In silico investigation on the effect of p27 phosphorylation in regulating Cdk2/CyclinA complex

Abstract

p27 is an intrinsically disordered protein which belongs to the Cip/Kip family. It inhibits the cyclin-dependent kinase (Cdk)/cyclin complexes which results in the regulation of cell cycle, during the G1 to S phase transition. Phosphorylation of p27 at specific sites such as Y74, Y88, T187, and P188 may alter its function. In vitro studies showed that phosphorylation of p27 at residues Y74 and Y88 resulted in enhancement of Cdk2 activity. However, the exact molecular details are unknown. This study uses molecular dynamics (MD) simulation and trajectory analyses to study the effect of phosphorylation of p27 at the Y74 and Y88 residues. We carried out MD simulation for 50 ns using AMBER20, and performed root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bonding analyses. We studied protein-protein interaction using PDBsum server. It has been found that there is an increase in binding affinity of phosphorylated p27 for Cdk2, but it weakens the Cdk2/cyclin A association. We observed shifts in RMSD, RMSF, and hydrogen bonding patterns which shows that there are conformational changes, thus providing insights into the increase in Cdk2 activity and its regulatory role in cell cycle.