Allostery without conformational change

Allostery is a strange-looking word for a relatively simple idea: regulation at a distance. Binding events at one location on a protein can influence binding events that are relatively far away. It is allostery—in the form of cooperative binding in hemoglobin—that makes our oxygen-delivery system work. Because it provides an alternative way to attack drug targets, allosteric regulation is an attractive possibility for new medicines; recent results suggest that allosteric inhibitors may have promise in the treatment of diseases related to hormone receptor activation. Yet, as interest increases in the therapeutic potential of allosteric drugs, structural biologists are re-evaluating what allostery really means.

In the classic view of allostery, binding of one ligand at one site provokes a large conformational change that alters the affinity of another site for its ligand. Without denying that this conception of remote regulation has proven phenomenally successful, we can still ask whether models of this kind cover the full breadth of possibilities. Chung-Jung Tsai, Antonio del Sol, and Ruth Nussinov ask precisely that in their article now in press at the Journal of Molecular Biology (1). They find, based on an allosteric protein "benchmark", that significant backbone deformations are not an essential characteristic of allosteric effects. They therefore state that allostery might arise not only from large conformational changes, but also from changes in dynamics.

This is not a new concept—the possibility that allostery could be driven by entropic effects was articulated as early as 1984 by Cooper and Dryden (2). It seems like an odd idea, in part (I believe) because most of the analogies we use to describe allostery involve obvious changes of shape. But even stably folded proteins undergo significant fluctuations—at a fundamental level, especially when it comes to side chains, their shape is fluid. This imparts a substantial configurational entropy, which could be important in regulating binding.

Almost any binding event, irrespective of the structural dynamics of the protein or ligand, results in a decrease in the entropy of the system because the translational and rotational degrees of freedom of the protein and ligand are no longer independent. It is normal, although not always the case, that binding a ligand also significantly reduces the configurational entropy of the protein. These entropic costs are offset by energetic benefits of binding.


So, let us consider a protein that binds two ligands at different sites (see my figure cave drawing at right; CE = configurational entropy), such that neither binding event significantly alters the overall conformation. Binding of ligand A, however, might still be expected to decrease the fluctuations in the immediate vicinity of the binding site. If that's all that happens, then binding of ligand A does not alter the binding of ligand B (case I). Let us imagine, however, that the rigidification spreads from the "A site" to the "B site" (case II). Such a rigidification might pre-organize the B site; in this case the entropic cost of binding B is reduced. Thus, the binding is enhanced. Obviously, this could work the opposite way as well. It is known that binding a ligand sometimes increases the configurational entropy of a protein. If this increased entropy is communicated to the B site, then the entropic penalty for binding B and rigidifying that site is increased (case III). So depending on the system, either positive or negative allostery is possible. Tsai et al. discuss these and other models in greater detail.

Is it in fact possible for dynamic effects to be "transmitted" through a protein? As Tsai, et al. point out, previous research indicates that it is, even in relatively small globular domains. Ernesto Fuentes demonstrated that peptide binding to a PDZ domain induced changes in side-chain dynamics on the back side of the protein (3). As I discussed previously, this communication pathway has been associated with an allosteric interaction between two PDZ domains in PTP-BL. Moreover, Andrew Lee and some weirdo demonstrated that similar effects occurred in a protein of the potato inhibitor I family that lacked any discernible allosteric behavior whatsoever (4). Beyond proving that dynamic effects are transmissible, results of this kind support the idea that allosteric potential is a property of proteins generally (5).

The Tsai et al. paper is meant to reinforce and develop the concept that allostery is not solely a feature of proteins or complexes that undergo large conformational rearrangements in response to particular ligand-binding events. Small changes in backbone conformation or altered dynamics may also be responsible for allosteric effects. This may sound significantly different from present views of allostery, but in a sense it does not alter the classic interpretation. Rather, this new view points to a deficiency in the classic understanding of "conformational change". A genuine understanding of a protein's structure is not captured by a single conformation, but rather by the structural dynamics of a conformational ensemble. In some cases, i.e. the classic examples, the structural effects of ligand binding take the form of a change in the energy distribution: a particular subset of conformations becomes lower in energy and thus becomes more populated. In others, however, binding results in an elimination of possible sub-states of a given backbone conformation. Both outcomes significantly change the conformational ensemble, and both of them can produce allosteric effects.

1. Tsai, C., del Sol, A., Nussinov, R. (2008). Allostery: Absence of a change in shape does not imply that allostery is not at play. Journal of Molecular Biology DOI: 10.1016/j.jmb.2008.02.034

2. Cooper, A., Dryden, D.T. (1984). Allostery without conformational change. European Biophysics Journal, 11(2), 103-109. DOI: 10.1007/BF00276625 OPEN ACCESS

3. Fuentes, E., Der C.J., and Lee A.L. (2004). Ligand-dependent Dynamics and Intramolecular Signaling in a PDZ Domain. Journal of Molecular Biology, 335(4), 1105-1115. DOI: 10.1016/j.jmb.2003.11.010

4. Clarkson, M., Gilmore, S., Edgell, M., Lee, A. (2006). Dynamic coupling and allosteric behavior in a nonallosteric protein. Biochemistry, 45(25), 7693-7699. DOI: 10.1021/bi060652l

5. Gunasekaran, K., Ma, B., Nussinov, R. (2004). Is allostery an intrinsic property of all dynamic proteins?. Proteins: Structure, Function, and Bioinformatics, 57(3), 433-443. DOI: 10.1002/prot.20232