Evaluation of CDK6 and p16/INK4a-Derived Peptides Interaction

Andrey Kazennov, Andrey Alekseenko, Vladimir Bozhenko, Tatiana Kulinich, Nikolay Shuvalov, Yaroslav Kholodov

Department of Computational Mathematics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
Russian Scientific Center of Roentgenoradiology, Moscow, Russia.

DOI: 10.4236/cmb.2013.33007                

Abstract

 The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for simulation, which was accelerated using NVIDIA GPUs.

Keywords

Cyclin-Dependent Kinases; Molecular Dynamics; Umbrella Sampling; GPU; SASA

Conflicts of Interest

The authors declare no conflicts of interest.

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