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

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

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


In human cell, cell cycle events are governed by several CDKs [1]. Cell-cycle dependent oscillations in CDK activity are induced by complex mechanisms that include binding to positive regulatory subunits and phosphorylation at positive and negative regulatory sites. For activation CDKs require binding to cyclins. CDKs obtain full activity at binding with adenosine triphosphate (ATP) by phosphorylation of a threonine residue in the CDK (Thr 160 in human CDK2) [2].  Activities of these enzymes are inhibited in several ways, for examples, (de)phosphorylation, interaction with various natural protein inhibitors [3]. CDK2 can be negatively regulated by phosphorylation on Tyr15 and to a lesser extent on Thr14 [4].

This work describes behavior of monomeric CDK2/ATP, CDK2/cyclinA/ATP complex, and pT160-CDK2/cyclinA/ATP complex (CDK2/cyclinA/ATP complex phosphorylated on Thr160 residue of CDK2) using the molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER software package [5]. The next MD study was performed on pY15,pT160-CDK2/cyclinA/ATP system. The system was prepared from pT160-CDK2/cyclinA/ATP by phosphorylation of the Tyr15 residue of CDK2. Results of conformational behavior of ATP and key residues for activation in these complexes will be presented. Activation of CDK2 involves various conformational changes, including the reorientation of the phosphate part of ATP and key residues involved in ATP binding site. Transformation of conformation of ATP phosphate in the pT160-CDK2/cyclinA complex is important to form substrate binding site, and is thought to be critical for catalysis.



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3. M. Otyepka, Z. Kříž, J. Koča, J. Biol. Struct. Dyn., 20 (2002) 141-154.

4. H. L. De Bondt, J. Rosenblatt, J. Jancarik, Nature, 363 (1993) 595-602.

5. D. A. Case et al., AMBER ver. 6.0, University of California, San Francisco, 1999.