Simulation of Different Truncated p16^INK4a Forms and In Silico Study of Interaction with Cdk4

Abstract

Protein-protein interactions studies can greatly increase the amount of structural and functional information pertaining to biologically active molecules and processes. The information obtained from such studies can lead to design and application of new modification in order to obtain a desired bioactivity. Many application packages and servers performing docking, such as HEX, DOT, AUTODOCK, and ZDOCK are now available for predicting the lowest free energy state of a protein complex. In this study, we have focused on cyclin-dependent kinase 4 (Cdk4), a key molecule in the regulation of cell cycle progression at the G1-S phase restriction point and p16INK4a, a tumor suppressor which inhibits Cdk4 activity. Truncated structures were created to find the more critical regions of p16 for interaction. The tertiary structures were determined by ProSAL, GENO3D Web Server. We evaluated their interactions with Cdk4 using two docking systems, HEX 4.5 and DOT 1. Calculations were performed on a high-speed computer. Minimizations and visualizations were carried out by PdbViewer 3.7. Considering shape and shape/electrostatic total energy, structures containing ANK II, III and IV motifs that lack the N-terminal region of the full length p16 molecule showed the best fit complexes among the p16 truncated forms. The free energies were compatible with that of p16 full length original form, the full length. It seems that the N-terminal of the molecule is not crucial for the interaction since the truncated structure containing only this region did not show a good total energy.

C‐terminal domain of p16INK4a is adequate in inducing cell cycle arrest, growth inhibition and CDK4/6 interaction similar to the full length protein in HT‐1080 fibrosarcoma cells

“…According to the in silico interaction studies of p16 truncated forms and CDK4 [Fahham et al, 2009], four truncated forms (including the ATG and the stop codon) were constructed by PCR‐based amplification with four pairs of primers (described in Table I) using p16 full length. Figure 1 shows the schematic presentation of the ankyrin repeats and the loops included in each construct.…”

“…In an attempt to identify the minimum stable and functionally active region of p16, the preliminary investigation was performed in silico in our team [Fahham et al, 2009]. In this regard, the protein was sequentially divided into smaller building blocks and eight truncated structures were created by homology modeling pertaining to the most critical regions of p16 for interaction and inhibition of CDK4 according to the previous investigations [Yang et al, 1995; Tevelev et al, 1996; Yang et al, 1996; Yarbrough et al, 1999].…”

“…In this study, to evaluate the functional region of p16, we have generated different truncated structures (including different ankyrin motifs and loops) based on our previous in silico screening of the eight truncated forms regarding their interaction with CDK4 [Fahham et al, 2009]. The effect of the generated truncated structures on growth inhibition and cell cycle were then evaluated in HT‐1080, p16‐deficient and wild type pRb fibrosarcoma cell line [Li et al, 1995; Whitaker et al, 1995; Roninson, 2003].…”

In silico study of fragile histidine triad interaction domains with MDM2 and p53

“…[26] Hex apparently accelerates the procedure compared with the typical FFT docking algorithms. [27]…”

Informatics of Drug Synergism in Naturally Occurring Anticancer Agents

“…An example of this type of study is our recent paper, in which the cyclin-dependent kinase 4 (Cdk4), a key molecule in the regulation of cell cycle progression at the G1-S phase restriction point and p16INK4a, a tumor suppressor that inhibits Cdk4 activity were studied [21]. Based on the docking results, it was found that the N-terminal of p16INK4a is not crucial for the interaction since the truncated structure containing only this region did not show a good total energy.…”