Aptamer affinity to P53 DBD: A molecular dynamics study

Abstract

Protein P53, as a tumor suppressor plays an important role in many biological processes. Its DNA binding domain (DBD) contains a Zn ion which has an important role in aggregation and binding. The presence of abnormal wild-type P53 and its mutations in high concentration can be indicative of a pathological cancer state. Because of the intrinsic disordering in its structure, finding structures to overcome disordering and to interact with this protein and its mutations is one of the challenges of scientists for using P53 as a biomarker to early diagnosis of cancers. Here, we used the molecular dynamics simulation to study the interaction of wild-type P53 DBD and its mutations with an aptamer to find one solution for the mentioned challenge. The analyses of RMSD, Electrostatic energy, Number of hydrogen binding are used to discuss the quality of interactions. Aptamer- protein binding free energy is calculated with free energy perturbation method and value of ΔG= -181 Kcal.mol−1 for the interaction of aptamer- R249S, allow us to introduce the aptamer as a material to capture and recognize of R249S.