Theoretical Prediction System of Stabilization Complex Conformation of DNA Binding Protein and the Binding Affinity for Each DNA Sequence

Abstract

Theoretical methods such as molecular mechanics and molecular dynamics are very useful in understanding the fundamentals of life sciences. We have established a procedure to predict the structure of a complex of p53 with an arbitrary DNA complex, and have made it possible to predict the binding energy of p53 to DNA from the configuration of molecular dynamics simulations of the complex structure. We performed validation studies using FTD, an anti-tumor drug that exerts its pharmacological effect by incorporation into DNA, and confirmed that the binding affinity of the p53-binding BAX sequence to the p53 tetramer was increased by FTD incorporation. This indicates that FTD tends to interact strongly with DNA-binding proteins when incorporated into DNA. On the other hand, the binding affinity of FTD-containing DNA was greatly reduced in p53-binding sequences extracted from FTD-resistant cells compared to that of normal DNA. In other words, it was suggested that randomly substituted thymidine for FTDs in resistant cells may have acquired resistance by entering positions that prevented binding to DNA-binding proteins. We believe that this procedure is a versatile procedure that can take into account the binding energies of not only the p53 protein, but also other DNA-binding proteins and other biomolecules, thus increasing the importance of computational science in the life sciences.