1
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Maiti S, Singh A, Maji T, Saibo NV, De S. Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. Curr Res Struct Biol 2024; 7:100138. [PMID: 38707546 PMCID: PMC11068507 DOI: 10.1016/j.crstbi.2024.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 05/07/2024] Open
Abstract
Eukaryotic proteins often feature long stretches of amino acids that lack a well-defined three-dimensional structure and are referred to as intrinsically disordered proteins (IDPs) or regions (IDRs). Although these proteins challenge conventional structure-function paradigms, they play vital roles in cellular processes. Recent progress in experimental techniques, such as NMR spectroscopy, single molecule FRET, high speed AFM and SAXS, have provided valuable insights into the biophysical basis of IDP function. This review discusses the advancements made in these techniques particularly for the study of disordered regions in proteins. In NMR spectroscopy new strategies such as 13C detection, non-uniform sampling, segmental isotope labeling, and rapid data acquisition methods address the challenges posed by spectral overcrowding and low stability of IDPs. The importance of various NMR parameters, including chemical shifts, hydrogen exchange rates, and relaxation measurements, to reveal transient secondary structures within IDRs and IDPs are presented. Given the high flexibility of IDPs, the review outlines NMR methods for assessing their dynamics at both fast (ps-ns) and slow (μs-ms) timescales. IDPs exert their functions through interactions with other molecules such as proteins, DNA, or RNA. NMR-based titration experiments yield insights into the thermodynamics and kinetics of these interactions. Detailed study of IDPs requires multiple experimental techniques, and thus, several methods are described for studying disordered proteins, highlighting their respective advantages and limitations. The potential for integrating these complementary techniques, each offering unique perspectives, is explored to achieve a comprehensive understanding of IDPs.
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Affiliation(s)
| | - Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Tanisha Maji
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Nikita V. Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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2
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Shankaranarayana AH, Meduri B, Pujar GV, Hariharapura RC, Sethu AK, Singh M, Bidye D. Restoration of p53 functions by suppression of mortalin-p53 sequestration: an emerging target in cancer therapy. Future Med Chem 2023; 15:2087-2112. [PMID: 37877348 DOI: 10.4155/fmc-2023-0061] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 10/26/2023] Open
Abstract
Functional inactivation of wild-type p53 is a major trait of cancerous cells. In many cases, such inactivation occurs by either TP53 gene mutations or due to overexpression of p53 binding partners. This review focuses on an overexpressed p53 binding partner called mortalin, a mitochondrial heat shock protein that sequesters both wild-type and mutant p53 in malignant cells due to changes in subcellular localization. Clinical evidence suggests a drastic depletion of the overall survival time of cancer patients with high mortalin expression. Therefore, mortalin-p53 sequestration inhibitors could be game changers in improving overall survival rates. This review explores the consequences of mortalin overexpression and challenges, status and strategies for accelerating drug discovery to suppress mortalin-p53 sequestration.
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Affiliation(s)
- Akshatha Handattu Shankaranarayana
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Bhagyalalitha Meduri
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Gurubasavaraj Veeranna Pujar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Raghu Chandrashekar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Arun Kumar Sethu
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Manisha Singh
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Durgesh Bidye
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
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3
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Nicolini F, Todorovski T, Puig E, Díaz-Lobo M, Vilaseca M, García J, Andreu D, Giralt E. How Do Cancer-Related Mutations Affect the Oligomerisation State of the p53 Tetramerisation Domain? Curr Issues Mol Biol 2023; 45:4985-5004. [PMID: 37367066 DOI: 10.3390/cimb45060317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Tumour suppressor p53 plays a key role in the development of cancer and has therefore been widely studied in recent decades. While it is well known that p53 is biologically active as a tetramer, the tetramerisation mechanism is still not completely understood. p53 is mutated in nearly 50% of cancers, and mutations can alter the oligomeric state of the protein, having an impact on the biological function of the protein and on cell fate decisions. Here, we describe the effects of a number of representative cancer-related mutations on tetramerisation domain (TD) oligomerisation defining a peptide length that permits having a folded and structured domain, thus avoiding the effect of the flanking regions and the net charges at the N- and C-terminus. These peptides have been studied under different experimental conditions. We have applied a variety of techniques, including circular dichroism (CD), native mass spectrometry (MS) and high-field solution NMR. Native MS allows us to detect the native state of complexes maintaining the peptide complexes intact in the gas phase; the secondary and quaternary structures were analysed in solution by NMR, and the oligomeric forms were assigned by diffusion NMR experiments. A significant destabilising effect and a variable monomer population were observed for all the mutants studied.
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Affiliation(s)
- Federica Nicolini
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Toni Todorovski
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Puig
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mireia Díaz-Lobo
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - David Andreu
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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4
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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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5
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Wang H, Guo M, Wei H, Chen Y. Targeting p53 pathways: mechanisms, structures, and advances in therapy. Signal Transduct Target Ther 2023; 8:92. [PMID: 36859359 PMCID: PMC9977964 DOI: 10.1038/s41392-023-01347-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/19/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
The TP53 tumor suppressor is the most frequently altered gene in human cancers, and has been a major focus of oncology research. The p53 protein is a transcription factor that can activate the expression of multiple target genes and plays critical roles in regulating cell cycle, apoptosis, and genomic stability, and is widely regarded as the "guardian of the genome". Accumulating evidence has shown that p53 also regulates cell metabolism, ferroptosis, tumor microenvironment, autophagy and so on, all of which contribute to tumor suppression. Mutations in TP53 not only impair its tumor suppressor function, but also confer oncogenic properties to p53 mutants. Since p53 is mutated and inactivated in most malignant tumors, it has been a very attractive target for developing new anti-cancer drugs. However, until recently, p53 was considered an "undruggable" target and little progress has been made with p53-targeted therapies. Here, we provide a systematic review of the diverse molecular mechanisms of the p53 signaling pathway and how TP53 mutations impact tumor progression. We also discuss key structural features of the p53 protein and its inactivation by oncogenic mutations. In addition, we review the efforts that have been made in p53-targeted therapies, and discuss the challenges that have been encountered in clinical development.
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Affiliation(s)
- Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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6
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Aguilar A, Wang S. Therapeutic Strategies to Activate p53. Pharmaceuticals (Basel) 2022; 16:24. [PMID: 36678521 PMCID: PMC9866379 DOI: 10.3390/ph16010024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
The p53 protein has appropriately been named the "guardian of the genome". In almost all human cancers, the powerful tumor suppressor function of p53 is compromised by a variety of mechanisms, including mutations with either loss of function or gain of function and inhibition by its negative regulators MDM2 and/or MDMX. We review herein the progress made on different therapeutic strategies for targeting p53.
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Affiliation(s)
- Angelo Aguilar
- The Rogel Cancer Center, Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- The Rogel Cancer Center, Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Solares MJ, Jonaid GM, Luqiu WY, Berry S, Khadela J, Liang Y, Evans MC, Pridham KJ, Dearnaley WJ, Sheng Z, Kelly DF. High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials. Chembiochem 2022; 23:e202200310. [PMID: 35789183 PMCID: PMC9574649 DOI: 10.1002/cbic.202200310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Indexed: 11/06/2022]
Abstract
Mutations in tumor suppressor genes, such as Tumor Protein 53 (TP53), are heavily implicated in aggressive cancers giving rise to gain- and loss-of-function phenotypes. While individual domains of the p53 protein have been studied extensively, structural information for full-length p53 remains incomplete. Functionalized microprocessor chips (microchips) with properties amenable to electron microscopy permitted us to visualize complete p53 assemblies for the first time. The new structures revealed p53 in an inactive dimeric state independent of DNA binding. Residues located at the protein-protein interface corresponded with modification sites in cancer-related hot spots. Changes in these regions may amplify the toxic effects of clinical mutations. Taken together, these results contribute advances in technology and imaging approaches to decode native protein models in different states of activation.
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Affiliation(s)
- Maria J Solares
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - William Y Luqiu
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Janki Khadela
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yanping Liang
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016, USA
| | - Madison C Evans
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin J Pridham
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhi Sheng
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
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8
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Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency. Int J Mol Sci 2022; 23:ijms23147960. [PMID: 35887312 PMCID: PMC9316806 DOI: 10.3390/ijms23147960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
The formation of a tetrameric assembly is essential for the ability of the tumor suppressor protein p53 to act as a transcription factor. Such a quaternary conformation is driven by a specific tetramerization domain, separated from the central DNA-binding domain by a flexible linker. Despite the distance, functional crosstalk between the two domains has been reported. This phenomenon can explain the pathogenicity of some inherited or somatically acquired mutations in the tetramerization domain, including the widespread R337H missense mutation present in the population in south Brazil. In this work, we combined computational predictions through extended all-atom molecular dynamics simulations with functional assays in a genetically defined yeast-based model system to reveal structural features of p53 tetramerization domains and their transactivation capacity and specificity. In addition to the germline and cancer-associated R337H and R337C, other rationally designed missense mutations targeting a significant salt-bridge interaction that stabilizes the p53 tetramerization domain were studied (i.e., R337D, D352R, and the double-mutation R337D plus D352R). The simulations revealed a destabilizing effect of the pathogenic mutations within the p53 tetramerization domain and highlighted the importance of electrostatic interactions between residues 337 and 352. The transactivation assay, performed in yeast by tuning the expression of wild-type and mutant p53 proteins, revealed that p53 tetramerization mutations could decrease the transactivation potential and alter transactivation specificity, in particular by better tolerating negative features in weak DNA-binding sites. These results establish the effect of naturally occurring variations at positions 337 and 352 on p53’s conformational stability and function.
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VATANSEVER B, AYGÜNEŞ JAFARİ D, GÜLER KARA H, SEVİNÇ E, KAYMAZ B, ALP G, ŞAHİN F, SAYDAM G, KOSOVA B. Importance of p53 gene polymorphisms in myelodysplastic syndrome disease. EGE TIP DERGISI 2022. [DOI: 10.19161/etd.1127363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim: Myelodysplastic syndrome (MDS) is a clonal disease with a high risk of conversion to acute myeloid leukemia, characterized by increased apoptosis and decreased hematopoiesis. The pathogenesis of MDS has not been fully explained. ~50% of cases have abnormal karyotype and this rate is around 80% in secondary MDS.
The p53 protein is an important regulator of stem cell homeostasis and is involved in a range of cellular events such as cell cycle regulation, apoptotic and inflammatory response. The TP53 gene, which has important roles in maintaining genomic integrity, is frequently mutated in cancers; however, some gene polymorphisms are known to be associated with cancer, as well as mutations. Our aim in the study is to determine the prevalence of four common p53 single nucleotide polymorphisms in MDS and their effects on disease development. For this reason, 100 cases followed up with the diagnosis of MDS or newly diagnosed in Ege University Faculty of Medicine, Department of Internal Medicine, Department of Hematology were included in the study.
Materials and Methods: DNAs isolated from peripheral blood leukocytes of MDS cases were studied by real-time PCR method, p53 polymorphisms (rs35163653, rs35993958, rs1800371, rs1042522) were determined by using appropriate probes and melting curve analysis.
Results: Among the four common p53 polymorphisms examined, especially the non-ancestral G allele in the rs1042522 polymorphism was observed to be increased in MDS cases (C: 30.3%; G: 69.7%). In this polymorphism, which is known to be functional, that is, affecting the function of the synthesized protein, the transition of the C nucleotide at position 417 to G (C>G) causes the coding of the amino acid proline at position 72 of the protein to arginine (P72R).
Conclusion: Our study is the first to investigate the p53 polymorphisms of rs35163653, rs35993958, rs1800371 and rs1042522 in the MDS disease group. Of these, rs1042522 polymorphism has been shown to be associated with cancer susceptibility and susceptibility, and it is thought that it may pose a high risk for MDS disease as well. In conclusion, rs1042522 polymorphism may be used as a marker in the diagnosis of MDS in the future by repeating this study for MDS disease with a larger case group.
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Affiliation(s)
- Bahar VATANSEVER
- Ege Üniversitesi Tıp Fakültesi, Hematoloji Bilim Dalı, İzmir, Türkiye
| | | | - Hale GÜLER KARA
- Ege Üniversitesi Tıp Fakültesi, Tıbbi Biyoloji Anabilim Dalı, İzmir, Türkiye
| | - Ege SEVİNÇ
- Ege Üniversitesi Tıp Fakültesi, Tıbbi Biyoloji Anabilim Dalı, İzmir, Türkiye
| | - Burçin KAYMAZ
- Ege Üniversitesi Tıp Fakültesi, Tıbbi Biyoloji Anabilim Dalı, İzmir, Türkiye
| | - Gülay ALP
- Ege Üniversitesi Tıp Fakültesi, Hematoloji Bilim Dalı, İzmir, Türkiye
| | - Fahri ŞAHİN
- Ege Üniversitesi Tıp Fakültesi, Hematoloji Bilim Dalı, İzmir, Türkiye
| | - Güray SAYDAM
- Ege Üniversitesi Tıp Fakültesi, Hematoloji Bilim Dalı, İzmir, Türkiye
| | - Buket KOSOVA
- Ege Üniversitesi Tıp Fakültesi, Tıbbi Biyoloji Anabilim Dalı, İzmir, Türkiye
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10
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Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53. J Mol Biol 2022; 434:167663. [PMID: 35659507 DOI: 10.1016/j.jmb.2022.167663] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 12/31/2022]
Abstract
The tumor protein 53 (p53) is involved in transcription-dependent and independent processes. Several p53 variants related to cancer have been found to impact protein stability. Other variants, on the contrary, might have little impact on structural stability and have local or long-range effects on the p53 interactome. Our group previously identified a loop in the DNA binding domain (DBD) of p53 (residues 207-213) which can recruit different interactors. Experimental structures of p53 in complex with other proteins strengthen the importance of this interface for protein-protein interactions. We here characterized with structure-based approaches somatic and germline variants of p53 which could have a marginal effect in terms of stability and act locally or allosterically on the region 207-213 with consequences on the cytosolic functions of this protein. To this goal, we studied 1132 variants in the p53 DBD with structure-based approaches, accounting also for protein dynamics. We focused on variants predicted with marginal effects on structural stability. We then investigated each of these variants for their impact on DNA binding, dimerization of the p53 DBD, and intramolecular contacts with the 207-213 region. Furthermore, we identified variants that could modulate long-range the conformation of the region 207-213 using a coarse-grain model for allostery and all-atom molecular dynamics simulations. Our predictions have been further validated using enhanced sampling methods for 15 variants. The methodologies used in this study could be more broadly applied to other p53 variants or cases where conformational changes of loop regions are essential in the function of disease-related proteins.
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11
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Jan YH, Heck DE, An Y, Laskin DL, Laskin JD. Nitrogen Mustard Alkylates and Cross-Links p53 in Human Keratinocytes. Chem Res Toxicol 2022; 35:636-650. [PMID: 35312310 PMCID: PMC9491701 DOI: 10.1021/acs.chemrestox.1c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytotoxic blistering agents such as sulfur mustard and nitrogen mustard (HN2) were synthesized for chemical warfare. Toxicity is due to reactive chloroethyl side chains that modify and damage cellular macromolecules including DNA and proteins. In response to DNA damage, cells initiate a DNA damage response directed at the recruitment and activation of repair-related proteins. A central mediator of the DNA damage response is p53, a protein that plays a critical role in regulating DNA repair. We found that HN2 causes cytosolic and nuclear accumulation of p53 in HaCaT keratinocytes; HN2 also induced post-translational modifications on p53 including S15 phosphorylation and K382 acetylation, which enhance p53 stability, promote DNA repair, and mediate cellular metabolic responses to stress. HN2 also cross-linked p53, forming dimers and high-molecular-weight protein complexes in the cells. Cross-linked multimers were also modified by K48-linked ubiquitination indicating that they are targets for proteasome degradation. HN2-induced modifications transiently suppressed the transcriptional activity of p53. Using recombinant human p53, HN2 alkylation was found to be concentration- and redox status-dependent. Dithiothreitol-reduced protein was more efficiently cross-linked indicating that p53 cysteine residues play a key role in protein modification. LC-MS/MS analysis revealed that HN2 directly alkylated p53 at C124, C135, C141, C176, C182, C275, C277, H115, H178, K132, and K139, forming both monoadducts and cross-links. The formation of intermolecular complexes was a consequence of HN2 cross-linked cysteine residues between two molecules of p53. Together, these data demonstrate that p53 is a molecular target for mustard vesicants. Modification of p53 likely mediates cellular responses to HN2 including DNA repair and cell survival contributing to vesicant-induced cytotoxicity.
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Affiliation(s)
- Yi-Hua Jan
- Department of Environmental and Occupational Health and Justice, Rutgers University School of Public Health, Piscataway, New Jersey 08854, United States
| | - Diane E Heck
- Department of Environmental Health Science, New York Medical College, Valhalla, New York 10595, United States
| | - Yunqi An
- Department of Pharmacology and Toxicology, Rutgers University Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854, United States
| | - Debra L Laskin
- Department of Pharmacology and Toxicology, Rutgers University Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854, United States
| | - Jeffrey D Laskin
- Department of Environmental and Occupational Health and Justice, Rutgers University School of Public Health, Piscataway, New Jersey 08854, United States
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12
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Nucleic acid actions on abnormal protein aggregation, phase transitions and phase separation. Curr Opin Struct Biol 2022; 73:102346. [PMID: 35247749 DOI: 10.1016/j.sbi.2022.102346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/06/2021] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
Liquid-liquid phase separation (LLPS) and phase transitions (PT) of proteins, which include the formation of gel- and solid-like species, have been characterized as physical processes related to the pathology of conformational diseases. Nucleic acid (NA)-binding proteins related to neurodegenerative disorders and cancer were shown by us and others to experience PT modulated by different NAs. Herein, we discuss recent work on phase separation and phase transitions of two amyloidogenic proteins, i.e. the prion protein (PrP) and p53, which undergo conformational changes and aggregate upon NA interaction. The role of different NAs in these processes is discussed to shed light on the relevance of PSs and PTs for both the functional and pathological roles of these mammalian proteins.
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13
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Marques MA, de Andrade GC, Silva JL, de Oliveira GAP. Protein of a thousand faces: The tumor-suppressive and oncogenic responses of p53. Front Mol Biosci 2022; 9:944955. [PMID: 36090037 PMCID: PMC9452956 DOI: 10.3389/fmolb.2022.944955] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022] Open
Abstract
The p53 protein is a pleiotropic regulator working as a tumor suppressor and as an oncogene. Depending on the cellular insult and the mutational status, p53 may trigger opposing activities such as cell death or survival, senescence and cell cycle arrest or proliferative signals, antioxidant or prooxidant activation, glycolysis, or oxidative phosphorylation, among others. By augmenting or repressing specific target genes or directly interacting with cellular partners, p53 accomplishes a particular set of activities. The mechanism in which p53 is activated depends on increased stability through post-translational modifications (PTMs) and the formation of higher-order structures (HOS). The intricate cell death and metabolic p53 response are reviewed in light of gaining stability via PTM and HOS formation in health and disease.
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Affiliation(s)
- Mayra A. Marques
- *Correspondence: Mayra A. Marques, ; Guilherme A. P. de Oliveira,
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14
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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15
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The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation. PLoS Biol 2021; 19:e3001364. [PMID: 34351910 PMCID: PMC8370613 DOI: 10.1371/journal.pbio.3001364] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/17/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
The naturally occurring Δ40p53 isoform heterotetramerizes with wild-type p53 (WTp53) to regulate development, aging, and stress responses. How Δ40p53 alters WTp53 function remains enigmatic because their co-expression causes tetramer heterogeneity. We circumvented this issue with a well-tested strategy that expressed Δ40p53:WTp53 as a single transcript, ensuring a 2:2 tetramer stoichiometry. Human MCF10A cell lines expressing Δ40p53:WTp53, WTp53, or WTp53:WTp53 (as controls) from the native TP53 locus were examined with transcriptomics (precision nuclear run-on sequencing [PRO-seq] and RNA sequencing [RNA-seq]), metabolomics, and other methods. Δ40p53:WTp53 was transcriptionally active, and, although phenotypically similar to WTp53 under normal conditions, it failed to induce growth arrest upon Nutlin-induced p53 activation. This occurred via Δ40p53:WTp53-dependent inhibition of enhancer RNA (eRNA) transcription and subsequent failure to induce mRNA biogenesis, despite similar genomic occupancy to WTp53. A different stimulus (5-fluorouracil [5FU]) also showed Δ40p53:WTp53-specific changes in mRNA induction; however, other transcription factors (TFs; e.g., E2F2) could then drive the response, yielding similar outcomes vs. WTp53. Our results establish that Δ40p53 tempers WTp53 function to enable compensatory responses by other stimulus-specific TFs. Such modulation of WTp53 activity may be an essential physiological function for Δ40p53. Moreover, Δ40p53:WTp53 functional distinctions uncovered herein suggest an eRNA requirement for mRNA biogenesis and that human p53 evolved as a tetramer to support eRNA transcription. How does Δ40p53, a naturally occurring isoform of p53 that is linked to accelerated aging, alter WTp53 function? Using an innovative approach, this study reveals that Δ40p53 suppresses enhancer RNA transcription and allows other stimulus-specific transcription factors to modulate the p53 transcriptional response.
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16
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Gomes AS, Ramos H, Inga A, Sousa E, Saraiva L. Structural and Drug Targeting Insights on Mutant p53. Cancers (Basel) 2021; 13:3344. [PMID: 34283062 PMCID: PMC8268744 DOI: 10.3390/cancers13133344] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 12/20/2022] Open
Abstract
p53 is a transcription factor with a pivotal role in cell homeostasis and fate. Its impairment is a major event in tumor onset and development. In fact, about half of human cancers bear TP53 mutations that not only halt the normal function of p53, but also may acquire oncogenic gain of functions that favor tumorigenesis. Although considered undruggable for a long time, evidence has proven the capability of many compounds to restore a wild-type (wt)-like function to mutant p53 (mutp53). However, they have not reached the clinic to date. Structural studies have strongly contributed to the knowledge about p53 structure, stability, dynamics, function, and regulation. Importantly, they have afforded relevant insights into wt and mutp53 pharmacology at molecular levels, fostering the design and development of p53-targeted anticancer therapies. Herein, we provide an integrated view of mutp53 regulation, particularly focusing on mutp53 structural traits and on targeting agents capable of its reactivation, including their biological, biochemical and biophysical features. With this, we expect to pave the way for the development of improved small molecules that may advance precision cancer therapy by targeting p53.
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Affiliation(s)
- Ana Sara Gomes
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (A.S.G.); (H.R.)
| | - Helena Ramos
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (A.S.G.); (H.R.)
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy;
| | - Emília Sousa
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Lucília Saraiva
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (A.S.G.); (H.R.)
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17
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Timofeev O, Stiewe T. Rely on Each Other: DNA Binding Cooperativity Shapes p53 Functions in Tumor Suppression and Cancer Therapy. Cancers (Basel) 2021; 13:2422. [PMID: 34067731 PMCID: PMC8155944 DOI: 10.3390/cancers13102422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022] Open
Abstract
p53 is a tumor suppressor that is mutated in half of all cancers. The high clinical relevance has made p53 a model transcription factor for delineating general mechanisms of transcriptional regulation. p53 forms tetramers that bind DNA in a highly cooperative manner. The DNA binding cooperativity of p53 has been studied by structural and molecular biologists as well as clinical oncologists. These experiments have revealed the structural basis for cooperative DNA binding and its impact on sequence specificity and target gene spectrum. Cooperativity was found to be critical for the control of p53-mediated cell fate decisions and tumor suppression. Importantly, an estimated number of 34,000 cancer patients per year world-wide have mutations of the amino acids mediating cooperativity, and knock-in mouse models have confirmed such mutations to be tumorigenic. While p53 cancer mutations are classically subdivided into "contact" and "structural" mutations, "cooperativity" mutations form a mechanistically distinct third class that affect the quaternary structure but leave DNA contacting residues and the three-dimensional folding of the DNA-binding domain intact. In this review we discuss the concept of DNA binding cooperativity and highlight the unique nature of cooperativity mutations and their clinical implications for cancer therapy.
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Affiliation(s)
- Oleg Timofeev
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Philipps-University, 35037 Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Philipps-University, 35037 Marburg, Germany
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18
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Wei H, Qu L, Dai S, Li Y, Wang H, Feng Y, Chen X, Jiang L, Guo M, Li J, Chen Z, Chen L, Zhang Y, Chen Y. Structural insight into the molecular mechanism of p53-mediated mitochondrial apoptosis. Nat Commun 2021; 12:2280. [PMID: 33863900 PMCID: PMC8052441 DOI: 10.1038/s41467-021-22655-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/24/2021] [Indexed: 01/07/2023] Open
Abstract
The tumor suppressor p53 is mutated in approximately half of all human cancers. p53 can induce apoptosis through mitochondrial membrane permeabilization by interacting with and antagonizing the anti-apoptotic proteins BCL-xL and BCL-2. However, the mechanisms by which p53 induces mitochondrial apoptosis remain elusive. Here, we report a 2.5 Å crystal structure of human p53/BCL-xL complex. In this structure, two p53 molecules interact as a homodimer, and bind one BCL-xL molecule to form a ternary complex with a 2:1 stoichiometry. Mutations at the p53 dimer interface or p53/BCL-xL interface disrupt p53/BCL-xL interaction and p53-mediated apoptosis. Overall, our current findings of the bona fide structure of p53/BCL-xL complex reveal the molecular basis of the interaction between p53 and BCL-xL, and provide insight into p53-mediated mitochondrial apoptosis. The structure of human tumor suppressor p53 in complex with the antiapoptotic protein BCL-xL reveals the basis of the p53–BCL-xL interaction and provides insight into the mechanisms of p53-mediated mitochondrial apoptosis.
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Affiliation(s)
- Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lingzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yilu Feng
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Longying Jiang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Ye Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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19
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Hosoya Y, Ohkanda J. Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. Molecules 2021; 26:2118. [PMID: 33917117 PMCID: PMC8067799 DOI: 10.3390/molecules26082118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid-liquid phase separations-which critically involve both intermolecular interactions between IDPs and their posttranslational modification-are analyzed to understand the potential of IDPs as new drug targets.
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Affiliation(s)
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano 399-4598, Japan;
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20
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Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
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Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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21
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Kamagata K, Kanbayashi S, Honda M, Itoh Y, Takahashi H, Kameda T, Nagatsugi F, Takahashi S. Liquid-like droplet formation by tumor suppressor p53 induced by multivalent electrostatic interactions between two disordered domains. Sci Rep 2020; 10:580. [PMID: 31953488 PMCID: PMC6969132 DOI: 10.1038/s41598-020-57521-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022] Open
Abstract
Early in vivo studies demonstrated the involvement of a tumor-suppressing transcription factor, p53, into cellular droplets such as Cajal and promyelocytic leukemia protein bodies, suggesting that the liquid-liquid phase separation (LLPS) might be involved in the cellular functions of p53. To examine this possibility, we conducted extensive investigations on the droplet formation of p53 in vitro. First, p53 itself was found to form liquid-like droplets at neutral and slightly acidic pH and at low salt concentrations. Truncated p53 mutants modulated droplet formation, suggesting the importance of multivalent electrostatic interactions among the N-terminal and C-terminal domains. Second, FRET efficiency measurements for the dimer mutants of p53 revealed that distances between the core domains and between the C-terminal domains were modulated in an opposite manner within the droplets. Third, the molecular crowding agents were found to promote droplet formation, whereas ssDNA, dsDNA, and ATP, to suppress it. Finally, the p53 mutant mimicking posttranslational phosphorylation did not form the droplets. We conclude that p53 itself has a potential to form droplets that can be controlled by cellular molecules and by posttranslational modifications, suggesting that LLPS might be involved in p53 function.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Masaya Honda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo, 135-0064, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
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22
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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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23
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Ghosh R, Kaypee S, Shasmal M, Kundu TK, Roy S, Sengupta J. Tumor Suppressor p53-Mediated Structural Reorganization of the Transcriptional Coactivator p300. Biochemistry 2019; 58:3434-3443. [DOI: 10.1021/acs.biochem.9b00333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raka Ghosh
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | | | - Tapas K. Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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24
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Zhou X, Hao Q, Lu H. Mutant p53 in cancer therapy-the barrier or the path. J Mol Cell Biol 2019; 11:293-305. [PMID: 30508182 PMCID: PMC6487791 DOI: 10.1093/jmcb/mjy072] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/11/2022] Open
Abstract
Since wild-type p53 is central for maintaining genomic stability and preventing oncogenesis, its coding gene TP53 is highly mutated in ~50% of human cancers, and its activity is almost abrogated in the rest of cancers. Approximately 80% of p53 mutations are single point mutations with several hotspot mutations. Besides loss of function and dominant-negative effect on the wild-type p53 activity, the hotspot p53 mutants also acquire new oncogenic functions, so-called 'gain-of-functions' (GOF). Because the GOF of mutant p53 is highly associated with late-stage malignance and drug resistance, these p53 mutants have become hot targets for developing novel cancer therapies. In this essay, we review some recent progresses in better understanding of the role of mutant p53 GOF in chemoresistance and the underlying mechanisms, and discuss the pros and cons of targeting mutant p53 for the development of anti-cancer therapies.
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Affiliation(s)
- Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, and Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Qian Hao
- Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
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25
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Liang Y, Dearnaley WJ, Alden NA, Solares MJ, Gilmore BL, Pridham KJ, Varano AC, Sheng Z, Alli E, Kelly DF. Correcting errors in the BRCA1 warning system. DNA Repair (Amst) 2018; 73:120-128. [PMID: 30503669 DOI: 10.1016/j.dnarep.2018.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Abstract
Given its important role in human health and disease, remarkably little is known about the full-length three-dimensional (3D) molecular architecture of the breast cancer type 1 susceptibility protein (BRCA1), or its mechanisms to engage the tumor suppressor, TP53 (p53). Here, we show how a prevalent cancer-related mutation in the C-terminal region of the full-length protein, BRCA15382insC, affects its structural properties, yet can be biochemically corrected to restore its functional capacity. As a downstream consequence of restoring the ubiquitin ligase activity of mutated BRCA15382insC, the DNA repair response of p53 was enhanced in cellular extracts naturally deficient in BRCA1 protein expression. Complementary structural insights of p53 tetramers bound to DNA in different stage of the repair process support these biochemical findings in the context of human cancer cells. Equally important, we show how this knowledge can be used to lower the viability of breast cancer cells by modulating the stability of the BRCA1 protein and its associated players.
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Affiliation(s)
- Yanping Liang
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA
| | - William J Dearnaley
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nick A Alden
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA
| | - Maria J Solares
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA; Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Brian L Gilmore
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA
| | - Kevin J Pridham
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA; Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - A Cameron Varano
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA; Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, 24061, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Zhi Sheng
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA
| | - Elizabeth Alli
- Comprehensive Cancer Center, Wake Forest School of Medicine, Wake Forest, NC, 27157, USA
| | - Deborah F Kelly
- Virgina Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, 24016, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA, 16802, USA.
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26
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Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A 2018; 115:E11302-E11310. [PMID: 30420502 DOI: 10.1073/pnas.1814051115] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atomic resolution characterization of the full-length p53 tetramer has been hampered by its size and the presence of extensive intrinsically disordered regions at both the N and C termini. As a consequence, the structural characteristics and dynamics of the disordered regions are poorly understood within the context of the intact p53 tetramer. Here we apply trans-intein splicing to generate segmentally 15N-labeled full-length p53 constructs in which only the resonances of the N-terminal transactivation domain (NTAD) are visible in NMR spectra, allowing us to observe this region of p53 with unprecedented detail within the tetramer. The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD). Chemical-shift changes and paramagnetic spin-labeling experiments reveal that the amphipathic AD1 and AD2 motifs of the NTAD interact with the DNA-binding surface of the DBD through primarily electrostatic interactions. Importantly, this interaction inhibits binding of nonspecific DNA to the DBD while having no effect on binding to a specific p53 recognition element. We conclude that the NTAD:DBD interaction functions to enhance selectivity toward target genes by inhibiting binding to nonspecific sites in genomic DNA. This work provides some of the highest-resolution data on the disordered N terminus of the nearly 180-kDa full-length p53 tetramer and demonstrates a regulatory mechanism by which the N terminus of p53 transiently interacts with the DBD to enhance target site discrimination.
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27
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Offutt TL, Ieong PU, Demir Ö, Amaro RE. Dynamics and Molecular Mechanisms of p53 Transcriptional Activation. Biochemistry 2018; 57:6528-6537. [PMID: 30388364 DOI: 10.1021/acs.biochem.8b01005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The "guardian of the genome", p53, functions as a tumor suppressor that responds to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Mutation of p53 disrupts its tumor suppressor function, leading to various types of human cancers. One particular mutant, R175H, is a structural mutant that inactivates the DNA damage response pathway and acquires oncogenic functions that promotes both cancer and drug resistance. Our current work aims to understand how p53 wild-type function is disrupted due to the R175H mutation. We use a series of atomistic integrative models built previously from crystal structures of the full-length p53 tetramer bound to DNA and model the R175H mutant using in silico site-directed mutagenesis. Explicitly solvated all-atom molecular dynamics (MD) simulations on wild-type and the R175H mutant p53 reveal insights into how wild-type p53 searches and recognizes DNA, and how this mechanism is disrupted as a result of the R175H mutation. Specifically, our work reveals the optimal quaternary DNA binding mode of the DNA binding domain and shows how this binding mode is altered via symmetry loss as a result of the R175H mutation, indicating a recognition mechanism that is reminiscent of the asymmetry seen in wild type p53 binding to nonspecific genomic elements. Altogether our work sheds new light into the hitherto unseen molecular mechanisms governing transcription factor, DNA recognition.
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Affiliation(s)
- Tavina L Offutt
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92092-0340 , United States
| | - Pek U Ieong
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92092-0340 , United States
| | - Özlem Demir
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92092-0340 , United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92092-0340 , United States
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28
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A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions. Nat Protoc 2018; 13:2864-2889. [DOI: 10.1038/s41596-018-0068-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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29
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Verkhivker GM. Biophysical simulations and structure-based modeling of residue interaction networks in the tumor suppressor proteins reveal functional role of cancer mutation hotspots in molecular communication. Biochim Biophys Acta Gen Subj 2018; 1863:210-225. [PMID: 30339916 DOI: 10.1016/j.bbagen.2018.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/19/2022]
Abstract
In the current study, we have combined molecular simulations and energetic analysis with dynamics-based network modeling and perturbation response scanning to determine molecular signatures of mutational hotspot residues in the p53, PTEN, and SMAD4 tumor suppressor proteins. By examining structure, energetics and dynamics of these proteins, we have shown that inactivating mutations preferentially target a group of structurally stable residues that play a fundamental role in global propagation of dynamic fluctuations and mediating allosteric interaction networks. Through integration of long-range perturbation dynamics and network-based approaches, we have quantified allosteric potential of residues in the studied proteins. The results have revealed that mutational hotspot sites often correspond to high centrality mediating centers of the residue interaction networks that are responsible for coordination of global dynamic changes and allosteric signaling. Our findings have also suggested that structurally stable mutational hotpots can act as major effectors of allosteric interactions and mutations in these positions are typically associated with severe phenotype. Modeling of shortest inter-residue pathways has shown that mutational hotspot sites can also serve as key mediating bridges of allosteric communication in the p53 and PTEN protein structures. Multiple regression models have indicated that functional significance of mutational hotspots can be strongly associated with the network signatures serving as robust predictors of critical regulatory positions responsible for loss-of-function phenotype. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of mutational hotspots, providing a plausible rationale for explaining and localizing disease-causing mutations in tumor suppressor genes.
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Affiliation(s)
- Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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30
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Assah E, Goh W, Zheng XT, Lim TX, Li J, Lane D, Ghadessy F, Tan YN. Rapid colorimetric detection of p53 protein function using DNA-gold nanoconjugates with applications for drug discovery and cancer diagnostics. Colloids Surf B Biointerfaces 2018; 169:214-221. [DOI: 10.1016/j.colsurfb.2018.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 12/11/2022]
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31
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Sinz A. Cross‐Linking/Mass Spectrometry for Studying Protein Structures and Protein–Protein Interactions: Where Are We Now and Where Should We Go from Here? Angew Chem Int Ed Engl 2018; 57:6390-6396. [DOI: 10.1002/anie.201709559] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/06/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of PharmacyMartin Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle (Saale) Germany
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32
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Sinz A. Vernetzung/Massenspektrometrie zur Untersuchung von Proteinstrukturen und Protein‐Protein‐Wechselwirkungen: Wo stehen wir und welchen Weg wollen wir einschlagen? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea Sinz
- Abteilung für Pharmazeutische Chemie & BioanalytikInstitut für PharmazieMartin-Luther-Universität Halle-Wittenberg Wolfgang-Langenbeck-Straße 4 06120 Halle (Saale) Deutschland
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33
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Gomes AS, Trovão F, Andrade Pinheiro B, Freire F, Gomes S, Oliveira C, Domingues L, Romão MJ, Saraiva L, Carvalho AL. The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding. Int J Mol Sci 2018; 19:ijms19041184. [PMID: 29652801 PMCID: PMC5979565 DOI: 10.3390/ijms19041184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 01/29/2023] Open
Abstract
The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and maintenance. For these reasons, the reactivation of p53 function is regarded as a promising strategy to halt cancer. In the present work, the recombinant mutant p53R280K DNA binding domain (DBD) was produced for the first time, and its crystal structure was determined in the absence of DNA to a resolution of 2.0 Å. The solved structure contains four molecules in the asymmetric unit, four zinc(II) ions, and 336 water molecules. The structure was compared with the wild-type p53 DBD structure, isolated and in complex with DNA. These comparisons contributed to a deeper understanding of the mutant p53R280K structure, as well as the loss of DNA binding related to halted transcriptional activity. The structural information derived may also contribute to the rational design of mutant p53 reactivating molecules with potential application in cancer treatment.
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Affiliation(s)
- Ana Sara Gomes
- LAQV-REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal.
| | - Filipa Trovão
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Benedita Andrade Pinheiro
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Filipe Freire
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Sara Gomes
- LAQV-REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal.
| | - Carla Oliveira
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
| | - Maria João Romão
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Lucília Saraiva
- LAQV-REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal.
| | - Ana Luísa Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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34
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Tsafou K, Tiwari PB, Forman-Kay JD, Metallo SJ, Toretsky JA. Targeting Intrinsically Disordered Transcription Factors: Changing the Paradigm. J Mol Biol 2018; 430:2321-2341. [PMID: 29655986 DOI: 10.1016/j.jmb.2018.04.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022]
Abstract
Increased understanding of intrinsically disordered proteins (IDPs) and protein regions has revolutionized our view of the relationship between protein structure and function. Data now support that IDPs can be functional in the absence of a single, fixed, three-dimensional structure. Due to their dynamic morphology, IDPs have the ability to display a range of kinetics and affinity depending on what the system requires, as well as the potential for large-scale association. Although several studies have shed light on the functional properties of IDPs, the class of intrinsically disordered transcription factors (TFs) is still poorly characterized biophysically due to their combination of ordered and disordered sequences. In addition, TF modulation by small molecules has long been considered a difficult or even impossible task, limiting functional probe development. However, with evolving technology, it is becoming possible to characterize TF structure-function relationships in unprecedented detail and explore avenues not available or not considered in the past. Here we provide an introduction to the biophysical properties of intrinsically disordered TFs and we discuss recent computational and experimental efforts toward understanding the role of intrinsically disordered TFs in biology and disease. We describe a series of successful TF targeting strategies that have overcome the perception of the "undruggability" of TFs, providing new leads on drug development methodologies. Lastly, we discuss future challenges and opportunities to enhance our understanding of the structure-function relationship of intrinsically disordered TFs.
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Affiliation(s)
- K Tsafou
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - P B Tiwari
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - J D Forman-Kay
- Molecular Medicine, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto M5G 1X8, Canada
| | - S J Metallo
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - J A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA.
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35
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Scaglione A, Monteonofrio L, Parisi G, Cecchetti C, Siepi F, Rinaldo C, Giorgi A, Verzili D, Zamparelli C, Savino C, Soddu S, Vallone B, Montemiglio LC. Effects of Y361-auto-phosphorylation on structural plasticity of the HIPK2 kinase domain. Protein Sci 2017; 27:725-737. [PMID: 29277937 DOI: 10.1002/pro.3367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/21/2017] [Accepted: 12/13/2017] [Indexed: 12/30/2022]
Abstract
The dual-specificity activity of the homeodomain interacting protein kinase 2 (HIPK2) is regulated by cis-auto-phosphorylation of tyrosine 361 (Y361) on the activation loop. Inhibition of this process or substitution of Y361 with nonphosphorylatable amino acid residues result in aberrant HIPK2 forms that show altered functionalities, pathological-like cellular relocalization, and accumulation into cytoplasmic aggresomes. Here, we report an in vitro characterization of wild type HIPK2 kinase domain and of two mutants, one at the regulating Y361 (Y361F, mimicking a form of HIPK2 lacking Y361 phosphorylation) and another at the catalytic lysine 228 (K228A, inactivating the enzyme). Gel filtration and thermal denaturation analyzes along with equilibrium binding experiments and kinase assays performed in the presence or absence of ATP-competitors were performed. The effects induced by mutations on overall stability, oligomerization and activity support the existence of different conformations of the kinase domain linked to Y361 phosphorylation. In addition, our in vitro data are consistent with both the cross-talk between the catalytic site and the activation loop of HIPK2 and the aberrant activities and accumulation previously reported for the Y361 nonphosphorylated HIPK2 in mammalian cells.
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Affiliation(s)
- Antonella Scaglione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy
| | - Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Cristina Cecchetti
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Francesca Siepi
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy
| | - Cinzia Rinaldo
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy.,CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, Rome, 00185, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Daniela Verzili
- CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, Rome, 00185, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Carmelinda Savino
- CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, Rome, 00185, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
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36
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Hage C, Iacobucci C, Rehkamp A, Arlt C, Sinz A. The First Zero-Length Mass Spectrometry-Cleavable Cross-Linker for Protein Structure Analysis. Angew Chem Int Ed Engl 2017; 56:14551-14555. [DOI: 10.1002/anie.201708273] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/04/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Christoph Hage
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
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37
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Hage C, Iacobucci C, Rehkamp A, Arlt C, Sinz A. The First Zero-Length Mass Spectrometry-Cleavable Cross-Linker for Protein Structure Analysis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Christoph Hage
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
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38
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Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis. Proc Natl Acad Sci U S A 2017; 114:10642-10647. [PMID: 28928145 DOI: 10.1073/pnas.1708194114] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray-scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge-charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge-charge interaction upon cleavage by caspases during cell pyroptosis.
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Murata A, Itoh Y, Mano E, Kanbayashi S, Igarashi C, Takahashi H, Takahashi S, Kamagata K. One-Dimensional Search Dynamics of Tumor Suppressor p53 Regulated by a Disordered C-Terminal Domain. Biophys J 2017; 112:2301-2314. [PMID: 28591603 DOI: 10.1016/j.bpj.2017.04.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 04/06/2017] [Accepted: 04/25/2017] [Indexed: 11/15/2022] Open
Abstract
Tumor suppressor p53 slides along DNA and finds its target sequence in drastically different and changing cellular conditions. To elucidate how p53 maintains efficient target search at different concentrations of divalent cations such as Ca2+ and Mg2+, we prepared two mutants of p53, each possessing one of its two DNA-binding domains, the CoreTet mutant having the structured core domain plus the tetramerization (Tet) domain, and the TetCT mutant having Tet plus the disordered C-terminal domain. We investigated their equilibrium and kinetic dissociation from DNA and search dynamics along DNA at various [Mg2+]. Although binding of CoreTet to DNA becomes markedly weaker at higher [Mg2+], binding of TetCT depends slightly on [Mg2+]. Single-molecule fluorescence measurements revealed that the one-dimensional diffusion of CoreTet along DNA consists of fast and slow search modes, the ratio of which depends strongly on [Mg2+]. In contrast, diffusion of TetCT consisted of only the fast mode. The disordered C-terminal domain can associate with DNA irrespective of [Mg2+], and can maintain an equilibrium balance of the two search modes and the p53 search distance. These results suggest that p53 modulates the quaternary structure of the complex between p53 and DNA under different [Mg2+] and that it maintains the target search along DNA.
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Affiliation(s)
- Agato Murata
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Chihiro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan.
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan.
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40
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Subekti DRG, Murata A, Itoh Y, Fukuchi S, Takahashi H, Kanbayashi S, Takahashi S, Kamagata K. The Disordered Linker in p53 Participates in Nonspecific Binding to and One-Dimensional Sliding along DNA Revealed by Single-Molecule Fluorescence Measurements. Biochemistry 2017; 56:4134-4144. [DOI: 10.1021/acs.biochem.7b00292] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Dwiky Rendra Graha Subekti
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Agato Murata
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Yuji Itoh
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Satoshi Fukuchi
- Faculty
of Engineering, Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Hiroto Takahashi
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Saori Kanbayashi
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Satoshi Takahashi
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kiyoto Kamagata
- Institute
for Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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41
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Chen Y, Gao T, Wang Y, Yang G. Investigating the Influence of Magnesium Ions on p53-DNA Binding Using Atomic Force Microscopy. Int J Mol Sci 2017; 18:ijms18071585. [PMID: 28754018 PMCID: PMC5536072 DOI: 10.3390/ijms18071585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
p53 is a tumor suppressor protein that plays a significant role in apoptosis and senescence, preserving genomic stability, and preventing oncogene expression. Metal ions, such as magnesium and zinc ions, have important influences on p53–DNA interactions for stabilizing the structure of the protein and enhancing its affinity to DNA. In the present study, we systematically investigated the interaction of full length human protein p53 with DNA in metal ion solution by atomic force microscopy (AFM). The p53–DNA complexes at various p53 concentrations were scanned by AFM and their images are used to measure the dissociation constant of p53–DNA binding by a statistical method. We found that the dissociation constant of p53 binding DNA is 328.02 nmol/L in physiological buffer conditions. The influence of magnesium ions on p53–DNA binding was studied by AFM at various ion strengths through visualization. We found that magnesium ions significantly stimulate the binding of the protein to DNA in a sequence-independent manner, different from that stimulated by zinc. Furthermore, the high concentrations of magnesium ions can promote p53 aggregation and even lead to the formation of self-assembly networks of DNA and p53 proteins. We propose an aggregation and self-assembly model based on the present observation and discuss its biological meaning.
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Affiliation(s)
- Yang Chen
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Tianyong Gao
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Yanwei Wang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
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42
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Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics. Arch Biochem Biophys 2017; 628:33-41. [PMID: 28501583 PMCID: PMC5553349 DOI: 10.1016/j.abb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/25/2023]
Abstract
Small-angle X-ray scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules. NMR is arguably the most powerful technique for the experimental analysis of dynamics. The joint application of these two highly complementary techniques provides an extremely useful approach that facilitates comprehensive characterization of biomacromolecular solutions. SAXS and NMR are effective and highly complementary techniques in structural biology. Constraints from SAXS can be readily incorporated in NMR structure calculations. High resolution NMR models of domains can serve as building blocks for SAXS-based rigid body modeling. Flexible systems can be well described using ensemble approaches combining SAXS and NMR. Dynamics studies can be enhanced by combining SAXS and NMR.
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43
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Arlt C, Flegler V, Ihling CH, Schäfer M, Thondorf I, Sinz A. An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full‐Length Wild‐Type Tetrameric p53 Tumor Suppressor. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609826] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Vanessa Flegler
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Mathias Schäfer
- Department Mass Spectrometry Institute of Organic Chemistry University of Cologne Greinstraße 4 50939 Cologne Germany
| | - Iris Thondorf
- Department of Technical Biochemistry 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 Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
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45
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Arlt C, Flegler V, Ihling CH, Schäfer M, Thondorf I, Sinz A. An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor. Angew Chem Int Ed Engl 2016; 56:275-279. [PMID: 27897373 DOI: 10.1002/anie.201609826] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/10/2016] [Indexed: 12/31/2022]
Abstract
We present an integrated approach for investigating the topology of proteins through native mass spectrometry (MS) and cross-linking/MS, which we applied to the full-length wild-type p53 tetramer. For the first time, the two techniques were combined in one workflow to obtain not only structural insight in the p53 tetramer, but also information on the cross-linking efficiency and the impact of cross-linker modification on the conformation of an intrinsically disordered protein (IDP). P53 cross-linking was monitored by native MS and as such, our strategy serves as a quality control for different cross-linking reagents. Our approach can be applied to the structural investigation of various protein systems, including IDPs and large protein assemblies, which are challenging to study by the conventional methods used for protein structure characterization.
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Affiliation(s)
- Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
| | - Vanessa Flegler
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
| | - Mathias Schäfer
- Department Mass Spectrometry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Iris Thondorf
- Department of Technical Biochemistry, 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, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
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46
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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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47
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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept. Int J Mol Sci 2016; 17:ijms17111874. [PMID: 27834926 PMCID: PMC5133874 DOI: 10.3390/ijms17111874] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/10/2023] Open
Abstract
Although it is one of the most studied proteins, p53 continues to be an enigma. This protein has numerous biological functions, possesses intrinsically disordered regions crucial for its functionality, can form both homo-tetramers and isoform-based hetero-tetramers, and is able to interact with many binding partners. It contains numerous posttranslational modifications, has several isoforms generated by alternative splicing, alternative promoter usage or alternative initiation of translation, and is commonly mutated in different cancers. Therefore, p53 serves as an important illustration of the protein structure–function continuum concept, where the generation of multiple proteoforms by various mechanisms defines the ability of this protein to have a multitude of structurally and functionally different states. Considering p53 in the light of a proteoform-based structure–function continuum represents a non-canonical and conceptually new contemplation of structure, regulation, and functionality of this important protein.
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48
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Costa DCF, de Oliveira GAP, Cino EA, Soares IN, Rangel LP, Silva JL. Aggregation and Prion-Like Properties of Misfolded Tumor Suppressors: Is Cancer a Prion Disease? Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023614. [PMID: 27549118 DOI: 10.1101/cshperspect.a023614] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Prion diseases are disorders that share several characteristics that are typical of many neurodegenerative diseases. Recently, several studies have extended the prion concept to pathological aggregation in malignant tumors involving misfolded p53, a tumor-suppressor protein. The aggregation of p53 and its coaggregation with p53 family members, p63 and p73, have been shown. Certain p53 mutants exert a dominant-negative regulatory effect on wild-type (WT) p53. The basis for this dominant-negative effect is that amyloid-like mutant p53 converts WT p53 into an aggregated species, leading to a gain-of-function (GoF) phenotype and the loss of its tumor-suppressor function. Recently, it was shown that p53 aggregates can be internalized by cells and can coaggregate with endogenous p53, corroborating the prion-like properties of p53 aggregates. The prion-like behavior of oncogenic p53 mutants provides an explanation for its dominant-negative and GoF properties, including the high metastatic potential of cancer cells carrying p53 mutations. The inhibition of p53 aggregation appears to represent a promising target for therapeutic intervention in patients with malignant tumors.
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Affiliation(s)
- Danielly C F Costa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto de Nutrição, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550-013, Brazil
| | - Guilherme A P de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Elio A Cino
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Iaci N Soares
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Luciana P Rangel
- Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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49
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Full-length p53 tetramer bound to DNA and its quaternary dynamics. Oncogene 2016; 36:1451-1460. [PMID: 27641333 DOI: 10.1038/onc.2016.321] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/15/2016] [Indexed: 01/04/2023]
Abstract
P53 is a major tumor suppressor that is mutated and inactivated in ~50% of all human cancers. Thus, reactivation of mutant p53 using small molecules has been a long sought-after anticancer therapeutic strategy. Full structural characterization of the full-length oligomeric p53 is challenging because of its complex architecture and multiple highly flexible regions. To explore p53 structural dynamics, here we developed a series of atomistic integrative models with available crystal structures of the full-length p53 (fl-p53) tetramer bound to three different DNA sequences: a p21 response element, a puma response element and a nonspecific DNA sequence. Explicitly solvated, all-atom molecular dynamics simulations of the three complexes (totaling nearly 1 μs of aggregate simulation time) yield final structures consistent with electron microscopy maps and, for the first time, show the direct interactions of the p53 C-terminal with DNA. Through a collective principal component analysis, we identify sequence-dependent differential quaternary binding modes of the p53 tetramer interfacing with DNA. Additionally, L1 loop dynamics of fl-p53 in the presence of DNA is revealed, and druggable pockets of p53 are identified via solvent mapping to aid future drug discovery studies.
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50
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Arlt C, Götze M, Ihling CH, Hage C, Schäfer M, Sinz A. Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker. Anal Chem 2016; 88:7930-7. [DOI: 10.1021/acs.analchem.5b04853] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Christian Arlt
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Michael Götze
- Institute
of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str.
3, D-06120 Halle
(Saale), Germany
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Christoph Hage
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Mathias Schäfer
- Institute
for Organic Chemistry, Department of Chemistry, University of Cologne, Greinstr. 4, D-50939 Cologne, Germany
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
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