Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations

  • Iveta Bártová
  • Jaroslav Koča
  • Michal Otyepka
Original Paper


The structures of fully active cyclin-dependent kinase-2 (CDK2) complexed with ATP and peptide substrate, CDK2 after the catalytic reaction, and CDK2 inhibited by phosphorylation at Thr14/Tyr15 were studied using molecular dynamics (MD) simulations. The structural details of the CDK2 catalytic site and CDK2 substrate binding box were described. Comparison of MD simulations of inhibited complexes of CDK2 was used to help understand the role of inhibitory phosphorylation at Thr14/Tyr15. Phosphorylation at Thr14/Tyr15 causes ATP misalignment for the phosphate-group transfer, changes in the Mg2+ coordination sphere, and changes in the H-bond network formed by CDK2 catalytic residues (Asp127, Lys129, Asn132). The inhibitory phosphorylation causes the G-loop to shift from the ATP binding site, which leads to opening of the CDK2 substrate binding box, thus probably weakening substrate binding. All these effects explain the decrease in kinase activity observed after inhibitory phosphorylation at Thr14/Tyr15 in the G-loop. Interaction of the peptide substrate, and the phosphorylated peptide product, with CDK2 was also studied and compared. These results broaden hypotheses drawn from our previous MD studies as to why a basic residue (Arg/Lys) is preferred at the P+2 substrate position.


View of the substrate binding site of the fully active cyclin-dependent kinase-2 (CDK2) (pT160-CDK2/cyclin A/ATP). The pThr160 activation site is located in the T-loop (yellow secondary structure). The G-loop, which partly forms the ATP binding site, is shown in blue. The Thr14 and Tyr15 inhibitory phosphorylation sites located in the G-loop are shown in licorice representation


CDK regulation Protein substrate Phosphorylation Cell cycle Molecular dynamics simulations 



We thank the Meta Center ( for computer time. The Czech Ministry of Education is acknowledged for financial support; grants: MSM6198959216, MSM0021622413 and LC06030.


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of Physical Chemistry and Centre for Biomolecular and Complex Molecular SystemsPalacký UniversityOlomoucCzech Republic
  2. 2.National Centre for Biomolecular Research, Faculty of ScienceMasaryk UniversityBrnoCzech Republic

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