Clustering of the structures of protein kinase activation loops: A new nomenclature for active and inactive kinase structures

Abstract

Targeting protein kinases is an important strategy for intervention in cancer. Inhibitors are directed at the conserved active conformation or a variety of inactive conformations. While attempts have been made to classify these conformations, a structurally rigorous catalogue of states has not been achieved. The kinase activation loop is crucial for catalysis and begins with the conserved DFGmotif (Asp-Phe-Gly). This motif is observed in two major classes of conformations, DFGin -an ensemble of active and inactive conformations where the Phe residue is in contact with the C-helix of the N-terminal lobe, and DFGout -an inactive form where Phe occupies the ATP site exposing the C-helix pocket. We have developed a clustering of kinase conformations based on the backbone dihedral angles of the sequence X-D-F, where X is the residue before the DFGmotif, and the DFG-Phe side-chain rotamer, utilizing a density-based clustering algorithm. We have identified 8 distinct conformations and labeled them based on their Ramachandran regions (A=alpha, B=beta, L=left) and the Phe rotamer (minus, plus, trans). Our clustering divides the DFGin group into six clusters including 'BLAminus,' which contains active structures, and two common inactive forms, 'BLBplus' and 'ABAminus.' DFGout structures we have are predominantly in the 'BBAminus' conformation, which is essentially required for binding Type II inhibitors. Structural features such as the C-helix position and the overall activation loop conformation are strongly associated with our clusters. Our structurally intuitive nomenclature will aid in understanding the conformational dynamics of these proteins and structure-based development of kinase drugs.