Activation segment of protein kinases: classification based on multidimensional analysis

Abstract

Activation segments (ASs) of protein kinases play crucial roles in regulation, rendering them prime candidates for therapeutic intervention. Their structural and sequence diversity makes them challenging to study systematically. This study proposes a novel classification of protein kinase ASs based on comprehensive analysis of their sequences, structures and conformational dynamics. Through sequence and structural analysis, we identified seven distinct classes of ASs that transcend traditional phylogenetic classifications. The analysis identified multiple highly conserved sequence motifs, including Y-X(2)-D-Y-Y, D-F-G-x(2)-R and P-x(2)-W-x-A-P-E, demonstrating correlations with functional characteristics. Secondary structure analysis demonstrated consistent patterns, notably two C-terminal α helices and N-terminal β sheets, with class-specific variations. Molecular dynamics simulations revealed differential stability patterns across conformational states (IN, OUT, SWP), with the OUT conformation showing remarkable stability in most classes. The 'Class II', characterized by three conserved motifs, stable secondary structure and consistent dynamics, exhibited unique structural and dynamic properties among the classes. This new classification system provides valuable insights for understanding kinase structure-function relationships.