nat Commun 11, 5841 (2020). https://doi.org/10.1038/s41467-020-19689-7

What they found was that by switching from trans to cis, the helix was stabilized and the binding affinity for the ligand increased (up to 120-fold, temperature-dependent) at that distant site (hence an allosteric event). This allosteric communication also worked in the other direction as the rate of cis-to-trans isomerisation increased when the ligand was bound (compared to the native isomerisation rate without ligand). This combination of a small peptide-binding domain and a photoswitch constitutes a very small allosteric system (the smallest known today?) which states can be controlled by light and ligands. The size and controllability of this systems might open up more in-depth studies on how a (or at least this) allosteric signal is transmitted inside a protein.

They further determined binding enthalpies, the difference in driving force for cis-to-trans isomerisation and resulting from that, a force that is transmitted through the allosteric events and therefore termed ‘allosteric force’. For more details on their theoretical considerations for this as well as the experiments have a look at their paper: Sensing the allosteric force.

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