The mechanism of inhibition of the cyclin‐dependent kinase‐2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK

Abstract

Molecular dynamics (MD) simulations were used to explain structural details of cyclin‐dependent kinase‐2 (CDK2) inhibition by phosphorylation at T14 and/or Y15 located in the glycine‐rich loop (G‐loop). Ten‐nanosecond‐long simulations of fully active CDK2 in a complex with a short peptide (HHASPRK) substrate and of CDK2 inhibited by phosphorylation of T14 and/or Y15 were produced. The inhibitory phosphorylations at T14 and/or Y15 show namely an ATP misalignment and a G‐loop shift (∼5 Å) causing the opening of the substrate binding box. The biological functions of the G‐loop and GxGxxG motif evolutionary conservation in protein kinases are discussed. The position of the ATP γ‐phosphate relative to the phosphorylation site (S/T) of the peptide substrate in the active CDK2 is described and compared with inhibited forms of CDK2. The MD results clearly provide an explanation previously not known as to why a basic residue (R/K) is preferred at the P 2 position in phosphorylated S/T peptide substrates.