Energetic redistribution in allostery to execute protein function.

A perturbation at one site of the protein could cause an effect at a distant site. This important biological phenomenon, termed the “allosteric effect,” is essential for protein regulation and cell signaling, playing an important role in cellular function. Its fundamental functional significance has inspired numerous works aiming to understand how allostery works. Allostery can involve large, or unobserved, subtle (mainly side-chain) conformational changes (1). Conformational changes are driven by enthalpy. The term “dynamic allostery” was coined by Cooper and Dryden in the early 1980s to describe allostery “even in the absence of a macromolecular conformational change” (2). Cooper andDryden argued that dynamic allostery is primarily an entropy effect. However, numerous works have been published over the last 20 y taking “dynamic allostery” to imply a complete absence of conformational change because the authors did not observe such changes (1). Importantly, “dynamic allostery” without observable conformational changes is still ruled by a population shift between two “distinct” states where a new energetic redistribution favorable for the allosteric (functional) state is either dominated by entropy, enthalpy, or both. Few studies questioned whether enthalpy plays a role in dynamic allostery as well (1). In PNAS, Kumawat and Chakrabarty (3) demonstrate that indeed even in dynamic allostery enthalpy plays a role by redistributing internal energies, especially electrostatic interaction energies, among residues upon perturbation (Fig. 1). Electrostatics is an established player in function. Decades ago, Warshel (4) and Warshel et al. (5) demonstrated its critical role in protein catalysis and Perutz (6) in allostery. Recently, rearrangements of electrostatic networks were reported for conformationally driven allostery (7, 8). The report of hidden electrostatic interactions in dynamic allostery in PNAS (3) argues that redistribution of electrostatic interaction energy could be universal in allosteric proteins, with or without significant conformational change. Proteins embrace redistribution of electrostatic interaction energies to execute their functions. For example, myosin, a motor protein, binds to the negatively charged ATP, which redistributes the electrostatic bond network, thus altering the charge of the actin-binding site, leading to myosin’s dissociation from actin (7). Thus, myosin redistributes electrostatic interaction energy in allostery to execute its function of dissociation from actin. The PDZ domain protein is a well-known cell signaling protein. The major functions of PDZ domains include recognition of the disordered C-terminal peptide motifs of hundreds of receptors and ion-channel proteins, dimerization with other modular domains, and phospholipid binding. As a dynamic regulator of cell signaling, PDZ function can be modulated allosterically (9). In the PDZ3 domain protein, the peptide recognition site is located at the hydrophobic β2–α2 region. Mutations of distal residues on the PDZ3 domain or deletion of the distal α3 helix (10) allosterically affect the binding affinity at the recognition site without causing significant conformational change. By contrast, binding of the peptide at the recognition site changes the dynamics of the PDZ3 domain, albeit still without large conformational change. Using molecular dynamics simulations and analysis of protein interaction energy, Kumawat and Chakrabarty (3) show that the perturbation of the binding of a peptide in the β2–α2 region leads to the side-chain rearrangement of certain charged residues to form new favorable electrostatic interactions. As a result, some of the previously favorable electrostatic interactions in the unbound state become unfavorable. Like a domino effect, additional side-chain rearrangements occur to release this energetic stress, altering the electrostatic and hydrogen bond network, especially in the Nand C-terminal regions, consistent with the known allosteric sites. How does this energetic redistribution affect PDZ3 function? PDZ domains are usually sequential on the protein chain. The energetic redistribution in one PDZ domain can propagate through an allo-network (11) to a second PDZ domain, thus affecting cell signaling. It is difficult to detect this dramatic redistribution of energy in experiments, because the energetic redistribution does not