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Updated: Mar 16, 2026

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay
Published on: May 3, 2018
Easy Identification of Residues Involved on Structural Differences Between Nonphosphorylated and Phosphorylated
Gonzalo Riadi1, Julio Caballero2
1Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile tel: +56 71 2 418 850; fax: +56 71 2 201 662.
Abstract:
The structures of proteins in Protein Data Bank (PDB) contain a lot of information that can be revealed through the use of tools to facilitate their organization and analysis. The increase in available structural data of nonphosphorylated and phosphorylated CDK2cyclin A (npCDK2cycA and pCDK2cycA) complexes has enabled a more realistic description of the fine structural details of the interface residues of these proteins. This work reports the application of two-dimensional network representations (TDNRs) to the structures deposited in PDB to distinguish the differences in the surface between both complexes due to phosphorylation. As a result, a detailed map of the hydrogen bonds (HBs) and hydrophobic interactions between the T-loop residues of CDK2 and the residues of cycA that are different among nonphosphorylated and phosphorylated complexes were described. In addition, we found some interesting subtle differences in the CDK2cycA interface between nonphosphorylated and phosphorylated complexes due to residues that are not located at the T-loop of CDK2. We noted that some HB interactions in CDK2cycA complex are reinforced when the CDK2 is phosphorylated.
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