title: 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 A) 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 gamma-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.
authors.affiliation: Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic.
authors.forename: Iveta
authors.initials: I
authors.lastname: Bártová
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
authors.forename: Zdenek
authors.initials: Z
authors.lastname: Kríz
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Koca
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D020816:Amino Acid Motifs; D001665:Binding Sites; D042846:CDC2-CDC28 Kinases / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D051357:Cyclin-Dependent Kinase 2; D004791:Enzyme Inhibitors / Q000737:chemistry*; D006801:Humans; D007477:Ions; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry; D010766:Phosphorylation; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012984:Software; D013237:Stereoisomerism; D013912:Threonine / Q000737:chemistry; D013997:Time Factors; D014443:Tyrosine / Q000737:chemistry; D014965:X-Rays
chemical_list: D004791:Enzyme Inhibitors; D007477:Ions; D010455:Peptides; D010710:Phosphates; D013912:Threonine; D014443:Tyrosine; D000255:Adenosine Triphosphate; D042846:CDC2-CDC28 Kinases; C495894:CDK2 protein, human; D051357:Cyclin-Dependent Kinase 2; D008274:Magnesium