R248Q mutation--Beyond p53-DNA binding.

Area of Science:

• Structural biology
• Molecular dynamics simulations
• Protein-DNA interactions

Background:

• The p53 tumor suppressor protein's DNA binding domain (DBD) is crucial for its function.
• Mutations in p53, such as R248Q, are common in cancer and affect DNA binding.
• The precise mechanisms of conformational changes and information propagation from mutation sites in p53 DBD are not fully understood.

Purpose of the Study:

• To investigate the steric and charge effects of R248 mutations on p53-DBD conformation using all-atom molecular dynamics (MD) simulations.
• To understand how mutations at R248 propagate conformational changes throughout the p53 DBD.
• To explore potential strategies for rescuing the function of R248Q mutants.

Main Methods:

• All-atom molecular dynamics (MD) simulations.
• Comparative analysis of wild-type p53 DBD and five R248 mutants (neutral arginine, R248A, R248W, R248Q).
• Analysis of conformational changes, dynamics, hydrogen bonding, and solvent exposure.

Main Results:

• Simulations reproduced experimentally observed global conformational changes for R248Q.
• Both charge and steric effects at R248 influence loop L3 dynamics.
• Mutations alter helix H2 and loop L1 dynamics, preventing major groove DNA interaction.
• R248Q mutation affects the zinc-binding pocket and increases solvent exposure of the S6/S7 turn, suggesting unfolding and aggregation propensity.
• Changes in the zinc-binding pocket of R248Q may explain its dominant-negative effects.

Conclusions:

• Steric and charge effects of R248 mutations significantly impact p53-DBD conformation and dynamics.
• The R248Q mutation induces specific structural alterations that likely contribute to its oncogenic activity.
• Proposed strategies based on simulation findings may help rescue R248Q mutant function.