Time-Resolved Fluorescence and Essential Dynamics Study on the Structural Heterogeneity of p53DBD Bound to the Anticancer p28 Peptide

Time-resolved fluorescence emission was combined with molecular dynamics (MD) simulations to investigate the DNA-binding domain (DBD) of the tumor suppressor p53 alone and its complex with the anticancer peptide p28 (DBD/p28). The fluorescence emission decay of the lone Trp residue, from both DBD and DBD/p28, was well-described by a stretched exponential function. Such a behavior was ascribed to heterogeneity in the Trp relaxation behavior, likely due to the coexistence of different conformational states. The increase of the stretching parameter, on passing from DBD to DBD/p28, indicates a reduced heterogeneity in the Trp146 environment for DBD/p28. Moreover, the effects of p28 on the global dynamics of DBD were analyzed by the essential dynamics method on 30 ns long MD trajectories of both DBD and DBD/p28. We found the establishment of wide-amplitude anharmonic modes throughout the DBD molecule, with a particularly high amplitude being detected in the DNA-binding region. These modes are significantly reduced when DBD is bound to p28, consistently with a structure stabilization. In summary, the results indicate that p28 binding has a strong effect on both the local and global heterogeneity of DBD, thus providing some hints to the understanding of its anticancer activity.