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Schubert SA, Ruano D, Joruiz SM, Stroosma J, Glavak N, Montali A, Pinto LM, Rodríguez-Girondo M, Barge-Schaapveld DQCM, Nielsen M, van Nesselrooij BPM, Mensenkamp AR, van Leerdam ME, Sharp TH, Morreau H, Bourdon JC, de Miranda NFCC, van Wezel T. Germline variant affecting p53β isoforms predisposes to familial cancer. Nat Commun 2024; 15:8208. [PMID: 39294166 PMCID: PMC11410958 DOI: 10.1038/s41467-024-52551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/06/2024] [Indexed: 09/20/2024] Open
Abstract
Germline and somatic TP53 variants play a crucial role during tumorigenesis. However, genetic variations that solely affect the alternatively spliced p53 isoforms, p53β and p53γ, are not fully considered in the molecular diagnosis of Li-Fraumeni syndrome and cancer. In our search for additional cancer predisposing variants, we identify a heterozygous stop-lost variant affecting the p53β isoforms (p.*342Serext*17) in four families suspected of an autosomal dominant cancer syndrome with colorectal, breast and papillary thyroid cancers. The stop-lost variant leads to the 17 amino-acid extension of the p53β isoforms, which increases oligomerization to canonical p53α and dysregulates the expression of p53's transcriptional targets. Our study reveals the capacity of p53β mutants to influence p53 signalling and contribute to the susceptibility of different cancer types. These findings underscore the significance of p53 isoforms and the necessity of comprehensive investigation into the entire TP53 gene in understanding cancer predisposition.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jordy Stroosma
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nikolina Glavak
- School of Medicine, University of Dundee, Dundee, UK
- Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Anna Montali
- School of Medicine, University of Dundee, Dundee, UK
| | - Lia M Pinto
- School of Medicine, University of Dundee, Dundee, UK
| | - Mar Rodríguez-Girondo
- Department of Biomedical Data Sciences, Section of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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2
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Safieh J, Chazan A, Saleem H, Vyas P, Danin-Poleg Y, Ron D, Haran TE. A molecular mechanism for the "digital" response of p53 to stress. Proc Natl Acad Sci U S A 2023; 120:e2305713120. [PMID: 38015851 PMCID: PMC10710088 DOI: 10.1073/pnas.2305713120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
The tumor suppressor protein p53 accumulates in response to cellular stress and consequently orchestrates the expression of multiple genes in a p53-level and time-dependent manner to overcome stress consequences, for which a molecular mechanism is currently unknown. Previously, we reported that DNA torsional flexibility distinguishes among p53 response elements (REs) and that transactivation at basal p53 levels is correlated with p53 REs flexibility. Here, we calculated the flexibility of ~200 p53 REs. By connecting functional outcomes of p53-target genes' activation to the calculated flexibility of their REs, we show that genes known to belong to pathways that are activated rapidly upon stress contain REs that are significantly more flexible relative to REs of genes known to be involved in pathways that are activated later in the response to stress. The global structural properties of several p53 REs belonging to different pathways were experimentally validated. Additionally, reporter-gene expression driven by flexible p53 REs occurred at lower p53 levels and with faster rates than expression from rigid REs. Furthermore, analysis of published endogenous mRNA levels of p53-target genes as a function of REs' flexibility showed that early versus late genes differ significantly in their flexibility properties of their REs and that highly flexible p53 REs enable high-activation level exclusively to early-response genes. Overall, we demonstrate that DNA flexibility of p53 REs contributes significantly to functional selectivity in the p53 system by facilitating the initial steps of p53-dependent target-genes expression, thereby contributing to survival versus death decisions in the p53 system.
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Affiliation(s)
- Jessy Safieh
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Ariel Chazan
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Hanna Saleem
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Pratik Vyas
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Yael Danin-Poleg
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Dina Ron
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Tali E. Haran
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
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3
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Sakaguchi S, Nakagawa N, Wahba HM, Wada J, Kamada R, Omichinski JG, Sakaguchi K. Highly Similar Tetramerization Domains from the p53 Protein of Different Mammalian Species Possess Varying Biophysical, Functional and Structural Properties. Int J Mol Sci 2023; 24:16620. [PMID: 38068946 PMCID: PMC10706167 DOI: 10.3390/ijms242316620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The p53 protein is a transcriptional regulatory factor and many of its functions require that it forms a tetrameric structure. Although the tetramerization domain of mammalian p53 proteins (p53TD) share significant sequence similarities, it was recently shown that the tree shrew p53TD is considerably more thermostable than the human p53TD. To determine whether other mammalian species display differences in this domain, we used biophysical, functional, and structural studies to compare the properties of the p53TDs from six mammalian model organisms (human, tree shrew, guinea pig, Chinese hamster, sheep, and opossum). The results indicate that the p53TD from the opossum and tree shrew are significantly more stable than the human p53TD, and there is a correlation between the thermostability of the p53TDs and their ability to activate transcription. Structural analysis of the tree shrew and opossum p53TDs indicated that amino acid substitutions within two distinct regions of their p53TDs can dramatically alter hydrophobic packing of the tetramer, and in particular substitutions at positions corresponding to F341 and Q354 of the human p53TD. Together, the results suggest that subtle changes in the sequence of the p53TD can dramatically alter the stability, and potentially lead to important changes in the functional activity, of the p53 protein.
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Affiliation(s)
- Shuya Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; (S.S.); (N.N.); (J.W.); (R.K.)
| | - Natsumi Nakagawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; (S.S.); (N.N.); (J.W.); (R.K.)
| | - Haytham M. Wahba
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada;
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 2722165, Egypt
| | - Junya Wada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; (S.S.); (N.N.); (J.W.); (R.K.)
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; (S.S.); (N.N.); (J.W.); (R.K.)
| | - James G. Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada;
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; (S.S.); (N.N.); (J.W.); (R.K.)
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4
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Ghosh A, Ganguly D. Structural impairment of p53 C-terminal due to the effect of phosphorylation and acetylation: a study on the interdependence of PTM. J Biomol Struct Dyn 2023:1-10. [PMID: 37937769 DOI: 10.1080/07391102.2023.2279270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023]
Abstract
The C-terminal of tumor suppressor protein p53 is intrinsically disordered while unbound. This particular segment often shows structural plasticity when bound to other binding partners. The disordered component undergoes a disordered to ordered transition upon recognition. Post-translational modifications (PTMs), namely phosphorylation and acetylation, significantly alter the structural motifs of the segment. Among the various types of PTMs, phosphorylation, and acetylation of p53 at both N- and C- terminals lead to stabilization and activation. It has been noted experimentally that phosphorylation often regulates (enhances or reduces) the acetylation at specific sites. The phosphorylation of Thr377 and Ser378 reduces the acetylation of Lys373 and Lys382. Mutations of Thr377 and Ser378 to neutral Ala enhance and phospho mimic Asp reduce the acetylation of Lys373 and Lys382. Simulations of several single-point and pair-wise mutated systems have been generated to compare how the presence or absence of phosphorylation favors or disfavors the acetylation by thermodynamic and conformational analysis. We are using implicit solvent replica exchange molecular dynamics simulations to get 200 ns well-converged conformational ensembles of each system. Different sets of systems having both single and double PTMs are simulated. The results admit the appreciable change in the secondary structural level upon specific PTM. Also, the residual structure of the unbound p53 with single-point PTM varies significantly with pair-wise modifications. These observations further shed light on the relationship between the interdependencies of the specific PTM sites and the secondary structural levels.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anamika Ghosh
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, Kolkata, India
| | - Debabani Ganguly
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, Kolkata, India
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5
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Hnath B, Chen J, Reynolds J, Choi E, Wang J, Zhang D, Sha CM, Dokholyan NV. Big versus small: The impact of aggregate size in disease. Protein Sci 2023; 32:e4686. [PMID: 37243896 PMCID: PMC10273386 DOI: 10.1002/pro.4686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Protein aggregation results in an array of different size soluble oligomers and larger insoluble fibrils. Insoluble fibrils were originally thought to cause neuronal cell deaths in neurodegenerative diseases due to their prevalence in tissue samples and disease models. Despite recent studies demonstrating the toxicity associated with soluble oligomers, many therapeutic strategies still focus on fibrils or consider all types of aggregates as one group. Oligomers and fibrils require different modeling and therapeutic strategies, targeting the toxic species is crucial for successful study and therapeutic development. Here, we review the role of different-size aggregates in disease, and how factors contributing to aggregation (mutations, metals, post-translational modifications, and lipid interactions) may promote oligomers opposed to fibrils. We review two different computational modeling strategies (molecular dynamics and kinetic modeling) and how they are used to model both oligomers and fibrils. Finally, we outline the current therapeutic strategies targeting aggregating proteins and their strengths and weaknesses for targeting oligomers versus fibrils. Altogether, we aim to highlight the importance of distinguishing the difference between oligomers and fibrils and determining which species is toxic when modeling and creating therapeutics for protein aggregation in disease.
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Affiliation(s)
- Brianna Hnath
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jiaxing Chen
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Joshua Reynolds
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Esther Choi
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jian Wang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Dongyan Zhang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Congzhou M. Sha
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Nikolay V. Dokholyan
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of Biochemistry & Molecular BiologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of ChemistryPenn State UniversityUniversity ParkPennsylvaniaUSA
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6
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Di Ianni A, Tüting C, Kipping M, Ihling CH, Köppen J, Iacobucci C, Arlt C, Kastritis PL, Sinz A. Structural assessment of the full-length wild-type tumor suppressor protein p53 by mass spectrometry-guided computational modeling. Sci Rep 2023; 13:8497. [PMID: 37231156 DOI: 10.1038/s41598-023-35437-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
The tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light on the structural and functional roles of p53's C-terminal region in full-length, wild-type human p53 tetramer and their importance for DNA binding. For this, we employed complementary techniques of structural mass spectrometry (MS) in an integrated approach with computational modeling. Our results show no major conformational differences in p53 between DNA-bound and DNA-free states, but reveal a substantial compaction of p53's C-terminal region. This supports the proposed mechanism of unspecific DNA binding to the C-terminal region of p53 prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in our integrative approach is envisioned to serve as general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered region (IDRs).
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Affiliation(s)
- Alessio Di Ianni
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Christian Tüting
- ZIK HALOmem and Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Marc Kipping
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Janett Köppen
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, Coppito, 67100, L'Aquila, Italy
| | - Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
| | - Panagiotis L Kastritis
- ZIK HALOmem and Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
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7
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Fine RL, Mao Y, Dinnen R, Rosal RV, Raffo A, Hochfeld U, Senatus P, Bruce JN, Nichols G, Wang H, Li Y, Brandt-Rauf PW. C-Terminal p53 Palindromic Tetrapeptide Restores Full Apoptotic Function to Mutant p53 Cancer Cells In Vitro and In Vivo. Biomedicines 2023; 11:137. [PMID: 36672645 PMCID: PMC9855826 DOI: 10.3390/biomedicines11010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/25/2022] [Accepted: 08/15/2022] [Indexed: 01/06/2023] Open
Abstract
We previously demonstrated that a synthetic monomer peptide derived from the C-terminus of p53 (aa 361−382) induced preferential apoptosis in mutant p53 malignant cells, but not normal cells. The major problem with the peptide was its short half-life (half-life < 10 min.) due to a random coil topology found in 3D proton NMR spectroscopy studies. To induce secondary/tertiary structures to produce more stability, we developed a peptide modelled after the tetrameric structure of p53 essential for activation of target genes. Starting with the above monomer peptide (aa 361−382), we added the nuclear localization sequence of p53 (aa 353−360) and the end of the C-terminal sequence (aa 383−393), resulting in a monomer spanning aa 353−393. Four monomers were linked by glycine to maximize flexibility and in a palindromic order that mimics p53 tetramer formation with four orthogonal alpha helices, which is required for p53 transactivation of target genes. This is now known as the 4 repeat-palindromic-p53 peptide or (4R-Pal-p53p). We explored two methods for testing the activity of the palindromic tetrapeptide: (1) exogenous peptide with a truncated antennapedia carrier (Ant) and (2) a doxycycline (Dox) inducer for endogenous expression. The exogenous peptide, 4R-Pal-p53p-Ant, contained a His tag at the N-terminal and a truncated 17aa Ant at the C-terminal. Exposure of human breast cancer MB-468 cells and human skin squamous cell cancer cells (both with mutant p53, 273 Arg->His) with purified peptide at 7 µM and 15 µM produced 52% and 75%, cell death, respectively. Comparatively, the monomeric p53 C-terminal peptide-Ant (aa 361−382, termed p53p-Ant), at 15 µM and 30 µM induced 15% and 24% cell death, respectively. Compared to the p53p-Ant, the exogenous 4R-pal-p53p-Ant was over five-fold more potent for inducing apoptosis at an equimolar concentration (15 µM). Endogenous 4R-Pal-p53p expression (without Ant), induced by Dox, resulted in 43% cell death in an engineered MB468 breast cancer stable cell line, while endogenous p53 C-terminal monomeric peptide expression produced no cell death due to rapid peptide degradation. The mechanism of apoptosis from 4R-Pal-p53p involved the extrinsic and intrinsic pathways (FAS, caspase-8, Bax, PUMA) for apoptosis, as well as increasing reactive oxygen species (ROS). All three death pathways were induced from transcriptional/translational activation of pro-apoptotic genes. Additionally, mRNA of p53 target genes (Bax and Fas) increased 14-fold and 18-fold, respectively, implying that the 4R-Pal-p53p restored full apoptotic potential to mutant p53. Monomeric p53p only increased Fas expression without a transcriptional or translational increase in Fas, and other genes and human marrow stem cell studies revealed no toxicity to normal stem cells for granulocytes, erythrocytes, monocytes, and macrophages (CFU-GEMM). Additionally, the peptide specifically targeted pre-malignant and malignant cells with mutant p53 and was not toxic to normal cells with basal levels of WT p53.
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Affiliation(s)
- Robert L. Fine
- Experimental Therapeutics Program, Division of Medical Oncology, College of Physicians and Surgeons of Columbia University, New York, NY 10314, USA
| | - Yuehua Mao
- Experimental Therapeutics Program, Division of Medical Oncology, College of Physicians and Surgeons of Columbia University, New York, NY 10314, USA
| | - Richard Dinnen
- Experimental Therapeutics Program, Division of Medical Oncology, College of Physicians and Surgeons of Columbia University, New York, NY 10314, USA
| | - Ramon V. Rosal
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY 10314, USA
| | - Anthony Raffo
- Experimental Therapeutics Program, Division of Medical Oncology, College of Physicians and Surgeons of Columbia University, New York, NY 10314, USA
| | - Uri Hochfeld
- Experimental Therapeutics Program, Division of Medical Oncology, College of Physicians and Surgeons of Columbia University, New York, NY 10314, USA
| | - Patrick Senatus
- Department of Neurosurgery, Neurologic Institute of New York, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeffrey N. Bruce
- Department of Neurosurgery, Neurologic Institute of New York, Columbia University Medical Center, New York, NY 10032, USA
| | - Gwen Nichols
- Experimental Therapeutics Program, Division of Medical Oncology, College of Physicians and Surgeons of Columbia University, New York, NY 10314, USA
| | - Hsin Wang
- Department of Chemistry, College of Staten Island, 2800 Victory Boulevard, New York, NY 10314, USA
| | - Yongliang Li
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY 10314, USA
| | - Paul W. Brandt-Rauf
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY 10314, USA
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
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8
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Ghosh A, Ganguly D. Structural modulation of p53TAD1-TAZ2 complex upon mutations and post-translational modification. J Biomol Struct Dyn 2023; 41:176-185. [PMID: 34787057 DOI: 10.1080/07391102.2021.2004235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The tumour suppressing p53 is a target for genetic alterations in human cancer. Native p53, found in latent state in cells, gets activated following various intracellular or extracellular responses. It plays imperative role in cell-cycle control, via growth-arrest, DNA repair and apoptosis, mainly regulated by post-translational modifications (PTM). However, the influence of PTMs on the activity of p53 is still under extensive experimental and computational study. There are numerous PTM sites in p53, which are reported to regulate its binding affinities with other proteins. Of the many, Thr18 at transactivational domain (TAD) of p53 is reported to amplify p53 activity upon phosphorylation. To understand the molecular basis of p53 recognition by its binding partner upon mutations and PTMs, we have exploited all atom molecular dynamic (MD) simulation of p53TAD1 bound to TAZ2 domain of p300. The MD simulation inferred that phosphorylated and mutated Thr18, as a phospho-mimic, bound with TAZ2, redistributed the charge environment of the interface, thereby modulating the stronger interactions with TAZ2 to enhance the binding efficiency. The electrostatic interactions due to different charge environment together with H-bonding and hydrophobic interaction dictate diverse binding approach between the two. The results of this computational study further explain the importance of the Thr18 as a PTM site in atomistic detail, hence shedding further light to the understanding of how PTMs are imperative for p53 activity to protect the cellular world.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anamika Ghosh
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Howrah, India
| | - Debabani Ganguly
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, Kolkata, India
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9
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Legartová S, Fagherazzi P, Goswami P, Brazda V, Lochmanová G, Koutná I, Bártová E. Irradiation potentiates p53 phosphorylation and p53 binding to the promoter and coding region of the TP53 gene. Biochimie 2023; 204:154-168. [PMID: 36167255 DOI: 10.1016/j.biochi.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 09/21/2022] [Indexed: 01/12/2023]
Abstract
An essential factor of the DNA damage response is 53BP1, a multimeric protein that inhibits the resection-dependent double-strand break (DBS) repair. The p53 protein is a tumor suppressor known as a guardian of the genome. Although the interaction between 53BP1 and its p53 partner is well-known in regulating gene expression, a question remains whether genome injury can affect the interaction between 53BP1 and p53 proteins or p53 binding to DNA. Here, using mass spectrometry, we determine post-translational modifications and interaction properties of 53BP1 and p53 proteins in non-irradiated and γ-irradiated cells. In addition, we used Atomic Force Microscopy (AFM) and Fluorescent Lifetime Imaging Microscopy combined with Fluorescence Resonance Energy Transfer (FLIM-FRET) for studies of p53 binding to DNA. Also, we used local laser microirradiation as a tool of advanced confocal microscopy, showing selected protein accumulation at locally induced DNA lesions. We observed that 53BP1 and p53 proteins accumulate at microirradiated chromatin but with distinct kinetics. The density of 53BP1 (53BP1pS1778) phosphorylated form was lower in DNA lesions than in the non-specified form. By mass spectrometry, we found 22 phosphorylations, 4 acetylation sites, and methylation of arginine 1355 within the DNA-binding domain of the 53BP1 protein (aa1219-1711). The p53 protein was phosphorylated on 8 amino acids and acetylated on the N-terminal domain. Post-translational modifications (PTMs) of 53BP1 were not changed in cells exposed to γ-radiation, while γ-rays increased the level of S6ph and S15ph in p53. Interaction analysis showed that 53BP1 and p53 proteins have 54 identical interaction protein partners, and AFM revealed that p53 binds to both non-specific and TP53-specific sequences (AGACATGCCTA GGCATGTCT). Irradiation by γ-rays enhanced the density of the p53 protein at the AGACATGCCTAGGCATGTCT region, and the binding of p53 S15ph to the TP53 promoter was potentiated in irradiated cells. These findings show that γ-irradiation, in general, strengthens the binding of phosphorylated p53 protein to the encoding gene.
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Affiliation(s)
- Soňa Legartová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Paolo Fagherazzi
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Pratik Goswami
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Vaclav Brazda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Gabriela Lochmanová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Irena Koutná
- The International Clinical Research Center of St. Anne's University Hospital in Brno (FNUSA-ICRC), Pekařská 53, 656 91, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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10
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Krois AS, Park S, Martinez-Yamout MA, Dyson HJ, Wright PE. Mapping Interactions of the Intrinsically Disordered C-Terminal Regions of Tetrameric p53 by Segmental Isotope Labeling and NMR. Biochemistry 2022; 61:2709-2719. [PMID: 36380579 PMCID: PMC9788666 DOI: 10.1021/acs.biochem.2c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The C-terminal region of the tumor suppressor protein p53 contains three domains, nuclear localization signal (NLS), tetramerization domain (TET), and C-terminal regulatory domain (CTD), which are essential for p53 function. Characterization of the structure and interactions of these domains within full-length p53 has been limited by the overall size and flexibility of the p53 tetramer. Using trans-intein splicing, we have generated full-length p53 constructs in which the C-terminal region is isotopically labeled with 15N for NMR analysis, allowing us to obtain atomic-level information on the C-terminal domains in the context of the full-length protein. Resonances of NLS and CTD residues have narrow linewidths, showing that these regions are largely solvent-exposed and dynamically disordered, whereas resonances from the folded TET are broadened beyond detection. Two regions of the CTD, spanning residues 369-374 and 381-388 and with high lysine content, make dynamic and sequence-independent interactions with DNA in regions that flank the p53 recognition element. The population of DNA-bound states increases as the length of the flanking regions is extended up to approximately 20 base pairs on either side of the recognition element. Acetylation of K372, K373, and K382, using a construct of the transcriptional coactivator CBP containing the TAZ2 and acetyltransferase domains, inhibits interaction of the CTD with DNA. This work provides high-resolution insights into the behavior of the intrinsically disordered C-terminal regions of p53 within the full-length tetramer and the molecular basis by which the CTD mediates DNA binding and specificity.
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Affiliation(s)
- Alexander S Krois
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - Sangho Park
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
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11
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Patil MR, Bihari A. A comprehensive study of p53 protein. J Cell Biochem 2022; 123:1891-1937. [PMID: 36183376 DOI: 10.1002/jcb.30331] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 01/10/2023]
Abstract
The protein p53 has been extensively investigated since it was found 43 years ago and has become a "guardian of the genome" that regulates the division of cells by preventing the growth of cells and dividing them, that is, inhibits the development of tumors. Initial proof of protein existence by researchers in the mid-1970s was found by altering and regulating the SV40 big T antigen termed the A protein. Researchers demonstrated how viruses play a role in cancer by employing viruses' ability to create T-antigens complex with viral tumors, which was discovered in 1979 following a viral analysis and cancer analog research. Researchers later in the year 1989 explained that in Murine Friend, a virus-caused erythroleukemia, commonly found that p53 was inactivated to suggest that p53 could be a "tumor suppressor gene." The TP53 gene, encoding p53, is one of human cancer's most frequently altered genes. The protein-regulated biological functions of all p53s include cell cycles, apoptosis, senescence, metabolism of the DNA, angiogenesis, cell differentiation, and immunological response. We tried to unfold the history of the p53 protein, which was discovered long back in 1979, that is, 43 years of research on p53, and how p53's function has been developed through time in this article.
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Affiliation(s)
- Manisha R Patil
- Department of Computer-Applications, School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Bihari
- Department of Computational Intelligence, School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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12
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Madarász K, Mótyán JA, Bedekovics J, Miltényi Z, Ujfalusi A, Méhes G, Mokánszki A. Deep Molecular and In Silico Protein Analysis of p53 Alteration in Myelodysplastic Neoplasia and Acute Myeloid Leukemia. Cells 2022; 11:3475. [PMID: 36359870 PMCID: PMC9654600 DOI: 10.3390/cells11213475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Mutation of the TP53 gene is one of the major drivers of myelodysplastic neoplasias (MDS) and acute myeloid leukemia with myelodysplasia-related changes (AML-MR). TP53 mutations present in these hematopoietic malignancies form a distinct molecular genetic cluster with a worse prognosis than without the alteration. However, besides well-characterized hot-spot variants, a significant proportion of TP53 alterations are of uncertain clinical significance. METHODS To enlighten so far unknown aspects, bone-marrow samples from altogether 77 patients are analyzed retrospectively with the diagnosis of AML-MR (26 cases), MDS-IB (12 cases), and MDS-LB (39 cases) according to WHO 2022 guidelines. Next-generation sequencing results are correlated with histological, cytogenetic, and survival data. RESULTS Twenty out of the 30 TP53 mutation types detected by NGS are not categorized in current public databases; thus, their clinical significance remained mysterious. Because of the interpretation difficulties and the absence of clinical correlations, pathogenicity is established based on in silico approaches. The 12 pathogenicity classification systems, as well as protein stability, protein-DNA, protein-protein interaction, and post-translational modification analyses are applied. We found statistically significant differences between AML/MDS groups considering p53 pathogenicity, protein structural changes, and overall survival. The largest number of abnormalities with the most severe consequences are found in AML-MR cases. CONCLUSIONS These molecular and in silico protein data further support that MDS with increased-blast (MDS-IB) is an intermediate group between AML-MR and MDS with low-blast (MDS-LB) patients, which frequently progresses to AML and is therefore considered a pre-leukemic condition.
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Affiliation(s)
- Kristóf Madarász
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Judit Bedekovics
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsófia Miltényi
- Department of Hematology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Anikó Ujfalusi
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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13
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Chen C, Fu G, Guo Q, Xue S, Luo SZ. Phase separation of p53 induced by its unstructured basic region and prevented by oncogenic mutations in tetramerization domain. Int J Biol Macromol 2022; 222:207-216. [PMID: 36108750 DOI: 10.1016/j.ijbiomac.2022.09.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 11/05/2022]
Abstract
Liquid-liquid phase separation (LLPS) drives the formation of extensive membrane-less compartments to regulate various cellular biological activities both physiologically and pathologically. It has been widely accepted that LLPS is closely related to amyloid diseases and increasing reports have linked this phenomenon to cancers. Mutations of tumor suppressor protein p53 exist in more than half of malignant tumors, making the protein vitally important in cancer research. Recently, p53 was reported to undergo phase separation, which may regulate the function of p53. The molecular mechanism of p53 phase separation and how this process relates to cancer remains largely unclear. Herein, we find that the disordered unstructured basic region (UBR) plays a crucial role in p53 LLPS, driven by electrostatic and hydrophobic interactions. Mutations in the tetramerization domain (TD) disrupt p53 phase separation by preventing the tetramer formation. Furthermore, our results have revealed that, in response to DNA damage in cell, the wild type (WT) p53 undergoes LLPS, while LLPS in oncogenic mutations is diminished or eliminated. The expression of the target gene of p53 decreased significantly with the mutations and cell survival increased with the mutations. Thus, we propose a novel mechanism of p53 carcinogenesis, whereby oncogenic mutations in TD impair the formation of p53 condensates, decreasing the activation of target genes and promoting cancer progression. This study helps to understand the behavior and function of p53 in a different aspect and may provide insights into cancer therapies targeting p53.
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Affiliation(s)
- Chen Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Gaohong Fu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Quanqiang Guo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Song Xue
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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14
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Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
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Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
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15
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Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. J Mol Biol 2021; 433:166900. [PMID: 33647288 DOI: 10.1016/j.jmb.2021.166900] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/31/2022]
Abstract
A large fraction of peptides or protein regions are disordered in isolation and fold upon binding. These regions, also called MoRFs, SLiMs or LIPs, are often associated with signaling and regulation processes. However, despite their importance, only a limited number of examples are available in public databases and their automatic detection at the proteome level is problematic. Here we present FLIPPER, an automatic method for the detection of structurally linear sub-regions or peptides that interact with another chain in a protein complex. FLIPPER is a random forest classification that takes the protein structure as input and provides the propensity of each amino acid to be part of a LIP region. Models are built taking into consideration structural features such as intra- and inter-chain contacts, secondary structure, solvent accessibility in both bound and unbound state, structural linearity and chain length. FLIPPER is accurate when evaluated on non-redundant independent datasets, 99% precision and 99% sensitivity on PixelDB-25 and 87% precision and 88% sensitivity on DIBS-25. Finally, we used FLIPPER to process the entire Protein Data Bank and identified different classes of LIPs based on different binding modes and partner molecules. We provide a detailed description of these LIP categories and show that a large fraction of these regions are not detected by disorder predictors. All FLIPPER predictions are integrated in the MobiDB 4.0 database.
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Affiliation(s)
| | - Paolo Bonato
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Marco Necci
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy.
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
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16
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17
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Moia R, Boggione P, Mahmoud AM, Kodipad AA, Adhinaveni R, Sagiraju S, Patriarca A, Gaidano G. Targeting p53 in chronic lymphocytic leukemia. Expert Opin Ther Targets 2020; 24:1239-1250. [PMID: 33016796 DOI: 10.1080/14728222.2020.1832465] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Genomic studies have allowed to identify molecular predictors for chronic lymphocytic leukemia (CLL) treatment tailoring. TP53 disruption is the strongest predictor of chemo-refractoriness and its assessment is the first decisional node in the disease treatment algorithm. AREAS COVERED The review covers the p53 biological pathway, its genetic alterations and clinical implications in CLL, and its druggable targets. The potential therapeutic options for TP53 disrupted patients are described, including: i) agents circumventing TP53 disruption; ii) targeted therapies restoring the physiological function of mutant p53; and iii) medicines potentiating p53 function. EXPERT OPINION The key approach to improve CLL outcome is treatment tailoring in individual patients. BCR and BCL2 inhibitors have significantly improved CLL survival, however TP53 disrupted patients still have a less favorable outcome than wild type cases, possibly because these novel drugs do not directly target p53 and do not restore the function of the disrupted p53 pathway. Emerging innovative molecules in cancer are able to restore the p53 mutant protein and/or potentiate the activity of the p53 wild type protein. If these compounds were confirmed as efficacious also for CLL, they would represent another step forward in the care of high risk CLL patients with TP53 abnormalities.
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Affiliation(s)
- Riccardo Moia
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Paola Boggione
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Abdurraouf Mokhtar Mahmoud
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Ahad Ahmed Kodipad
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Ramesh Adhinaveni
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Sruthi Sagiraju
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Andrea Patriarca
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale , Novara, Italy
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18
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Krüger A, Stier A, Fischbach A, Bürkle A, Hauser K, Mangerich A. Interactions of p53 with poly(ADP-ribose) and DNA induce distinct changes in protein structure as revealed by ATR-FTIR spectroscopy. Nucleic Acids Res 2019; 47:4843-4858. [PMID: 30892621 PMCID: PMC6511852 DOI: 10.1093/nar/gkz175] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/22/2019] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Due to multiple domains and in part intrinsically disordered regions, structural analyses of p53 remain a challenging task, particularly in complex with DNA and other macromolecules. Here, we applied a novel attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic approach to investigate changes in secondary structure of full-length p53 induced by non-covalent interactions with DNA and poly(ADP-ribose) (PAR). To validate our approach, we confirmed a positive regulatory function of p53’s C-terminal domain (CTD) with regard to sequence-specific DNA binding and verified that the CTD mediates p53–PAR interaction. Further, we demonstrate that DNA and PAR interactions result in distinct structural changes of p53, indicating specific binding mechanisms via different domains. A time-dependent analysis of the interplay of DNA and PAR binding to p53 revealed that PAR represents p53’s preferred binding partner, which efficiently controls p53–DNA interaction. Moreover, we provide infrared spectroscopic data on PAR pointing to the absence of regular secondary structural elements. Finally, temperature-induced melting experiments via CD spectroscopy show that DNA binding stabilizes the structure of p53, while PAR binding can shift the irreversible formation of insoluble p53 aggregates to higher temperatures. In conclusion, this study provides detailed insights into the dynamic interplay of p53 binding to DNA and PAR at a formerly inaccessible molecular level.
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Affiliation(s)
- Annika Krüger
- Department of Biology, University of Konstanz, Konstanz 78464, Germany.,Department of Chemistry, University of Konstanz, Konstanz 78464, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz 78464, Germany.,Zukunftskolleg, University of Konstanz, Konstanz 78464, Germany
| | - Anna Stier
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Arthur Fischbach
- Department of Biology, University of Konstanz, Konstanz 78464, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz 78464, Germany.,Zukunftskolleg, University of Konstanz, Konstanz 78464, Germany
| | - Alexander Bürkle
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, Konstanz 78464, Germany
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
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19
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Nakagawa N, Sakaguchi S, Nomura T, Kamada R, Omichinski JG, Sakaguchi K. The tetramerization domain of the tree shrew p53 protein displays unique thermostability despite sharing high sequence identity with the human p53 protein. Biochem Biophys Res Commun 2019; 521:681-686. [PMID: 31690451 DOI: 10.1016/j.bbrc.2019.10.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/17/2019] [Indexed: 01/11/2023]
Abstract
The p53 protein plays a number of roles in protecting organisms from different genotoxic stresses and this includes DNA damage induced by acetaldehyde, a metabolite of alcohol. Since the common tree shrew ingests high levels of alcohol as part of its normal diet, this suggests that its p53 protein may possess unique properties. Using a combination of biophysical and modeling studies, we demonstrate that the tetramerization domain of the tree shrew p53 protein is considerably more stable than the corresponding domain from humans despite sharing almost 90% sequence identity. Based on modeling and mutagenesis studies, we determine that a glutamine to methionine substitution at position 354 plays a key role in this difference. Given the link between stability of the p53 tetramerization domain and its transcriptional activity, the results suggest that this enhanced stability could lead to important consequences at p53-regulated genes in the tree shrew.
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Affiliation(s)
- Natsumi Nakagawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Shuya Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Takao Nomura
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - James G Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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20
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Ghate NB, Kim J, Shin Y, Situ A, Ulmer TS, An W. p32 is a negative regulator of p53 tetramerization and transactivation. Mol Oncol 2019; 13:1976-1992. [PMID: 31293051 PMCID: PMC6717765 DOI: 10.1002/1878-0261.12543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/03/2019] [Accepted: 07/08/2019] [Indexed: 01/10/2023] Open
Abstract
p53 is a sequence-specific transcription factor, and proper regulation of p53 transcriptional activity is critical for orchestrating different tumor-suppressive mechanisms. p32 is a multifunctional protein which interacts with a large number of viral proteins and transcription factors. Here, we investigate the effect of p32 on p53 transactivation and identify a novel mechanism by which p32 alters the functional characteristics of p53. Specifically, p32 attenuates p53-dependent transcription through impairment of p53 binding to its response elements on target genes. Upon p32 expression, p53 levels bound at target genes are decreased, and p53 target genes are inactivated, strongly indicating that p32 restricts p53 occupancy and function at target genes. The primary mechanism contributing to the observed action of p32 is the ability of p32 to interact with the p53 tetramerization domain and to block p53 tetramerization, which in turn enhances nuclear export and degradation of p53, leading to defective p53 transactivation. Collectively, these data establish p32 as a negative regulator of p53 function and suggest the therapeutic potential of targeting p32 for cancer treatment.
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Affiliation(s)
- Nikhil Baban Ghate
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Jinman Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Alan Situ
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Tobias S. Ulmer
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic InstituteUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
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21
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Martinelli AHS, Lopes FC, John EBO, Carlini CR, Ligabue-Braun R. Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies. Int J Mol Sci 2019; 20:ijms20061322. [PMID: 30875980 PMCID: PMC6471803 DOI: 10.3390/ijms20061322] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.
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Affiliation(s)
- Anne H S Martinelli
- Department of Molecular Biology and Biotechnology & Department of Biophysics, Biosciences Institute-IB, (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Fernanda C Lopes
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Elisa B O John
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Célia R Carlini
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 91410-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Department of Pharmaceutical Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre CEP 90050-170, RS, Brazil.
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22
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Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol 2019; 20:199-210. [DOI: 10.1038/s41580-019-0110-x] [Citation(s) in RCA: 452] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Probing initial transient oligomerization events facilitating Huntingtin fibril nucleation at atomic resolution by relaxation-based NMR. Proc Natl Acad Sci U S A 2019; 116:3562-3571. [PMID: 30808748 DOI: 10.1073/pnas.1821216116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The N-terminal region of the huntingtin protein, encoded by exon-1, comprises an amphiphilic domain (httNT), a polyglutamine (Q n ) tract, and a proline-rich sequence. Polyglutamine expansion results in an aggregation-prone protein responsible for Huntington's disease. Here, we study the earliest events involved in oligomerization of a minimalistic construct, httNTQ7, which remains largely monomeric over a sufficiently long period of time to permit detailed quantitative NMR analysis of the kinetics and structure of sparsely populated [Formula: see text] oligomeric states, yet still eventually forms fibrils. Global fitting of concentration-dependent relaxation dispersion, transverse relaxation in the rotating frame, and exchange-induced chemical shift data reveals a bifurcated assembly mechanism in which the NMR observable monomeric species either self-associates to form a productive dimer (τex ∼ 30 μs, K diss ∼ 0.1 M) that goes on to form a tetramer ([Formula: see text] μs; K diss ∼ 22 μM), or exchanges with a "nonproductive" dimer that does not oligomerize further (τex ∼ 400 μs; K diss ∼ 0.3 M). The excited state backbone chemical shifts are indicative of a contiguous helix (residues 3-17) in the productive dimer/tetramer, with only partial helical character in the nonproductive dimer. A structural model of the productive dimer/tetramer was obtained by simulated annealing driven by intermolecular paramagnetic relaxation enhancement data. The tetramer comprises a D 2 symmetric dimer of dimers with largely hydrophobic packing between the helical subunits. The structural model, validated by EPR distance measurements, illuminates the role of the httNT domain in the earliest stages of prenucleation and oligomerization, before fibril formation.
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24
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Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ. SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Sci Rep 2017; 7:8007. [PMID: 28808256 PMCID: PMC5556074 DOI: 10.1038/s41598-017-08321-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/07/2017] [Indexed: 12/21/2022] Open
Abstract
We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with a demonstrated accuracy of 0.95 and sensitivity of 0.98 on an independent test set. The predictor was developed using an ensemble machine learning approach with up-sampling of the minor class. It was trained on 53 complexes using various features, based on both protein 3D structure and sequence. The SpotOn web interface is freely available at: http://milou.science.uu.nl/services/SPOTON/.
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Affiliation(s)
- Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal. .,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands.
| | - Panagiotis I Koukos
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Rita Melo
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal.,Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066, Bobadela LRS, Portugal
| | - Jose G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Antonio J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Joerg Schaarschmidt
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Mikael Trellet
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Zeynep H Gümüş
- Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joaquim Costa
- CMUP/FCUP, Centro de Matemática da Universidade do Porto, Faculdade de Ciências, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands.
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25
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Oligomerization of the tetramerization domain of p53 probed by two- and three-color single-molecule FRET. Proc Natl Acad Sci U S A 2017; 114:E6812-E6821. [PMID: 28760960 DOI: 10.1073/pnas.1700357114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a method that combines two- and three-color single-molecule FRET spectroscopy with 2D FRET efficiency-lifetime analysis to probe the oligomerization process of intrinsically disordered proteins. This method is applied to the oligomerization of the tetramerization domain (TD) of the tumor suppressor protein p53. TD exists as a monomer at subnanomolar concentrations and forms a dimer and a tetramer at higher concentrations. Because the dissociation constants of the dimer and tetramer are very close, as we determine in this paper, it is not possible to characterize different oligomeric species by ensemble methods, especially the dimer that cannot be readily separated. However, by using single-molecule FRET spectroscopy that includes measurements of fluorescence lifetime and two- and three-color FRET efficiencies with corrections for submillisecond acceptor blinking, we show that it is possible to obtain structural information for individual oligomers at equilibrium and to determine the dimerization kinetics. From these analyses, we show that the monomer is intrinsically disordered and that the dimer conformation is very similar to that of the tetramer but the C terminus of the dimer is more flexible.
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26
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Macrophage migration inhibitory factor: A multifaceted cytokine implicated in multiple neurological diseases. Exp Neurol 2017; 301:83-91. [PMID: 28679106 DOI: 10.1016/j.expneurol.2017.06.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/06/2017] [Accepted: 06/21/2017] [Indexed: 12/12/2022]
Abstract
Macrophage migration inhibitory factor (MIF) is a conserved cytokine found as a homotrimer protein. It is found in a wide spectrum of cell types in the body including neuronal and non-neuronal cells. MIF is implicated in several biological processes; chemo-attraction, cytokine activity, and receptor binding, among other functions. More recently, a chaperone-like activity has been added to its repertoire. In this review, we focus on the implication of MIF in the central nervous system and peripheries, its role in neurological disorders, and the mechanisms by which MIF is regulated. Numerous studies have associated MIF with various disease settings. MIF plays an important role in advocating tumorigenic processes, Alzheimer's disease, and is also upregulated in autism-spectrum disorders and spinal cord injury where it contributes to the severity of the injured area. The protective effect of MIF has been reported in amyotrophic lateral sclerosis by its reduction of aggregated misfolded SOD1, subsequently reducing the severity of this disease. Interestingly, a protective as well as pathological role for MIF has been implicated in stroke and cerebral ischemia, as well as depression. Thus, the role of MIF in neurological disorders appears to be diverse with both beneficial and adversary effects. Furthermore, its modulation is rather complex and it is regulated by different proteins, either on a molecular or protein level. This complexity might be dependent on the pathophysiological context and/or cellular microenvironment. Hence, further clarification of its diverse roles in neurological pathologies is warranted to provide new mechanistic insights which may lead in the future to the development of therapeutic strategies based on MIF, to fight some of these neurological disorders.
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27
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Liu D, Wu WH, Liu YJ, Wu XL, Cao Y, Song B, Li X, Zhang WB. Topology Engineering of Proteins in Vivo Using Genetically Encoded, Mechanically Interlocking SpyX Modules for Enhanced Stability. ACS CENTRAL SCIENCE 2017; 3:473-481. [PMID: 28573210 PMCID: PMC5445526 DOI: 10.1021/acscentsci.7b00104] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 05/11/2023]
Abstract
Recombinant proteins are traditionally limited to linear configuration. Herein, we report in vivo protein topology engineering using highly efficient, mechanically interlocking SpyX modules named AXB and BXA. SpyX modules are protein domains composed of p53dim (X), SpyTag (A), and SpyCatcher (B). The p53dim guides the intertwining of the two nascent protein chains followed by autocatalytic isopeptide bond formation between SpyTag and SpyCatcher to fulfill the interlocking, leading to a variety of backbone topologies. Direct expression of AXB or BXA produces protein catenanes with distinct ring sizes. Recombinant proteins containing SpyX modules are obtained either as mechanically interlocked obligate dimers if the protein of interest is fused to the N- or C-terminus of SpyX modules, or as star proteins if the protein is fused to both N- and C-termini. As examples, cellular syntheses of dimers of (GB1)2 (where GB1 stands for immunoglobulin-binding domain B1 of streptococcal protein G) and of four-arm elastin-like star proteins were demonstrated. Comparison of the catenation efficiencies in different constructs reveals that BXA is generally much more effective than AXB, which is rationalized by the arrangement of three domains in space. Mechanical interlocking induces considerable stability enhancement. Both AXB and BXA have a melting point ∼20 °C higher than the linear controls and the BXA catenane has a melting point ~2 °C higher than the cyclic control BX'A. Notably, four-arm elastin-like star proteins demonstrate remarkable tolerance against trypsin digestion. The SpyX modules provide a convenient and versatile approach to construct unconventional protein topologies via the "assembly-reaction" synergy, which opens a new horizon in protein science for stability enhancement and function reinforcement via topology engineering.
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Affiliation(s)
- Dong Liu
- Key
Laboratory of Polymer Chemistry & Physics of Ministry of Education,
Center for Soft Matter Science and Engineering, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Wen-Hao Wu
- Key
Laboratory of Polymer Chemistry & Physics of Ministry of Education,
Center for Soft Matter Science and Engineering, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Ya-Jie Liu
- Key
Laboratory of Polymer Chemistry & Physics of Ministry of Education,
Center for Soft Matter Science and Engineering, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xia-Ling Wu
- Key
Laboratory of Polymer Chemistry & Physics of Ministry of Education,
Center for Soft Matter Science and Engineering, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yang Cao
- Key
Laboratory of Polymer Chemistry & Physics of Ministry of Education,
Center for Soft Matter Science and Engineering, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Bo Song
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Xiaopeng Li
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Wen-Bin Zhang
- Key
Laboratory of Polymer Chemistry & Physics of Ministry of Education,
Center for Soft Matter Science and Engineering, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Tel: + 86 10 6276 6876. Fax: + 86 10 6275 1710. E-mail:
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28
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Sakaguchi T, Janairo JIB, Lussier-Price M, Wada J, Omichinski JG, Sakaguchi K. Oligomerization enhances the binding affinity of a silver biomineralization peptide and catalyzes nanostructure formation. Sci Rep 2017; 7:1400. [PMID: 28469202 PMCID: PMC5431226 DOI: 10.1038/s41598-017-01442-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/28/2017] [Indexed: 01/27/2023] Open
Abstract
Binding affinity and specificity are crucial factors that influence nanostructure control by biomineralization peptides. In this paper, we analysed the role that the oligomeric state of a silver biomineralization peptide plays in regulating the morphology of silver nanostructure formation. Oligomerization was achieved by conjugating the silver specific TBP biomineralization peptide to the p53 tetramerization domain peptide (p53Tet). Interestingly, the TBP-p53Tet tetrameric peptide acted as a growth catalyst, controlling silver crystal growth, which resulted in the formation of hexagonal silver nanoplates without consuming the peptide. The TBP-p53Tet peptide caps the surface of the silver crystals, which enhances crystal growth on specific faces and thereby regulates silver nanostructure formation in a catalytic fashion. The present findings not only provide an efficient strategy for controlling silver nanostructure formation by biomineralization peptides, but they also demonstrate that in this case the oligomeric peptides play a unique catalytic role.
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Affiliation(s)
- Tatsuya Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jose Isagani B Janairo
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Mathieu Lussier-Price
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Junya Wada
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - James G Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Kazuyasu Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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29
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Kamada R, Toguchi Y, Nomura T, Imagawa T, Sakaguchi K. Tetramer formation of tumor suppressor protein p53: Structure, function, and applications. Biopolymers 2017; 106:598-612. [PMID: 26572807 DOI: 10.1002/bip.22772] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 01/10/2023]
Abstract
Tetramer formation of p53 is essential for its tumor suppressor function. p53 not only acts as a tumor suppressor protein by inducing cell cycle arrest and apoptosis in response to genotoxic stress, but it also regulates other cellular processes, including autophagy, stem cell self-renewal, and reprogramming of differentiated cells into stem cells, immune system, and metastasis. More than 50% of human tumors have TP53 gene mutations, and most of them are missense mutations that presumably reduce tumor suppressor activity of p53. This review focuses on the role of the tetramerization (oligomerization), which is modulated by the protein concentration of p53, posttranslational modifications, and/or interactions with its binding proteins, in regulating the tumor suppressor function of p53. Functional control of p53 by stabilizing or inhibiting oligomer formation and its bio-applications are also discussed. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 598-612, 2016.
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Affiliation(s)
- Rui Kamada
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yu Toguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Takao Nomura
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Toshiaki Imagawa
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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30
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Martin TG, Bharat TAM, Joerger AC, Bai XC, Praetorius F, Fersht AR, Dietz H, Scheres SHW. Design of a molecular support for cryo-EM structure determination. Proc Natl Acad Sci U S A 2016; 113:E7456-E7463. [PMID: 27821763 PMCID: PMC5127339 DOI: 10.1073/pnas.1612720113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air-water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.
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Affiliation(s)
- Thomas G Martin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Tanmay A M Bharat
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Andreas C Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Xiao-Chen Bai
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Florian Praetorius
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom;
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31
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Beckerman R, Yoh K, Mattia-Sansobrino M, Zupnick A, Laptenko O, Karni-Schmidt O, Ahn J, Byeon IJ, Keezer S, Prives C. Lysines in the tetramerization domain of p53 selectively modulate G1 arrest. Cell Cycle 2016; 15:1425-38. [PMID: 27210019 DOI: 10.1080/15384101.2016.1170270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Functional in a tetrameric state, the protein product of the p53 tumor suppressor gene confers its tumor-suppressive activity by transactivating genes which promote cell-cycle arrest, senescence, or programmed cell death. How p53 distinguishes between these divergent outcomes is still a matter of considerable interest. Here we discuss the impact of 2 mutations in the tetramerization domain that confer unique properties onto p53. By changing lysines 351 and 357 to arginine, thereby blocking all post-translational modifications of these residues, DNA binding and transcriptional regulation by p53 remain virtually unchanged. On the other hand, by changing these lysines to glutamine (2KQ-p53), thereby neutralizing their positive charge and potentially mimicking acetylation, p53 is impaired in the induction of cell cycle arrest and yet can still effectively induce cell death. Surprisingly, when 2KQ-p53 is expressed at high levels in H1299 cells, it can bind to and transactivate numerous p53 target genes including p21, but not others such as miR-34a and cyclin G1 to the same extent as wild-type p53. Our findings show that strong induction of p21 is not sufficient to block H1299 cells in G1, and imply that modification of one or both of the lysines within the tetramerization domain may serve as a mechanism to shunt p53 from inducing cell cycle arrest.
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Affiliation(s)
| | - Kathryn Yoh
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | | | | | - Oleg Laptenko
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Orit Karni-Schmidt
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Jinwoo Ahn
- b Department of Structural Biology , University of Pittsburgh , Pittsburgh , PA , USA
| | - In-Ja Byeon
- b Department of Structural Biology , University of Pittsburgh , Pittsburgh , PA , USA
| | - Susan Keezer
- c Cell Signaling Technology, Inc. , Danvers , MA , USA
| | - Carol Prives
- a Department of Biological Sciences , Columbia University , New York , NY , USA
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32
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Khalili M, Wales DJ. Computer Simulations of Peptides from the p53 DNA Binding Domain. J Chem Theory Comput 2015; 5:1380-92. [PMID: 26609726 DOI: 10.1021/ct8005387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have studied the dynamics and thermodynamics of two of the four evolutionarily conserved segments from the p53 DNA binding domain, using molecular dynamics and replica exchange simulations. These two regions contain well-defined elements of secondary structure (a β hairpin for region II and an α helix for region V) and bind to DNA in the intact protein. They are also mutational hot spots. The goal of our study was to determine the stability and folding propensity of these peptides in isolation. We used three force fields and solvent models (CHARMM19 with EEF1, CHARMM27 with GBMV, GROMOS96 with SPC). The predicted stability, folding propensity, and secondary structures depend upon the potential. Secondary structure predictors identify helical propensity for region II, in agreement with one of the force fields (CHARMM/GBMV). However, the other two potentials favor β structure for this peptide, although the conformations may differ from the crystal. For region V secondary structure predictions are unclear. Only one force field (CHARMM/GBMV) produces low-lying free energy minima that retain some of the α helical structure from the crystal structure. The other two potentials appear to favor β structure for this peptide.
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Affiliation(s)
- Mey Khalili
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, MITRE Corporation, 7515 Colshire Drive, McLean, Virginia 22102, and Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, MITRE Corporation, 7515 Colshire Drive, McLean, Virginia 22102, and Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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33
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Joerger AC, Wilcken R, Andreeva A. Tracing the evolution of the p53 tetramerization domain. Structure 2015; 22:1301-1310. [PMID: 25185827 PMCID: PMC4155161 DOI: 10.1016/j.str.2014.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 10/25/2022]
Abstract
The tetrameric transcription factors p53, p63, and p73 evolved from a common ancestor and play key roles in tumor suppression and development. Surprisingly, p63 and p73 require a second helix in their tetramerization domain for the formation of stable tetramers that is absent in human p53, raising questions about the evolutionary processes leading to diversification. Here we determined the crystal structure of the zebrafish p53 tetramerization domain, which contains a second helix, reminiscent of p63 and p73, combined with p53-like features. Through comprehensive phylogenetic analyses, we systematically traced the evolution of vertebrate p53 family oligomerization domains back to the beginning of multicellular life. We provide evidence that their last common ancestor also had an extended p63/p73-like domain and pinpoint evolutionary events that shaped this domain during vertebrate radiation. Domain compaction and transformation of a structured into a flexible, intrinsically disordered region may have contributed to the expansion of the human p53 interactome.
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Affiliation(s)
- Andreas C Joerger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Rainer Wilcken
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Antonina Andreeva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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34
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Arlt C, Ihling CH, Sinz A. Structure of full-length p53 tumor suppressor probed by chemical cross-linking and mass spectrometry. Proteomics 2015; 15:2746-55. [PMID: 25728495 DOI: 10.1002/pmic.201400549] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/15/2015] [Accepted: 02/24/2015] [Indexed: 11/12/2022]
Abstract
The tumor suppressor p53 presents a great challenge for 3D structural analysis due to its inherent flexibility. In this work, we gained insight into the structure of full-length wild-type human p53 in solution by chemical cross-linking/MS. This approach allowed us obtaining structural information of free wild-type p53 in solution without making use of the ultrastable quadruple p53 variant. The cross-links within one p53 monomer are in good agreement with the small-angle X-ray scattering based model of full-length p53. Our cross-linking data between different p53 molecules in the tetramer however indicate a large degree of flexibility in the C-terminal regulatory domain of full-length p53 in the absence of DNA. The cross-links suggest that the C-terminal regulatory domains are much closer to each other, resulting in a more compact arrangement of the p53 tetramer than perceived by the small-angle X-ray scattering model.
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Affiliation(s)
- Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Leroy B, Anderson M, Soussi T. TP53 mutations in human cancer: database reassessment and prospects for the next decade. Hum Mutat 2014; 35:672-88. [PMID: 24665023 DOI: 10.1002/humu.22552] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/04/2014] [Indexed: 12/18/2022]
Abstract
More than 50% of human tumors carry TP53 gene mutations and in consequence more than 45,000 somatic and germline mutations have been gathered in the UMD TP53 database (http://p53.fr). Analyses of these mutations have been invaluable for bettering our knowledge on the structure-function relationships within the TP53 protein and the high degree of heterogeneity of the various TP53 mutants in human cancer. In this review, we discuss how with the release of the sequences of thousands of tumor genomes issued from high-throughput sequencing, the description of novel TP53 mutants is now reaching a plateau indicating that we are close to the full set of mutants that target the elusive tumor-suppressive activity of this protein. We performed an extensive and thorough analysis of the TP53 mutation database, focusing particularly on specific sets of mutations that were overlooked in the past because of their low frequencies, for example, synonymous mutations, splice mutations, or mutations-targeting residues subject to posttranslational modifications. We also discuss the evolution of the statistical methods used to differentiate TP53 passenger mutations and artifactual data from true mutations, a process vital to the release of an accurate TP53 mutation database that will in turn be an invaluable tool for both clinicians and researchers.
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Affiliation(s)
- Bernard Leroy
- Université Pierre et Marie Curie-Paris 6, Paris, 75005, France
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36
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Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC. Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases. Chem Rev 2014; 114:6844-79. [PMID: 24830552 PMCID: PMC4100540 DOI: 10.1021/cr400713r] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Vrushank Davé
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, United States
| | - Prerna Malaney
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Steven J. Metallo
- Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, United States
| | - Ravi Ramesh Pathak
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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TP53 mutations occur in 15.7% of ALL and are associated with MYC-rearrangement, low hypodiploidy, and a poor prognosis. Blood 2014; 124:251-8. [PMID: 24829203 DOI: 10.1182/blood-2014-02-558833] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
TP53 is the most extensively studied gene in cancer. However, data on frequency and the prognostic impact of TP53 mutations in acute lymphoblastic leukemia (ALL) remain scarce. Thus, we aimed at identifying the mutation frequency of TP53, its association with cytogenetic subgroups, and its impact on survival in a large cohort of 625 patients with ALL. Our data revealed an overall mutation incidence of 15.7%, which increases with age. Correlation with cytogenetic subgroups showed that mutations were most frequent in ALL with low hypodiploidy or MYC-rearrangements. Furthermore, for a large number of patients, both TP53 alleles were altered, either by 2 TP53 mutations (12%) or by a TP53 mutation and a TP53 deletion in the second allele (39%). A high TP53 mutation load was correlated to low hypodiploidy, high hyperdiploidy, and a complex karyotype. Moreover, a higher mutation load was found in B-lineage ALL compared with T-lineage ALL. Similar to other cancers, the median overall survival was significantly shorter in patients with TP53 mutation compared with patients with wild-type TP53. This effect was especially pronounced when both TP53 alleles were affected, either by 2 TP53 mutations or by both a mutation and an accompanying TP53 deletion.
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38
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Lang V, Pallara C, Zabala A, Lobato-Gil S, Lopitz-Otsoa F, Farrás R, Hjerpe R, Torres-Ramos M, Zabaleta L, Blattner C, Hay RT, Barrio R, Carracedo A, Fernandez-Recio J, Rodríguez MS, Aillet F. Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity. Mol Oncol 2014; 8:1026-42. [PMID: 24816189 DOI: 10.1016/j.molonc.2014.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 03/19/2014] [Accepted: 04/02/2014] [Indexed: 11/26/2022] Open
Abstract
The tumor suppressor p53 regulates the expression of genes involved in cell cycle progression, senescence and apoptosis. Here, we investigated the effect of single point mutations in the oligomerization domain (OD) on tetramerization, transcription, ubiquitylation and stability of p53. As predicted by docking and molecular dynamics simulations, p53 OD mutants show functional defects on transcription, Mdm2-dependent ubiquitylation and 26S proteasome-mediated degradation. However, mutants unable to form tetramers are well degraded by the 20S proteasome. Unexpectedly, despite the lower structural stability compared to WT p53, p53 OD mutants form heterotetramers with WT p53 when expressed transiently or stably in cells wild type or null for p53. In consequence, p53 OD mutants interfere with the capacity of WT p53 tetramers to be properly ubiquitylated and result in changes of p53-dependent protein expression patterns, including the pro-apoptotic proteins Bax and PUMA under basal and adriamycin-induced conditions. Importantly, the patient derived p53 OD mutant L330R (OD1) showed the more severe changes in p53-dependent gene expression. Thus, in addition to the well-known effects on p53 stability, ubiquitylation defects promote changes in p53-dependent gene expression with implications on some of its functions.
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Affiliation(s)
- Valérie Lang
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | - Chiara Pallara
- Joint BSC-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Carrer Jordi Girona 29, 08034 Barcelona, Spain.
| | - Amaia Zabala
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Sofia Lobato-Gil
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | | | - Rosa Farrás
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012 Valencia, Spain.
| | - Roland Hjerpe
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Monica Torres-Ramos
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Lorea Zabaleta
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | - Christine Blattner
- Karlsruher Institute of Technology, Institute of Toxicology and Genetics, Fritz-Erler-Straße 23, 76133 Karlsruhe, Germany.
| | - Ronald T Hay
- Center for Interdisciplinary Research, School of Life Sciences, University of Dundee, Dow Street, DD15EH Scotland, United Kingdom.
| | - Rosa Barrio
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Arkaitz Carracedo
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain; Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, E-48080 Bilbao, Spain.
| | - Juan Fernandez-Recio
- Joint BSC-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Carrer Jordi Girona 29, 08034 Barcelona, Spain.
| | - Manuel S Rodríguez
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | - Fabienne Aillet
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
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Janairo JIB, Sakaguchi T, Hara K, Fukuoka A, Sakaguchi K. Effects of biomineralization peptide topology on the structure and catalytic activity of Pd nanomaterials. Chem Commun (Camb) 2014; 50:9259-62. [DOI: 10.1039/c4cc04350b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Three dimensional porous structures of Pd were formed through a designed peptide with precisely defined topological features. The hierarchical materials exhibited excellent catalytic performance in the reduction of nitrophenol isomers with preference for the meta isomer.
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Affiliation(s)
| | - Tatsuya Sakaguchi
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-080, Japan
| | - Kenji Hara
- Catalysis Research Center
- Hokkaido University
- Sapporo 001-0021, Japan
| | - Atsushi Fukuoka
- Catalysis Research Center
- Hokkaido University
- Sapporo 001-0021, Japan
| | - Kazuyasu Sakaguchi
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-080, Japan
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40
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Chillemi G, Davidovich P, D'Abramo M, Mametnabiev T, Garabadzhiu AV, Desideri A, Melino G. Molecular dynamics of the full-length p53 monomer. Cell Cycle 2013; 12:3098-108. [PMID: 23974096 DOI: 10.4161/cc.26162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The p53 protein is frequently mutated in a very large proportion of human tumors, where it seems to acquire gain-of-function activity that facilitates tumor onset and progression. A possible mechanism is the ability of mutant p53 proteins to physically interact with other proteins, including members of the same family, namely p63 and p73, inactivating their function. Assuming that this interaction might occurs at the level of the monomer, to investigate the molecular basis for this interaction, here, we sample the structural flexibility of the wild-type p53 monomeric protein. The results show a strong stability up to 850 ns in the DNA binding domain, with major flexibility in the N-terminal transactivations domains (TAD1 and TAD2) as well as in the C-terminal region (tetramerization domain). Several stable hydrogen bonds have been detected between N-terminal or C-terminal and DNA binding domain, and also between N-terminal and C-terminal. Essential dynamics analysis highlights strongly correlated movements involving TAD1 and the proline-rich region in the N-terminal domain, the tetramerization region in the C-terminal domain; Lys120 in the DNA binding region. The herein presented model is a starting point for further investigation of the whole protein tetramer as well as of its mutants.
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41
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Yun HY, Huh SH. Fluorescence Study Gives a Hint to Understand How the p53 DNA Binding Domain Recognizes Its Specific Binding Site on DNA Fragments. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.4.1300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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Domain-domain interactions in full-length p53 and a specific DNA complex probed by methyl NMR spectroscopy. Proc Natl Acad Sci U S A 2012; 109:15752-6. [PMID: 22972749 DOI: 10.1073/pnas.1214176109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The tumor suppressor p53 is a homotetramer of 4 × 393 residues. Its core domain and tetramerization domain are linked and flanked by intrinsically disordered sequences, which hinder its full structural characterization. There is an outstanding problem of the state of the tetramerization domain. Structural studies on the isolated tetramerization domain show it is in a folded tetrameric conformation, but there are conflicting models from electron microscopy of the full-length protein, one of which proposes that the domain is not tetramerically folded and the tetrameric protein is stabilized by interactions between the N and C termini. Here, we present methyl-transverse relaxation optimized NMR spectroscopy (methyl-TROSY) investigations on the full-length and separate domains of the protein with its methionine residues enriched with (13)C to probe its quaternary structure. We obtained high-quality spectra of both the full-length tetrameric p53 and its DNA complex, observing the environment at 11 specific methyl sites. The tetramerization domain was as tetramerically folded in the full-length constructs as in the isolated domain. The N and C termini were intrinsically disordered in both the full-length protein and its complex with a 20-residue specific DNA sequence. Additionally, we detected in the interface of the core (DNA-binding) and N-terminal parts of the protein a slow conformational exchange process that was modulated by specific recognition of DNA, indicating allosteric processes.
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43
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Wada J, Kamada R, Imagawa T, Chuman Y, Sakaguchi K. Inhibition of tumor suppressor protein p53-dependent transcription by a tetramerization domain peptide via hetero-oligomerization. Bioorg Med Chem Lett 2012; 22:2780-3. [PMID: 22429466 DOI: 10.1016/j.bmcl.2012.02.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 12/28/2022]
Abstract
Tumor suppressor protein p53 induces cell cycle arrest, apoptosis, and senescence in response to cellular stresses. The p53 tetramer formation is essential for its functions. Despite of these crucial functions of p53 for integrity of genome, activation of the p53 signal pathway causes low induced pluripotent stem (iPS) cell generation efficiency. In this study, we report transient inhibition of p53-dependent transcription using a p53 tetramerization domain peptide that contains cell penetrating and nuclear localization signals. The peptide was efficiently introduced into cells and inhibited p21 expression via hetero-tetramerization with endogenous p53 protein. This method can be applied towards safe and efficient iPS cell generation.
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Affiliation(s)
- Junya Wada
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-ku, Sapporo, Japan
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44
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Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol 2012; 30:159-64. [PMID: 22252508 DOI: 10.1038/nbt.2106] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/19/2011] [Indexed: 01/13/2023]
Abstract
To better understand the molecular mechanisms and genetic basis of human disease, we systematically examine relationships between 3,949 genes, 62,663 mutations and 3,453 associated disorders by generating a three-dimensional, structurally resolved human interactome. This network consists of 4,222 high-quality binary protein-protein interactions with their atomic-resolution interfaces. We find that in-frame mutations (missense point mutations and in-frame insertions and deletions) are enriched on the interaction interfaces of proteins associated with the corresponding disorders, and that the disease specificity for different mutations of the same gene can be explained by their location within an interface. We also predict 292 candidate genes for 694 unknown disease-to-gene associations with proposed molecular mechanism hypotheses. This work indicates that knowledge of how in-frame disease mutations alter specific interactions is critical to understanding pathogenesis. Structurally resolved interaction networks should be valuable tools for interpreting the wealth of data being generated by large-scale structural genomics and disease association studies.
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Affiliation(s)
- Xiujuan Wang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
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45
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Natan E, Joerger AC. Structure and kinetic stability of the p63 tetramerization domain. J Mol Biol 2011; 415:503-13. [PMID: 22100306 PMCID: PMC3277882 DOI: 10.1016/j.jmb.2011.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/27/2011] [Accepted: 11/03/2011] [Indexed: 12/14/2022]
Abstract
The p53 family of transcription factors--comprising p53, p63 and p73--plays an important role in tumor prevention and development. Essential to their function is the formation of tetramers, allowing cooperative binding to their DNA response elements. We solved crystal structures of the human p63 tetramerization domain, showing that p63 forms a dimer of dimers with D₂ symmetry composed of highly intertwined monomers. The primary dimers are formed via an intramolecular β-sheet and hydrophobic helix packing (H1), a hallmark of all p53 family members. Like p73, but unlike p53, p63 requires a second helix (H2) to stabilize the architecture of the tetramer. In order to investigate the impact of structural differences on tetramer stability, we measured the subunit exchange reaction of p53 family homotetramers by nanoflow electrospray mass spectrometry. There were differences in both the kinetics and the pattern of the exchange reaction, with the p53 and p63 tetramers exhibiting much faster exchange kinetics than p73. The structural similarity between p63 and p73 rationalizes previous observations that p63 and p73 form mixed tetramers, and the kinetic data reveal the dissociation of the p73 homotetramers as the rate-limiting step for heterotetramer formation. Differential stability of the tetramers may play an important role in the cross talk between different isoforms and regulation of p53, p63 and p73 function in the cell cycle.
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Affiliation(s)
- Eviatar Natan
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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46
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Nomura T, Kamada R, Ito I, Sakamoto K, Chuman Y, Ishimori K, Shimohigashi Y, Sakaguchi K. Probing phenylalanine environments in oligomeric structures with pentafluorophenylalanine and cyclohexylalanine. Biopolymers 2011; 95:410-9. [PMID: 21280026 DOI: 10.1002/bip.21594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Stabilization of protein structures and protein-protein interactions are critical in the engineering of industrially useful enzymes and in the design of pharmaceutically valuable ligands. Hydrophobic interactions involving phenylalanine residues play crucial roles in protein stability and protein-protein/peptide interactions. To establish an effective method to explore the hydrophobic environments of phenylalanine residues, we present a strategy that uses pentafluorophenylalanine (F5Phe) and cyclohexylalanine (Cha). In this study, substitution of F5Phe or Cha for three Phe residues at positions 328, 338, and 341 in the tetramerization domain of the tumor suppressor protein p53 was performed. These residues are located at the interfaces of p53-p53 interactions and are important in the stabilization of the tetrameric structure. The stability of the p53 tetrameric structure did not change significantly when F5Phe-containing peptides at positions Phe328 or Phe338 were used. In contrast, the substitution of Cha for Phe341 in the hydrophobic core enhanced the stability of the tetrameric structure with a T(m) value of 100 degrees C. Phe328 and Phe338 interact with each other through pi-interactions, whereas Phe341 is buried in the surrounding alkyl side-chains of the hydrophobic core of the p53 tetramerization domain. Furthermore, high pressure-assisted denaturation analysis indicated improvement in the occupancy of the hydrophobic core. Considerable stabilization of the p53 tetramer was achieved by filling the identified cavity in the hydrophobic core of the p53 tetramer. The results indicate the status of the Phe residues, indicating that the "pair substitution" of Cha and F5Phe is highly suitable for probing the environments of Phe residues.
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Affiliation(s)
- Takao Nomura
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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47
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Interaction of the p53 DNA-binding domain with its n-terminal extension modulates the stability of the p53 tetramer. J Mol Biol 2011; 409:358-68. [PMID: 21457718 PMCID: PMC3176915 DOI: 10.1016/j.jmb.2011.03.047] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/22/2011] [Accepted: 03/23/2011] [Indexed: 12/30/2022]
Abstract
The tetrameric tumor suppressor p53 plays a pivotal role in the control of the cell cycle and provides a paradigm for an emerging class of oligomeric, multidomain proteins with structured and intrinsically disordered regions. Many of its biophysical and functional properties have been extrapolated from truncated variants, yet the exact structural and functional role of certain segments of the protein is unclear. We found from NMR and X-ray crystallography that the DNA-binding domain (DBD) of human p53, usually defined as residues 94-292, extends beyond these domain boundaries. Trp91, in the hinge region between the disordered proline-rich N-terminal domain and the DBD, folds back onto the latter and has a cation-π interaction with Arg174. These additional interactions increase the melting temperature of the DBD by up to 2 °C and inhibit aggregation of the p53 tetramer. They also modulate the dissociation of the p53 tetramer. The absence of the Trp91/Arg174 packing presumably allows nonnative DBD-DBD interactions that both nucleate aggregation and stabilize the interface. These data have important implications for studies of multidomain proteins in general, highlighting the fact that weak ordered-disordered domain interactions can modulate the properties of proteins of complex structure.
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48
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An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity. EMBO J 2011; 30:2167-76. [PMID: 21522129 DOI: 10.1038/emboj.2011.127] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/24/2011] [Indexed: 01/23/2023] Open
Abstract
The p53 tumour suppressor gene, the most frequently mutated gene in human cancer, encodes a transcription factor that contains sequence-specific DNA binding and homo-tetramerization domains. Interestingly, the affinities of p53 for specific and non-specific DNA sites differ by only one order of magnitude, making it hard to understand how this protein recognizes its specific DNA targets in vivo. We describe here the structure of a p53 polypeptide containing both the DNA binding and oligomerization domains in complex with DNA. The structure reveals that sequence-specific DNA binding proceeds via an induced fit mechanism that involves a conformational switch in loop L1 of the p53 DNA binding domain. Analysis of loop L1 mutants demonstrated that the conformational switch allows DNA binding off-rates to be regulated independently of affinities. These results may explain the universal prevalence of conformational switching in sequence-specific DNA binding proteins and suggest that proteins like p53 rely more on differences in binding off-rates, than on differences in affinities, to recognize their specific DNA sites.
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49
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Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. J Am Chem Soc 2011; 133:6288-98. [PMID: 21466200 PMCID: PMC3080108 DOI: 10.1021/ja111318m] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR can be difficult due to slow tumbling of the system and the difficulty in identifying NOE interactions across protein interfaces. Here, we present an automated method (RosettaOligomers) for determining the solution structures of oligomeric systems using only chemical shifts, sparse NOEs, and domain orientation restraints from residual dipolar couplings (RDCs) without a need for a previously determined structure of the monomeric subunit. The method integrates previously developed Rosetta protocols for solving the structures of monomeric proteins using sparse NMR data and for predicting the structures of both nonintertwined and intertwined symmetric oligomers. We illustrated the performance of the method using a benchmark set of nine protein dimers, one trimer, and one tetramer with available experimental data and various interface topologies. The final converged structures are found to be in good agreement with both experimental data and previously published high-resolution structures. The new approach is more readily applicable to large oligomeric systems than conventional structure-determination protocols, which often require a large number of NOEs, and will likely become increasingly relevant as more high-molecular weight systems are studied by NMR.
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Affiliation(s)
- Nikolaos G Sgourakis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA
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50
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Chun PW, Lewis MS. Planck-Benzinger thermal work function: thermodynamic characterization of the carboxy-terminus of p53 peptide fragments. Protein J 2010; 29:617-30. [PMID: 21086029 DOI: 10.1007/s10930-010-9286-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The thermodynamic parameters for six p53 carboxy-terminus peptide fragments as determined by analytical ultracentrifugal analysis were compared over the experimental temperature range of 275-310 K to evaluate the Gibbs free energy change as a function of temperature, ΔG°(T), from 0 to 400 K using our general linear third-order fitting function, ΔG°(T) = α + βT² + γT³. Data obtained at the typical experimental temperature range are not sufficient to accurately describe the variations observed in the oligomerization of these p53 fragments. It is necessary to determine a number of thermodynamic parameters, all of which can be precisely assessed using this general third-order linear fitting function. These are the heat of reaction, innate temperature-invariant enthalpy, compensatory temperatures and the thermodynamic molecular switch occurring at the thermal set point. This methodology can be used to distinguish the characteristic structure and stability of p53 carboxy-terminal fragments or other p53 mutants. It should be used for the thermodynamic characterization of any interacting biological system.
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Affiliation(s)
- Paul W Chun
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610-0245, USA.
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