title: Easy Identification of Residues Involved on Structural Differences Between Nonphosphorylated and Phosphorylated CDK2Cyclin A Complexes Using Two-Dimensional Networks.
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 CDK2cyclin A (npCDK2cycA and pCDK2cycA) 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 CDK2cycA 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 CDK2cycA complex are reinforced when the CDK2 is phosphorylated.
authors.affiliation: Centro 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.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Riadi
authors.affiliation: Centro 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. jcaballero@utalca.cl, jmcr77@yahoo.com.
authors.forename: Julio
authors.initials: J
authors.lastname: Caballero
keywords: CDK2; Cyclin A; Cyclin-dependent kinase; Phosphorylated proteins; Proteinprotein interface; Two-dimensional networks