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During the last decade, the classical view of a protein existing in equilibrium between discrete conformational states has undergone a radical transformation. Experimental observations, particularly those obtained from NMR-detected hydrogen/deuterium exchange, indicate that even under native conditions proteins need to be considered as complex statistical ensembles (see for example refs. 1–13). In the view pioneered by Englander and coworkers (1, 2, 4, 7, 8, 14) proteins undergo local unfolding reactions scattered throughout their entire structures. These unfolding reactions occur independently of each other, may involve only a few amino acids, and give rise to a large number of states in which each state is defined by the presence of one or several locally unfolded regions. This collection of states defines the native-state ensemble. The immediate, and perhaps most relevant, consequence of these observations is that the Gibbs energy of stabilization of a protein is not uniformly distributed throughout its three-dimensional structure. There are regions with high stability constants and regions with low stability constants (13, 15). Furthermore, under native conditions cooperativity appears to be local or regional rather than global. The implications of these findings have been mostly discussed in relation to the protein folding problem; however, their biological implications are tremendous because the native state is the functionally relevant state. If cooperativity is local or regional rather than global, how do distal sites communicate with each other? How do regulatory allosteric interactions take place? How are the functional properties of a protein related to the distribution of states within the native ensemble, and how does ligand binding affect this distribution and modulate function? Is the location of stable and unstable regions a random event or it is dictated by functional considerations? How are protein function and stability related? The tools to …

Can allosteric regulation be predicted from structure?