A MOLECULAR DYNAMICS STUDY OF THE CYCLIN-DEPENDENT KINASE-2 (CDK2) WITH SUBSTRATE PEPTIDE (HHASPRK) INHIBITION BY PHOSPHORYLATION
| Authors | |
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| Year of publication | 2004 |
| Type | Article in Proceedings |
| Conference | Acta Univ. Palacki. Olomouc., Fac. Rer. Nat., Chemica 43S |
| MU Faculty or unit | |
| Citation | |
| Field | Biochemistry |
| Keywords | cell cycle; CDK regulation; phosphorylated tyrosine; threonine |
| Description | The cyclin-dependent kinase-2, CDK2, controls the eukaryotic cell cycle at the G1 S boundary. CDK2 catalyzes the phosphoryl transfer of the adenosine-5-triphosphate (ATP) ?-phosphate to serine or threonine hydroxyl in the protein substrate. The CDK2 activity is regulated by complex mechanism including binding to positive regulatory subunit (Cyclin A or Cyclin E) and phosphorylation at positive regulatory site in the activation segment (T-loop) [1]. The CDK2 activity is inhibited in several ways, for example, by (de)phosphorylation, interaction with various artificial and natural protein inhibitors [2,3], etc. The CDK2 can be also negatively regulated by phosphorylation at Y15 and, to a lesser extent, at T14 residue in the inhibition segment (G-loop) [4]. Mechanism of the CDK2 inhibition by phosphorylation is known from the kinetics experiments but the structural aspects of inhibition remains unclear. The first attempt to explain the mechanism of inhibition by phosphorylation came from molecular dynamics simulations on the fully active CDK2 but without any peptide substrate [5]. This work broadens the previous study describing behavior of the fully active CDK2 (pT160-CDK2/Cyclin A/ATP complex) with bound the substrate peptide (HHASPRK) and CDK2 inhibited by phosphorylation at T14, Y15, and T14/Y15 residues in the G-loop using molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER 6.0 software package [6]. The inhibited complexes of CDK2 were prepared from X-ray structure of the pT160-CDK2/Cyclin A/HHASPRK/ATP complex (1QMZ PDB ID code) by in silico phosphorylation of the T14 and/or Y15 residues. Enzyme dynamics was studied during 15 ns long trajectory for the fully active CDK2 and 10 ns long trajectories for all inhibited CDK2. Differences in conformational behavior of key residues for substrate binding and phosphoryl transfer of fully active vs. inhibited CDK2 will be presented and compared to the previous work [5]. |
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