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Updated: Jun 13, 2025
Yeast As a Chassis for Developing Functional Assays to Study Human P53
Published on: August 4, 2019
Structural dynamics of the wild-type p53 DNA-binding domain and hotspot mutants reveal oncogenic conformational
Ziqian Zhao1, Gang Wang1, Xiaoxiao Wu1
1Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai, 200438, China. qianzhenyu@sus.edu.cn.
Abstract:
The tumor suppressor protein p53, widely known for the potency and diversity of its functions, acts as a critical barrier to tumorigenesis. Mutations in p53, particularly within its DNA-binding domain (DBD), compromise its tumor suppressing function in over 40% of human tumors. Diverse p53 mutants adopt three major types of oncogenic effects, namely the loss-of-function effect, dominant-negative effect and gain-of-function effect. However, the conformational mechanisms by which hotspot mutations (e.g., R175H, R273H/C) drive p53 dysfunction remain elusive. Here, we performed microsecond-level molecular dynamics simulations to dissect the structural dynamics of wild-type p53DBD and three oncogenic mutants. In wild-type p53DBD, multi-state conformational switching of the L1 loop was governed by hydrophobic interactions (A119/V122-P278) and an intra-loop hydrogen bond network. Notably, a previously unidentified β-hairpin conformation within the L1 loop was discovered, suggesting a latent regulatory motif. Mutations at R273 disrupted the H2 α-helix integrity, inducing helix-to-coil transitions that destabilized the DNA-binding interface. In contrast, R175H mutation triggered allosteric flexibility in both L2 and L3 loops, distorting the DNA contact surface through synergistic loop rearrangements. Interaction network analysis further revealed that these mutations remodeled non-local residue couplings, with R273H/C primarily destabilizing local interactions and R175H perturbing long-range communication with the LSH motif. Our findings provide structural insights into wild-type p53's complex activities and link mutation-specific conformational shifts to p53's loss/gain-of-function phenotypes, offering new avenues for restoring p53 activity in cancers.
Insights
Mutations in the tumor suppressor p53 (protein 53) DNA-binding domain disrupt its function. Molecular dynamics reveal how specific mutations alter p53 protein structure, impacting cancer development and offering therapeutic targets.
Area of Science:
- Structural Biology
- Molecular Oncology
- Protein Dynamics
Background:
- The tumor suppressor protein p53 is crucial for preventing cancer.
- Mutations in p53's DNA-binding domain (DBD) are common in human tumors, leading to loss-of-function, dominant-negative, or gain-of-function effects.
- The precise conformational mechanisms driving p53 dysfunction due to hotspot mutations remain unclear.
Purpose of the Study:
- To investigate the structural dynamics of wild-type p53DBD and oncogenic mutants using molecular dynamics simulations.
- To elucidate the conformational mechanisms by which hotspot mutations (R175H, R273H/C) lead to p53 dysfunction.
- To link mutation-specific conformational changes to p53's altered functional phenotypes in cancer.
Main Methods:
- Microsecond-level molecular dynamics simulations of wild-type p53DBD and three oncogenic mutants (R175H, R273H/C).
- Analysis of structural dynamics, including loop conformations and helix integrity.
- Interaction network analysis to assess residue couplings and communication pathways.
Main Results:
- Wild-type p53DBD exhibits multi-state conformational switching in the L1 loop, involving hydrophobic interactions and hydrogen bonds, and reveals a novel beta-hairpin conformation.
- R273 mutations destabilize the H2 alpha-helix, leading to helix-to-coil transitions and disruption of the DNA-binding interface.
- R175H mutation induces allosteric flexibility in L2 and L3 loops, altering the DNA contact surface via loop rearrangements and perturbing long-range interactions.
Conclusions:
- Specific p53 mutations induce distinct conformational changes that underlie their oncogenic effects.
- R273 mutations primarily affect local DNA-binding interactions, while R175H impacts long-range communication within the protein.
- These findings provide structural insights into p53 dysfunction and suggest potential strategies for restoring its tumor-suppressive activity in cancer.
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