The mechanism by which protein conformation changes in response to binding of a second protein (or small effector) has been well characterized, but poorly understood. In the mid-1960’s seminal publications by Monod, Wyman, and Changeux (1965) and Koshland, Nemethy, and Filmer (1966) described what are now termed the “concerted” and “sequential” models, respectively. These models of allosteric regulation describe coupling between ligand binding and subunit conformation and coupling of conformations between different subunits. In the concerted (MWC) model, all subunits switch conformation simultaneously; in the sequential model, binding of a ligand changes shape of only the connecting subunit. Without knowing how probable the allosterically activated sates are in the absence of the allosteric ligands, it is difficult to know what structural and energetic features of a protein must be present in order for the signal transduction to occur (Hilser, Science, 653, 327, 2010).
An alternative model, proposed by Eigen (1967) considers both types of change as being probabilistic leading to the concept of conformational spread (where each conformational state change occurs with a time constant which can be greater or less than that of ligand binding).
Allostery, or allosteric regulation, is utilized by a wide range of proteins whose activity is switched from an “on” to an “off” position – natural examples of control loops with feedback from downstream products or feed forward from upstream substrates. Typically the regulatory site of an allosteric protein is physically distinct from its active site. Examples include many receptor-mediated processes, enzymes involved in metabolism, and motor proteins. Allosteric sites represent novel drug targets particularly since these modulators have a decreased potential for toxic effects since modulators with limited cooperativity will have a readily determined maximum effect. Recent studies suggest that regional changes in the conformational heterogeneity of proteins (i.e., local unfolding) often accompany allosteric transitions.
Recently, Bai and coworkers (Science, 685, 327, 2010), demonstrated that the bacterial flagellar switch that controls the direction of flagellar rotation during chemotaxis has a highly cooperative response. They used high-resolution optical microscopy to observe switching of single motors and identified a stochastic (non-deterministic, i.e. “random”) multistate behavior of the switch. These observations are in agreement with models of allostery following a conformational spread behavior. Another group (Yuan et al., J Mol Biol 394, 390, 2009) explained that the dependence of conformational switching resulting from varying mechanical loads on the flagella could be explained by conformational spreading.
The ensemble model allows a more productive, theory-based, evaluation of the impact of amino acid substitutions based on analysis of the effects on the energetic of each conformational state and their interactions. Within the scope of this ensemble view of allostery, one can better assess the cooperative energetics for molecular interactions at local and non-local levels within a protein. Validation of this tool, as presented in the recently published experiments, may facilitate protein design for engineering organisms, pharmaceuticals, and cellular devices. It appears that this ensemble model greatly redefines and simplifies this design task.
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