1
|
Osterburg C, Ferniani M, Antonini D, Frombach AS, D'Auria L, Osterburg S, Lotz R, Löhr F, Kehrloesser S, Zhou H, Missero C, Dötsch V. Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree. Cell Death Dis 2023; 14:274. [PMID: 37072394 PMCID: PMC10113246 DOI: 10.1038/s41419-023-05796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023]
Abstract
The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. Mutations in the DNA binding domain (DBD) of p53 have been studied in great detail, enabling a general mechanism-based classification. In this study we provide a detailed investigation of all currently known mutations in the p63 DBD, which are associated with developmental syndromes, by measuring their impact on transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes. Here we propose a classification of the p63 DBD mutations based on the four different mechanisms of DNA binding impairment which we identified: direct DNA contact, zinc finger region, H2 region, and dimer interface mutations. The data also demonstrate that, in contrast to p53 cancer mutations, no p63 mutation induces global unfolding and subsequent aggregation of the domain. The dimer interface mutations that affect the DNA binding affinity by disturbing the interaction between the individual DBDs retain partial DNA binding capacity which correlates with a milder patient phenotype.
Collapse
Affiliation(s)
- Christian Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Marco Ferniani
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Dario Antonini
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Ann-Sophie Frombach
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Ludovica D'Auria
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Susanne Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Rebecca Lotz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Sebastian Kehrloesser
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Huiqing Zhou
- Departments of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
- Departments of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy.
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany.
| |
Collapse
|
2
|
Lima IDM, Pedrote MM, Marques MA, Sousa GDSD, Silva JL, de Oliveira GAP, Cino EA. Water Leakage Pathway Leads to Internal Hydration of the p53 Core Domain. Biochemistry 2023; 62:35-43. [PMID: 36535020 DOI: 10.1021/acs.biochem.2c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The gene encoding the p53 tumor suppressor protein is the most frequently mutated oncogene in cancer patients; yet, generalized strategies for rescuing the function of different p53 mutants remain elusive. This work investigates factors that may contribute to the low inherent stability of the wild-type p53 core domain (p53C) and structurally compromised Y220C mutant. Pressure-induced unfolding of p53C was compared to p63C, the p53 family member with the highest stability, the engineered superstable p53C hexamutant (p53C HM), and lower stability p53C Y220C cancer-associated mutant. The following pressure unfolding values (P50% bar) were obtained: p53C 3346, p53C Y220C 2217, p53C HM 3943, and p63C 4326. Molecular dynamics (MD) simulations revealed that p53C Y220C was most prone to water infiltration, followed by p53C, whereas the interiors of p53C HM and p63C remained comparably dry. A strong correlation (r2 = 0.92) between P50% and extent of interior hydration was observed. The pathways of individual water molecule entry and exit were mapped and analyzed, revealing a common route preserved across the p53 family involving a previously reported pocket, along with a novel surface cleft, both of which appear to be targetable by small molecules. Potential determinants of propensity to water incursion were assessed, including backbone hydrogen bond protection and combined sequence and structure similarity. Collectively, our results indicate that p53C has an intrinsic susceptibility to water leakage, which is exacerbated in a structural class mutant, suggesting that there may be a common avenue for rescuing p53 function.
Collapse
Affiliation(s)
- Igor D M Lima
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte31270-901, Brazil
| | - Murilo M Pedrote
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Centrum of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro21941-901, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Centrum of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro21941-901, Brazil
| | - Gileno Dos S de Sousa
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Centrum of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro21941-901, Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Centrum of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro21941-901, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Centrum of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro21941-901, Brazil
| | - Elio A Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte31270-901, Brazil
| |
Collapse
|
3
|
Bizzarri AR. Conformational Heterogeneity and Frustration of the Tumor Suppressor p53 as Tuned by Punctual Mutations. Int J Mol Sci 2022; 23:12636. [PMID: 36293489 PMCID: PMC9604312 DOI: 10.3390/ijms232012636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 12/02/2022] Open
Abstract
The conformational heterogeneity of the p53 tumor suppressor, the wild-type (p53wt) and mutated forms, was investigated by a computational approach, including the modeling and all atoms of the molecular dynamics (MD) simulations. Four different punctual mutations (p53R175H, p53R248Q, p53R273H, and p53R282W) which are known to affect the DNA binding and belong to the most frequent hot-spot mutations in human cancers, were taken into consideration. The MD trajectories of the wild-type and mutated p53 forms were analyzed by essential dynamics to extract the relevant collective motions and by the frustration method to evaluate the degeneracy of the energy landscape. We found that p53 is characterized by wide collective motions and its energy landscape exhibits a rather high frustration level, especially in the regions involved in the binding to physiological ligands. Punctual mutations give rise to a modulation of both the collective motions and the frustration of p53, with different effects depending on the mutation. The regions of p53wt and of the mutated forms characterized by a high frustration level are also largely involved in the collective motions. Such a correlation is discussed also in connection with the intrinsic disordered character of p53 and with its central functional role.
Collapse
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| |
Collapse
|
4
|
Osterburg C, Dötsch V. Structural diversity of p63 and p73 isoforms. Cell Death Differ 2022; 29:921-937. [PMID: 35314772 PMCID: PMC9091270 DOI: 10.1038/s41418-022-00975-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 01/25/2023] Open
Abstract
Abstract
The p53 protein family is the most studied protein family of all. Sequence analysis and structure determination have revealed a high similarity of crucial domains between p53, p63 and p73. Functional studies, however, have shown a wide variety of different tasks in tumor suppression, quality control and development. Here we review the structure and organization of the individual domains of p63 and p73, the interaction of these domains in the context of full-length proteins and discuss the evolutionary origin of this protein family.
Facts
Distinct physiological roles/functions are performed by specific isoforms.
The non-divided transactivation domain of p63 has a constitutively high activity while the transactivation domains of p53/p73 are divided into two subdomains that are regulated by phosphorylation.
Mdm2 binds to all three family members but ubiquitinates only p53.
TAp63α forms an autoinhibited dimeric state while all other vertebrate p53 family isoforms are constitutively tetrameric.
The oligomerization domain of p63 and p73 contain an additional helix that is necessary for stabilizing the tetrameric states. During evolution this helix got lost independently in different phylogenetic branches, while the DNA binding domain became destabilized and the transactivation domain split into two subdomains.
Open questions
Is the autoinhibitory mechanism of mammalian TAp63α conserved in p53 proteins of invertebrates that have the same function of genomic quality control in germ cells?
What is the physiological function of the p63/p73 SAM domains?
Do the short isoforms of p63 and p73 have physiological functions?
What are the roles of the N-terminal elongated TAp63 isoforms, TA* and GTA?
Collapse
|
5
|
Hidden electrostatic energy contributions define dynamic allosteric communications within p53 during molecular recognition. Biophys J 2021; 120:4512-4524. [PMID: 34478701 DOI: 10.1016/j.bpj.2021.08.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/03/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022] Open
Abstract
Molecular recognition is fundamental to transcription regulation. As a transcription factor, the tumor suppressor p53 has to recognize either specific DNA sequences or repressor protein partners. However, the molecular mechanism underlying the p53 conformational switch from the DNA-bound to repressor-bound states is not fully characterized. The highly charged nature of these interacting molecules prompted us to explore the nonbonded energy contributions behind molecular recognition of either a DNA or the repressor protein iASPP by p53 DNA binding domain (p53DBD), using molecular dynamics simulation followed by rigorous analyses of energy terms. Our results illuminate the allosteric pathway by which iASPP binding to p53 diminishes binding affinity between p53 and DNA. Even though the p53DBD uses a common framework of residues for recognizing both DNA and iASPP, a comparison of the electrostatics in the two p53DBD complexes revealed significant differences in residue-wise contributions to the electrostatic energy. We found that an electrostatic allosteric communication path exists in the presence of both substrates. It consists of evolutionarily conserved residues, from residue K120 of the binding loop L1 to a distal residue R213 of p53DBD. K120 is near the DNA in the p53DBD-DNA complex, whereas iASPP binding moves it away from its DNA binding position in the p53DBD-iASPP complex. The "energy hubs" (the residues show a higher degree of connectivity with other residues in the electrostatic networks) determined from the electrostatic network analysis established that this conformational change in K120 completely rewires the electrostatic network from K120 to R213, thereby impeding DNA binding. Furthermore, we found shifting populations of hydrogen bonds and salt bridges reduce pairwise electrostatic energies within p53DBD in its DNA-bound state.
Collapse
|
6
|
Bizzarri AR, Cannistraro S. Temperature Modulation of the DBDp53 Structure as Monitored by Static and Time-Resolved Fluorescence Combined with Molecular Dynamics Simulations. J Phys Chem B 2021; 125:10166-10173. [PMID: 34493041 DOI: 10.1021/acs.jpcb.1c05909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Trp146 of the p53 DNA-binding domain (DBD) was investigated by static and time-resolved fluorescence combined with molecular dynamics (MD) simulations at different temperatures (25, 30, 37, and 45 °C). Static emission spectra exhibit an intensity maximum at 30 °C without any substantial peak shift, while the time-resolved fluorescence displays a peculiar stretched exponential decay, indicative of a structural disorder, at all of the investigated temperatures. The stretched exponential parameter was found to increase at 37 °C. An analysis of the MD simulation trajectories evidenced the occurrence of jumps in the temporal evolution of the distances between Trp146 and residues Arg110, Asp228, Cys229, and Gln144, which are mainly responsible for Trp146 fluorescence quenching. The times that these quenchers spend close to or far from Trp146 can provide an explanation for the static fluorescence behavior. Further essential dynamics analysis of the MD trajectories indicates a significant restriction of protein global motions above 37 °C. These results are consistent with a decrease in the structural heterogeneity of DBD as the temperature increases. The results are also discussed in view of understanding how temperature can modulate the p53 capability to binding partners, including DNA.
Collapse
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, Viterbo 01100, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, Viterbo 01100, Italy
| |
Collapse
|
7
|
Gangele K, Gulati K, Joshi N, Kumar D, Poluri KM. Molecular insights into the differential structure-dynamics-stability features of interleukin-8 orthologs: Implications to functional specificity. Int J Biol Macromol 2020; 164:3221-3234. [PMID: 32853623 DOI: 10.1016/j.ijbiomac.2020.08.176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
Chemokines are a sub-group of chemotactic cytokines that regulate the leukocyte migration by binding to G-protein coupled receptors (GPCRs) and cell surface glycosaminoglycans (GAGs). Interleukin-8 (CXCL8/IL8) is one of the most essential CXC chemokine that has been reported to be involved in various pathophysiological conditions. Structure-function relationships of human IL8 have been studied extensively. However, no such detailed information is available on IL8 orthologs, although they exhibit significant functional divergence. In order to unravel the differential structure-dynamics-stability-function relationship of IL8 orthologs, comparative molecular analysis was performed on canine (laurasians) and human (primates) IL8 proteins using in-silico molecular evolutionary analysis and solution NMR spectroscopy methods. The residue level NMR studies suggested that, although the overall structural architecture of canine IL8 is similar to that of human IL8, systematic differences were observed in their backbone dynamics and low-energy excited states due to amino acid substitutions. Further, these substitutions also resulted in attenuation of stability and heparin binding affinity in the canine IL8 as compared to its human counterpart. Indeed, structural and sequence analysis evidenced for specificity of molecular interactions with cognate receptor (CXCR1) and glycosaminoglycan (heparin), thus providing evidence for a noticeable functional specificity and divergence between the two IL8 orthologs.
Collapse
Affiliation(s)
- Krishnakant Gangele
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nidhi Joshi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| |
Collapse
|
8
|
Abstract
BACKGROUND Beast cancer is the most common women cancer worldwide, while two third of them are ER alpha positive breast cancer. Among the ER alpha positive breast cancer, about 80% are P53 wild type, indicating the potential tumor suppression role in ER alpha positive breast cancer. Since P53 is an important safeguard to inhibit cell malignant transformation, reactivating P53 signaling could a plausible approach to treat breast cancer. METHODS TRIM3 protein levels were measured by western blot, while the P53 classical target genes were measured by real-time PCR. WST1 assay were used to measure cell proliferation, while cleaved caspase-3 was used to detect cell apoptosis. Protein stability and ubiquitin assay were used to detect the P53 protein ubiquitin and stability. The immuno-precipitation assays were used to detect the protein interactions. Immuno-staining was used to detect the protein localization of P53 and TRIM3, while the ubiquitin-based immuno-precipitation assays were used to detect the specific ubiquitination manner of P53. RESULTS In our study, we identified TRIM3 as an endogenous inhibitor for P53 signaling. TRIM3 depletion inhibited breast cancer cell proliferation and promoted apoptosis. In addition, TRIM3 depletion increased P53 protein level in breast cancer cell. Further investigation showed that TRIM3 could associate with P53 and promote P53 K48-linked ubiquitination and degradation. CONCLUSION Our study identified a novel post-translational modification mechanism between TRIM3 and P53. TRIM3 depletion or blockage could be a promising strategy to rescue P53 signaling and inhibit breast cancer progression.
Collapse
|
9
|
Bizzarri AR, Cannistraro S. Time-Resolved Fluorescence and Essential Dynamics Study on the Structural Heterogeneity of p53DBD Bound to the Anticancer p28 Peptide. J Phys Chem B 2020; 124:9820-9828. [PMID: 33103427 DOI: 10.1021/acs.jpcb.0c06778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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.
Collapse
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Pradhan MR, Siau JW, Kannan S, Nguyen MN, Ouaray Z, Kwoh CK, Lane DP, Ghadessy F, Verma CS. Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket. Nucleic Acids Res 2019; 47:1637-1652. [PMID: 30649466 PMCID: PMC6393305 DOI: 10.1093/nar/gky1314] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 11/25/2018] [Accepted: 01/09/2019] [Indexed: 01/01/2023] Open
Abstract
The DNA binding domain (DBD) of the tumor suppressor p53 is the site of several oncogenic mutations. A subset of these mutations lowers the unfolding temperature of the DBD. Unfolding leads to the exposure of a hydrophobic β-strand and nucleates aggregation which results in pathologies through loss of function and dominant negative/gain of function effects. Inspired by the hypothesis that structural changes that are associated with events initiating unfolding in DBD are likely to present opportunities for inhibition, we investigate the dynamics of the wild type (WT) and some aggregating mutants through extensive all atom explicit solvent MD simulations. Simulations reveal differential conformational sampling between the WT and the mutants of a turn region (S6-S7) that is contiguous to a known aggregation-prone region (APR). The conformational properties of the S6-S7 turn appear to be modulated by a network of interacting residues. We speculate that changes that take place in this network as a result of the mutational stress result in the events that destabilize the DBD and initiate unfolding. These perturbations also result in the emergence of a novel pocket that appears to have druggable characteristics. FDA approved drugs are computationally screened against this pocket.
Collapse
Affiliation(s)
- Mohan R Pradhan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Jia Wei Siau
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Minh N Nguyen
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Zohra Ouaray
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Chemistry, University of Southampton, SO17 1BJ, United Kingdom
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Farid Ghadessy
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| |
Collapse
|
12
|
Signorelli S, Cannistraro S, Bizzarri AR. Raman Evidence of p53-DBD Disorder Decrease upon Interaction with the Anticancer Protein Azurin. Int J Mol Sci 2019; 20:ijms20123078. [PMID: 31238511 PMCID: PMC6627904 DOI: 10.3390/ijms20123078] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 12/30/2022] Open
Abstract
Raman spectroscopy, which is a suitable tool to elucidate the structural properties of intrinsically disordered proteins, was applied to investigate the changes in both the structure and the conformational heterogeneity of the DNA-binding domain (DBD) belonging to the intrinsically disordered protein p53 upon its binding to Azurin, an electron-transfer anticancer protein from Pseudomonas aeruginosa. The Raman spectra of the DBD and Azurin, isolated in solution or forming a complex, were analyzed by a combined analysis based on peak inspection, band convolution, and principal component analysis (PCA). In particular, our attention was focused on the Raman peaks of Tyrosine and Tryptophan residues, which are diagnostic markers of protein side chain environment, and on the Amide I band, of which the deconvolution allows us to extract information about α-helix, β-sheet, and random coil contents. The results show an increase of the secondary structure content of DBD concomitantly with a decrease of its conformational heterogeneity upon its binding to Azurin. These findings suggest an Azurin-induced conformational change of DBD structure with possible implications for p53 functionality.
Collapse
Affiliation(s)
- Sara Signorelli
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia, 01100 Viterbo, Italy.
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia, 01100 Viterbo, Italy.
| | - Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia, 01100 Viterbo, Italy.
| |
Collapse
|
13
|
Chitrala KN, Nagarkatti M, Nagarkatti P, Yeguvapalli S. Analysis of the TP53 Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach. Int J Mol Sci 2019; 20:ijms20122962. [PMID: 31216622 PMCID: PMC6627686 DOI: 10.3390/ijms20122962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk factors, estrogen levels play a crucial role. Among the estrogen receptors, estrogen receptor alpha (ERα) is known to interact with tumor suppressor protein p53 directly thereby repressing its function. Previously, we have studied the impact of deleterious breast cancer-associated non-synonymous single nucleotide polymorphisms (nsnps) rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 gene on the p53 DNA-binding core domain. In the present study, we aimed to analyze the impact of these mutations on p53–ERα interaction. To this end, we, have modelled the full-length structure of human p53 and validated its quality using PROCHECK and subjected it to energy minimization using NOMAD-Ref web server. Three-dimensional structure of ERα activation function-2 (AF-2) domain was downloaded from the protein data bank. Interactions between the modelled native and mutant (R110P, P278A, P151T) p53 with ERα was studied using ZDOCK. Machine learning predictions on the interactions were performed using Weka software. Results from the protein–protein docking showed that the atoms, residues and solvent accessibility surface area (SASA) at the interface was increased in both p53 and ERα for R110P mutation compared to the native complexes indicating that the mutation R110P has more impact on the p53–ERα interaction compared to the other two mutants. Mutations P151T and P278A, on the other hand, showed a large deviation from the native p53-ERα complex in atoms and residues at the surface. Further, results from artificial neural network analysis showed that these structural features are important for predicting the impact of these three mutations on p53–ERα interaction. Overall, these three mutations showed a large deviation in total SASA in both p53 and ERα. In conclusion, results from our study will be crucial in making the decisions for hormone-based therapies against breast cancer.
Collapse
Affiliation(s)
- Kumaraswamy Naidu Chitrala
- Department of Zoology, Sri Venkateswara University, Tirupati 517502, India.
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
| | | |
Collapse
|
14
|
Cino EA, Soares IN, Pedrote MM, de Oliveira GAP, Silva JL. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds. Sci Rep 2016; 6:32535. [PMID: 27600721 PMCID: PMC5013286 DOI: 10.1038/srep32535] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/10/2016] [Indexed: 11/23/2022] Open
Abstract
The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy.
Collapse
Affiliation(s)
- Elio A Cino
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Iaci N Soares
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Murilo M Pedrote
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, RJ, Brazil
| |
Collapse
|
15
|
Identification of p53-target genes in Danio rerio. Sci Rep 2016; 6:32474. [PMID: 27581768 PMCID: PMC5007497 DOI: 10.1038/srep32474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/08/2016] [Indexed: 11/22/2022] Open
Abstract
To orchestrate the genomic response to cellular stress signals, p53 recognizes and binds to DNA containing specific and well-characterized p53-responsive elements (REs). Differences in RE sequences can strongly affect the p53 transactivation capacity and occur even between closely related species. Therefore, the identification and characterization of a species-specific p53 Binding sistes (BS) consensus sequence and of the associated target genes may help to provide new insights into the evolution of the p53 regulatory networks across different species. Although p53 functions were studied in a wide range of species, little is known about the p53-mediated transcriptional signature in Danio rerio. Here, we designed and biochemically validated a computational approach to identify novel p53 target genes in Danio rerio genome. Screening all the Danio rerio genome by pattern-matching-based analysis, we found p53 RE-like patterns proximal to 979 annotated Danio rerio genes. Prioritization analysis identified a subset of 134 candidate pattern-related genes, 31 of which have been investigated in further biochemical assays. Our study identified runx1, axin1, traf4a, hspa8, col4a5, necab2, and dnajc9 genes as novel direct p53 targets and 12 additional p53-controlled genes in Danio rerio genome. The proposed combinatorial approach resulted to be highly sensitive and robust for identifying new p53 target genes also in additional animal species.
Collapse
|
16
|
Ouaray Z, ElSawy KM, Lane DP, Essex JW, Verma C. Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain. Proteins 2016; 84:1443-61. [DOI: 10.1002/prot.25089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/26/2016] [Accepted: 06/13/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Zahra Ouaray
- School of Chemistry; University of Southampton; Southampton SO17 1BJ United Kingdom
- Bioinformatics Institute, Agency for Science, Technology and Research; Singapore 138671 Singapore
| | - Karim M. ElSawy
- York Centre for Complex Systems Analysis (YCCSA), University of York; York YO10 5GE United Kingdom
- Department of Chemistry; College of Science, Qassim University; Buraydah 52571 Saudi Arabia
| | - David P. Lane
- p53 Laboratory; Agency for Science, Technology and Research; Singapore 138648 Singapore
| | - Jonathan W. Essex
- School of Chemistry; University of Southampton; Southampton SO17 1BJ United Kingdom
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research; Singapore 138671 Singapore
- School of Biological Sciences; Nanyang Technological University; 637551 Singapore
- Department of Biological Sciences; National University of Singapore; 117543 Singapore
| |
Collapse
|
17
|
Singh MI, Jain V. Molecular Dissection of the Homotrimeric Sliding Clamp of T4 Phage: Two Domains of a Subunit Display Asymmetric Characteristics. Biochemistry 2016; 55:588-96. [DOI: 10.1021/acs.biochem.5b01204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manika Indrajit Singh
- Microbiology
and Molecular
Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Vikas Jain
- Microbiology
and Molecular
Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| |
Collapse
|
18
|
Lion M, Raimondi I, Donati S, Jousson O, Ciribilli Y, Inga A. Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay. PLoS One 2015; 10:e0116177. [PMID: 25668429 PMCID: PMC4323202 DOI: 10.1371/journal.pone.0116177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/16/2014] [Indexed: 11/18/2022] Open
Abstract
Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course of evolution. We present a new approach to investigate transactivation capacity of sequence-specific TFs in evolutionary studies. Saccharomyces cerevisiae was used as an in vivo test tube and p53 proteins derived from human and five commonly used animal models were chosen as proof of concept. p53 is a highly conserved master regulator of environmental stress responses. Previous reports indicated conserved p53 DNA binding specificity in vitro, even for evolutionary distant species. We used isogenic yeast strains where p53-dependent transactivation was measured towards chromosomally integrated p53 response elements (REs). Ten REs were chosen to sample a wide range of DNA binding affinity and transactivation capacity for human p53 and proteins were expressed at two levels using an inducible expression system. We showed that the assay is amenable to study thermo-sensitivity of frog p53, and that chimeric constructs containing an ectopic transactivation domain could be rapidly developed to enhance the activity of proteins, such as fruit fly p53, that are poorly effective in engaging the yeast transcriptional machinery. Changes in the profile of relative transactivation towards the ten REs were measured for each p53 protein and compared to the profile obtained with human p53. These results, which are largely independent from relative p53 protein levels, revealed widespread evolutionary divergence of p53 transactivation specificity, even between human and mouse p53. Fruit fly and human p53 exhibited the largest discrimination among REs while zebrafish p53 was the least selective.
Collapse
Affiliation(s)
- Mattia Lion
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Ivan Raimondi
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Stefano Donati
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Olivier Jousson
- Laboratory of Microbial Genomics, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
- * E-mail:
| |
Collapse
|
19
|
|
20
|
Ji X, Huang Q, Yu L, Nussinov R, Ma B. Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs. Int J Mol Sci 2014; 15:13275-98. [PMID: 25075982 PMCID: PMC4159794 DOI: 10.3390/ijms150813275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 02/06/2023] Open
Abstract
p53 protein has about thirty phosphorylation sites located at the N- and C-termini and in the core domain. The phosphorylation sites are relatively less mutated than other residues in p53. To understand why and how p53 phosphorylation sites are rarely mutated in human cancer, using a bioinformatics approaches, we examined the phosphorylation site and its nearby flanking residues, focusing on the consensus phosphorylation motif pattern, amino-acid correlations within the phosphorylation motifs, the propensity of structural disorder of the phosphorylation motifs, and cancer mutations observed within the phosphorylation motifs. Many p53 phosphorylation sites are targets for several kinases. The phosphorylation sites match 17 consensus sequence motifs out of the 29 classified. In addition to proline, which is common in kinase specificity-determining sites, we found high propensity of acidic residues to be adjacent to phosphorylation sites. Analysis of human cancer mutations in the phosphorylation motifs revealed that motifs with adjacent acidic residues generally have fewer mutations, in contrast to phosphorylation sites near proline residues. p53 phosphorylation motifs are mostly disordered. However, human cancer mutations within phosphorylation motifs tend to decrease the disorder propensity. Our results suggest that combination of acidic residues Asp and Glu with phosphorylation sites provide charge redundancy which may safe guard against loss-of-function mutations, and that the natively disordered nature of p53 phosphorylation motifs may help reduce mutational damage. Our results further suggest that engineering acidic amino acids adjacent to potential phosphorylation sites could be a p53 gene therapy strategy.
Collapse
Affiliation(s)
- Xiaona Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Long Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|