A Molecular Dynamics Study of the Cyclin-Dependent Kinase-2 (CDK2) with Substrate Peptide (HHASPRK), Inhibition of CDK2 by Phosphorylation

I. Bártová1, M. Otyepka2, Z. Kříž1, and J. Koča1


1National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.

2Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř. Svobody 26, 771 46 Olomouc, Czech Republic.


The cyclin-dependent kinase, CDK2, regulates the eukaryotic cell cycle at the G1 – S boundary. CDKs activity is regulated by complex mechanism including binding to positive regulatory subunit and phosphorylation at positive and/or negative regulatory sites [1]. For activation CDK2 requires binding to Cyclin A or Cyclin E. The CDK2 obtains full activity after phosphorylation of the threonine residue (T160) in the activation segment (T-loop) [2]. CDK2 catalyzes the phosphoryl transfer of the adenosine-5´-triphosphate (ATP) g-phosphate to serine or threonine hydroxyl in the protein substrate. The CDKs activity is inhibited in several ways, for example, by (de)phosphorylation, interaction with various natural protein inhibitors [3,4], etc. The CDK2 can be negatively regulated by phosphorylation at Y15 and, to a lesser extent, at T14 in the glycine-rich loop (G-loop) [5].

This work describes behavior of the fully active CDK2 (pT160-CDK2/Cyclin A/ATP complex) with substrate peptide (HHASPRK) and CDK2 inhibited by phosphorylation at T14, Y15, and T14/Y15 residues altogether in the G-loop using molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER software package [6]. Inhibited complexes of CDK2 were prepared from pT160-CDK2/Cyclin A/HHASPRK/ATP (1QMZ PDB ID code) by phosphorylation of the T14 and/or Y15 residues. Enzyme dynamics was studied during 8 ns long trajectory. Differences in conformational behavior of key residues for substrate binding and phosphoryl transfer of fully active vs. inhibited CDK2 will be presented.


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