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Aptamer Affinity to P53 DBD: A Molecular Dynamics Study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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Koulgi S, Achalere A, Sonavane U, Joshi R. Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain. J Chem Inf Model 2022; 62:6449-6461. [PMID: 35614540 DOI: 10.1021/acs.jcim.2c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The transcription factor p53 is one of the most widely studied cancer proteins. Its temperature-sensitive nature suggests reduction in functionality at physiological temperatures. Temperature-induced conformational variations and their impact on its functional ability still remain unexplored. A total of 20.8 μs molecular dynamics simulations of wildtype p53 in the apo and the DNA-bound states have been performed at 300 K and 310 K. Further, Markov State Modeling (MSM) analyses were performed, considering Cα-Cα distances as reaction coordinates. Filtering of these distances based on correlation with the time-independent components (tICs) resulted in 16 and 32 distances for apo and DNA-bound systems, respectively. Individual MSM analyses using these filtered distances were performed for both p53 systems. These Cα-Cα residue pairs belonged to the N-terminal, S6/7 β-turn, loop L2, loop L3, and hydrophobic core residues. At physiological temperatures, apo-p53 exhibits exposure of its hydrophobic core, where the temperature-sensitive hotspot residues were also located. This exposure was the result of the S6/7 β-turn and N-terminal moving apart. In the DNA-bound p53 system, loop L1 attains an open conformation at physiological temperatures, which weakens the DNA binding. It is already known that p53 mutants that lack DNA binding also tend to show similar conformational variations. The S6/7 β-turn along with the already known functionally important loop L2 may pose as regions to be targeted to overcome the loss in binding of temperature-sensitive wildtype p53. Rescue strategies directed toward these temperature-sensitive regions may be useful to recuperate its strong binding at physiological temperatures.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Archana Achalere
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
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Tang Y, Yao Y, Wei G. Unraveling the Allosteric Mechanism of Four Cancer-related Mutations in the Disruption of p53-DNA Interaction. J Phys Chem B 2021; 125:10138-10148. [PMID: 34403252 DOI: 10.1021/acs.jpcb.1c05638] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The p53 protein plays active roles in the physiological regulation of cell cycle as well as in cancer developments. In more than half of human cancers, the protein is inactivated by mutations located primarily in its DNA-binding domain (DBD), and some mutations located in the β-sandwich region of DBD are reported to decrease p53-DNA binding affinities. To understand the long-range correlation between p53 β-sandwich and DNA, and the allosteric mechanism of β-sandwich mutations in the disruption of p53-DNA interactions, we first identify three regions with a strong correlation with DNA based on microsecond molecular dynamics (MD) simulations of wild-type p53-DNA complex and then perform multiple MD simulations on four cancer-related mutants L145Q, P151S, Y220C, and G266R, which are located in these three regions. Our simulations show that these mutations allosterically destabilize the structural stability of the DNA-binding groove in p53 and disrupt the p53-DNA interactions. Network analyses reveal optimal correlation paths through which the mutation-induced allosteric signal passes to DNA, and the disturbance effect of these mutations on the global connectivity and dynamical correlation of the p53-DNA complex. This work paves the way for the in-depth understanding of the mutation-induced loss in p53's DNA-recognition ability and the pathological mechanism of cancer development.
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Affiliation(s)
- Yiming Tang
- Department of Physics, State Key Laboratory of Surface physics, and Key Laboratory for Computational Physical Science (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Yifei Yao
- Department of Physics, State Key Laboratory of Surface physics, and Key Laboratory for Computational Physical Science (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface physics, and Key Laboratory for Computational Physical Science (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
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Bizzarri AR, Cannistraro S. Toward Cancer Diagnostics of the Tumor Suppressor p53 by Surface Enhanced Raman Spectroscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:s20247153. [PMID: 33327383 PMCID: PMC7764831 DOI: 10.3390/s20247153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 05/10/2023]
Abstract
The tumor suppressor p53 protein plays a crucial role in many biological processes. The presence of abnormal concentrations of wild-type p53, or some of its mutants, can be indicative of a pathological cancer state. p53 represents therefore a valuable biomarker for tumor screening approaches and development of suitable biosensors for its detection deserves a high interest in early diagnostics. Here, we revisit our experimental approaches, combining Surface Enhanced Raman Spectroscopy (SERS) and nanotechnological materials, for ultrasensitive detection of wild-type and mutated p53, in the perspective to develop biosensors to be used in clinical diagnostics. The Raman marker is provided by a small molecule (4-ATP) acting as a bridge between gold nanoparticles (NPs) and a protein biomolecule. The Azurin copper protein and specific antibodies of p53 were used as a capture element for p53 (wild-type and its mutants). The developed approaches allowed us to reach a detection level of p53 down to 10-17 M in both buffer and serum. The implementation of the method in a biosensor device, together with some possible developments are discussed.
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Tan YS, Mhoumadi Y, Verma CS. Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting. J Mol Cell Biol 2020; 11:306-316. [PMID: 30726928 PMCID: PMC6487789 DOI: 10.1093/jmcb/mjz009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/14/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
The transcription factor p53 plays pivotal roles in numerous biological processes, including the suppression of tumours. The rich availability of biophysical data aimed at understanding its structure–function relationships since the 1990s has enabled the application of a variety of computational modelling techniques towards the establishment of mechanistic models. Together they have provided deep insights into the structure, mechanics, energetics, and dynamics of p53. In parallel, the observation that mutations in p53 or changes in its associated pathways characterize several human cancers has resulted in a race to develop therapeutic modulators of p53, some of which have entered clinical trials. This review describes how computational modelling has played key roles in understanding structural-dynamic aspects of p53, formulating hypotheses about domains that are beyond current experimental investigations, and the development of therapeutic molecules that target the p53 pathway.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore
| | - Yasmina Mhoumadi
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
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Bizzarri AR, Cannistraro S. Investigation of a Direct Interaction between miR4749 and the Tumor Suppressor p53 by Fluorescence, FRET and Molecular Modeling. Biomolecules 2020; 10:biom10020346. [PMID: 32098369 PMCID: PMC7072324 DOI: 10.3390/biom10020346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/10/2020] [Accepted: 02/20/2020] [Indexed: 01/09/2023] Open
Abstract
The interactions between the DNA binding domain (DBD) of the tumor suppressor p53 and miR4749, characterized by a high sequence similarity with the DNA Response Element (RE) of p53, was investigated by fluorescence spectroscopy combined with computational modeling and docking. Fluorescence quenching experiments witnessed the formation of a specific complex between DBD and miR4749 with an affinity of about 105 M. Förster Resonance Energy Transfer (FRET) allowed us to measure a distance of 3.9 ± 0.3 nm, between the lone tryptophan of DBD and an acceptor dye suitably bound to miR4749. Such information, combined with a computational modeling approach, allowed us to predict possible structures for the DBD-miR4749 complex. A successive docking refinement, complemented with binding free energy calculations, led us to single out a best model for the DBD-miR4749 complex. We found that the interaction of miR4749 involves the DBD L3 loop and the H1 helix, close to the Zn-finger motif; with this suggesting that miR4749 could directly inhibit the p53 interaction with DNA. These results might inspire new therapeutic strategies finalized to restore the p53 functional activity.
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Olotu FA, Soliman MES. Dynamic perspectives into the mechanisms of mutation-induced p53-DNA binding loss and inactivation using active perturbation theory: Structural and molecular insights toward the design of potent reactivators in cancer therapy. J Cell Biochem 2018; 120:951-966. [PMID: 30160791 DOI: 10.1002/jcb.27458] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/19/2018] [Indexed: 01/08/2023]
Abstract
The DNA-binding ability of p53 represents the crux of its tumor suppressive activities, which involves transcriptional activation of target genes responsible for apoptosis and cell-cycle arrest. Mutational occurrences within or in close proximity to the DNA-binding surface of p53 have accounted for the loss of direct DNA-binding ability and inactivation implicated in many cases of cancer. Moreover, the design of therapeutic compounds that can restore DNA-binding ability in p53 mutants has been identified as a way forward in curtailing their oncogenic activities. However, there is still the need for more insights into evaluate the perturbations that occur at the DNA-binding interface of mp53 relative to DNA-binding loss, inactivation, and design of potent reactivators, hence the purpose of this study. Therefore, we evaluated p53-structural (R175H) and contact (R273C) mutational effects using tunnel perturbation analysis and other computational tools. We identified significant perturbations in the active tunnels of p53, which resulted in altered geometry and loss, unlike in the wild-type p53. This corroborated with structural, DNA-binding, and interaction network analysis, which showed that loss of flexibility, repulsion of DNA-interactive residues, and instability occurred at the binding interface of both mutants. Also, these mutations altered bonding interactions and network topology at the DNA-binding interface, resulting in the reduction of p53-DNA binding proximity and affinity. Therefore, these findings would aid the structure-based design of novel chemical entities capable of restoring p53-DNA binding and activation.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, Department of Pharmaceutical Chemistry, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, Department of Pharmaceutical Chemistry, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
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Jiang Z, Xu W, Dan G, Liu Y, Xiong J. P53 and Murine Double Mimute 2 (MDM2) Expression Changes and Significance in Different Types of Endometrial Lesions. Med Sci Monit 2016; 22:4786-4793. [PMID: 27924072 PMCID: PMC5158131 DOI: 10.12659/msm.898616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Endometrial lesions are common in obstetrics and gynecology, including endometrial polyps, uterine adenomyosis, and malignant endometrial adenocarcinoma. Endometrial lesions seriously affect women’s health, fertility, quality of life, and life safety. As a pro-apoptosis gene, p53 is considered to be closely related with human tumors. Murine double mimute 2 (MDM2) is an oncogene that can promote tumor occurrence and development. P53 and MDM2 expression and significance in different types of endometrial lesions have not been fully elucidated. Material/Methods Normal endometrium, endometrial polyps, uterine adenomyosis, and endometrial adenocarcinoma tissue samples were collected. Real-time PCR was used to detect p53 and MDM2 mRNA expression. Immunohistochemical staining and Western blot analysis were applied to test p53 and MDM2 protein expression. Their correlation with clinical staging of endometrial adenocarcinoma was analyzed. Results P53 and MDM2 mRNA and protein expression were significantly elevated in the endometrial polyps group and the endometrial adenocarcinoma group compared with the normal control group (P<0.05). Their levels increased more obviously in endometrial adenocarcinoma compared with endometrial polyps (P<0.05). P53 and MDM2 mRNA and protein expression were slightly enhanced in uterine adenomyosis compared with normal controls, but this difference lacked statistical significance (P>0.05). P53 and MDM2 mRNA and protein level showed a positive correlation. Significantly higher expression of p53 or MDM2 was observed in patients with stage III compared to those in patients with stage II. Higher expression was also observed in patients with stage II than in patients with stage I. Conclusions P53 and MDM2 mRNA and protein were elevated in endometrial polyps and endometrial adenocarcinoma and their expressions were correlated with clinical staging of endometrial adenocarcinoma. They can promote cancer occurrence and development, and can be treated to assist diagnosis and provide a reference for treatment.
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Affiliation(s)
- Zhongyong Jiang
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Wanqing Xu
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Gang Dan
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Yuan Liu
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Jie Xiong
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
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