Role of a Novel PH-Kinase Domain Interface in PKB/Akt Regulation: Structural Mechanism for Allosteric Inhibition

Abstract

Protein kinase B (PKB/Akt) belongs to the AGC superfamily of related serine/threonine protein kinases. It is a key regulator downstream of various growth factors and hormones and is involved in malignant transformation and chemo-resistance. Full-length PKB protein has not been crystallised, thus studying the molecular mechanisms that are involved in its regulation in relation to its structure have not been simple. Recently, the dynamics between the inactive and active conformer at the molecular level have been described. The maintenance of PKB's inactive state via the interaction of the PH and kinase domains prevents its activation loop to be phosphorylated by its upstream activator, phosphoinositide-dependent protein kinase-1 (PDK1). By using a multidisciplinary approach including molecular modelling, classical biochemical assays, and Förster resonance energy transfer (FRET)/two-photon fluorescence lifetime imaging microscopy (FLIM), a detailed model depicting the interaction between the different domains of PKB in its inactive conformation was demonstrated. These findings in turn clarified the molecular mechanism of PKB inhibition by AKT inhibitor VIII (a specific allosteric inhibitor) and illustrated at the molecular level its selectivity towards different PKB isoforms. Furthermore, these findings allude to the possible function of the C-terminus in sustaining the inactive conformer of PKB. This study presents essential insights into the quaternary structure of PKB in its inactive conformation. An understanding of PKB structure in relation to its function is critical for elucidating its mode of activation and discovering how to modulate its activity. The molecular mechanism of inhibition of PKB activation by the specific drug AKT inhibitor VIII has critical implications for determining the mechanism of inhibition of other allosteric inhibitors and for opening up opportunities for the design of new generations of modulator drugs. A critical protein in cell-signalling pathways, called protein kinase B, regulates many aspects of cell biology from metabolism to proliferation and survival, by modifying other proteins with the addition of a phosphate group. Hence, deregulation of its activity has acute consequences on cell function. Increased activity of a tumour-promoting form of protein kinase B or of upstream regulatory proteins has been observed in tumours, while impaired protein kinase B function has been linked to diabetes. Therefore, understanding the molecular mechanism of protein kinase B activation will help reveal how its activity might be regulated to limit disease progression. Toward this end, we studied how protein kinase B structure relates to its function, to identify molecular mechanisms regulating its kinase activity, modifying its cellular localization, and altering its binding to other proteins. By determining the spatial organization of different regions of the protein in inactive protein kinase B, we discovered a cavity at the interface of two distinct functional regions of the inactive form. We also localized the C-terminal end of the protein to the apex of the cavity, suggesting a role of this domain in regulating the inactive form of the protein. This represents a novel example of negative regulation by inhibition across these different regions of the protein. From these findings, we elucidated the mechanism of action of a highly specific protein kinase B inhibitor, AKT inhibitor VIII. We determined that simultaneous binding of the inhibitor to the two different functional regions, through the cavity, “locks” protein kinase B in an inactive conformation and prevents regulatory proteins from accessing the C-terminal domain.