Structural aspects of protein kinase control-role of conformational flexibility.

Protein kinases catalyze the phosphotransfer reaction fundamental to most signaling and regulatory processes in the eukaryotic cell. Absolute control of individual protein kinase activity is, therefore, of utmost importance to signaling fidelity in the cell. Mechanisms for activity modulation, including complete and reversible inactivation, have been shown by crystal structures of many active and inactive protein kinases. The structures of inactivated kinases, compared with those of active and catalytically competent kinases such as the protein kinase A catalytic subunit, highlight recurring structural alterations among a set of elements of the catalytic kinase core. These 'activity modulation sites' apparently comprise the principal evolved mechanisms for control of enzyme activity in the catalytic domain. In combination, they enable diverse physiological regulatory mechanisms operative for most protein kinases. Identification and characterization of these sites should impact strategies for discovery and design of target-specific therapeutic drugs as the range of structural variations for specific kinases becomes known. The principle site, the ATP-binding pocket, is the target of many physiological regulators and also most experimental or therapeutic inhibitors, which typically block it in a competitive or allosteric fashion. Co-crystallization studies with protein kinase A and other kinases have revealed binding features of several classes of protein kinase inhibitors. Ligand-induced structural changes are common and tend to optimize buried surface areas. The ability to optimize binding energies arising from the hydrophobic effect creates a logarithmic dependence of binding energy on buried surface areas. Exceptions to this rule arise for specific inhibitor classes, and possibly also as artifacts of structure determination.