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Fang T, Wang J, Sun S, Deng X, Xue M, Han F, Sun B, Chen L. JinLiDa granules alleviates cardiac hypertrophy and inflammation in diabetic cardiomyopathy by regulating TP53. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155659. [PMID: 38759318 DOI: 10.1016/j.phymed.2024.155659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/14/2024] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND JinLiDa granules (JLD) is a traditional Chinese medicine (TCM) used to treat type 2 diabetes mellitus with Qi and Yin deficiency. Clinical evidence has shown that JLD can alleviate diabetic cardiomyopathy, but the exact mechanism is not yet clear. PURPOSE The purpose of this study was to examine the potential role and mechanism of JLD in the treatment of diabetic cardiomyopathy through network pharmacological analysis and basic experiments. METHODS The targets of JLD associated with diabetic cardiomyopathy were examined by network pharmacology. Protein interaction analysis was performed on the targets, and the associated pathways were searched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Diabetic mice were treated with low or high doses of JLD by gavage, and AC16 and H9C2 cardiomyocytes exposed to high-glucose conditions were treated with JLD. The analysis results were verified by various experimental techniques to examine molecular mechanisms. RESULTS Network pharmacological analysis revealed that JLD acted on the tumor suppressor p53 (TP53) during inflammation and fibrosis associated with diabetic cardiomyopathy. The results of basic experiments showed that after JLD treatment, ventricular wall thickening in diabetic mouse hearts was attenuated, cardiac hypertrophy and myocardial inflammation were alleviated, and the expression of cardiac hypertrophy- and inflammation-related factors in cardiomyocytes exposed to a high-glucose environment was decreased. Cardiomyocyte morphology also improved after JLD treatment. TP53 expression and the tumor necrosis factor (TNF) and transforming growth factor beta-1 (TGFβ1) signaling pathways were significantly altered, and inhibiting TP53 expression effectively alleviated the activation of the TNF and TGFβ1 signaling pathways under high glucose conditions. Overexpression of TP53 activated these signaling pathways. CONCLUSIONS JLD acted on TP53 to regulate the TNF and TGFβ1 signaling pathways, effectively alleviating cardiomyocyte hypertrophy and inflammation in high glucose and diabetic conditions. Our study provides a solid foundation for the future treatment of diabetic cardiomyopathy with JLD.
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Affiliation(s)
- Ting Fang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Jingyi Wang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Shengnan Sun
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Xiaoqing Deng
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Mei Xue
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Fei Han
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Bei Sun
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China.
| | - Liming Chen
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China.
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Haase A, Alefeld E, Yalinci F, Meenen DV, Busch MA, Dünker N. Gastric Inhibitory Polypeptide Receptor (GIPR) Overexpression Reduces the Tumorigenic Potential of Retinoblastoma Cells. Cancers (Basel) 2024; 16:1656. [PMID: 38730608 PMCID: PMC11083251 DOI: 10.3390/cancers16091656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Retinoblastoma (RB) is the most common malignant intraocular tumor in early childhood. Gene expression profiling revealed that the gastric inhibitory polypeptide receptor (GIPR) is upregulated following trefoil factor family peptide 1 (TFF1) overexpression in RB cells. In the study presented, we found this G protein-coupled transmembrane receptor to be co-expressed with TFF1, a new diagnostic and prognostic RB biomarker for advanced subtype 2 RBs. Functional analyses in two RB cell lines revealed a significant reduction in cell viability and growth and a concomitant increase in apoptosis following stable, lentiviral GIPR overexpression, matching the effects seen after TFF1 overexpression. In chicken chorioallantoic membrane (CAM) assays, GIPR-overexpressing RB cells developed significantly smaller CAM tumors. The effect of GIPR overexpression in RB cells was reversed by the GIPR inhibitor MK0893. The administration of recombinant TFF1 did not augment GIPR overexpression effects, suggesting that GIPR does not serve as a TFF1 receptor. Investigations of potential GIPR up- and downstream mediators suggest the involvement of miR-542-5p and p53 in GIPR signaling. Our results indicate a tumor suppressor role of GIPR in RB, suggesting its pathway as a new potential target for future retinoblastoma therapy.
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Cavalu S, Saber S, Hamad RS, Abdel-Reheim MA, Elmorsy EA, Youssef ME. Orexins in apoptosis: a dual regulatory role. Front Cell Neurosci 2024; 18:1336145. [PMID: 38699177 PMCID: PMC11064656 DOI: 10.3389/fncel.2024.1336145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
The orexins, also referred to as hypocretins, are neuropeptides that originate from the lateral hypothalamus (LH) region of the brain. They are composed of two small peptides, orexin-A, and orexin-B, which are broadly distributed throughout the central and peripheral nervous systems. Orexins are recognized to regulate diverse functions, involving energy homeostasis, the sleep-wake cycle, stress responses, and reward-seeking behaviors. Additionally, it is suggested that orexin-A deficiency is linked to sleepiness and narcolepsy. The orexins bind to their respective receptors, the orexin receptor type 1 (OX1R) and type 2 (OX2R), and activate different signaling pathways, which results in the mediation of various physiological functions. Orexin receptors are widely expressed in different parts of the body, including the skin, muscles, lungs, and bone marrow. The expression levels of orexins and their receptors play a crucial role in apoptosis, which makes them a potential target for clinical treatment of various disorders. This article delves into the significance of orexins and orexin receptors in the process of apoptosis, highlighting their expression levels and their potential contributions to different diseases. The article offers an overview of the existing understanding of the orexin/receptor system and how it influences the regulation of apoptosis.
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Affiliation(s)
- Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Rabab S. Hamad
- Biological Sciences Department, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
- Central Laboratory, Theodor Bilharz Research Institute, Giza, Egypt
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, Egypt
| | - Elsayed A. Elmorsy
- Department of Pharmacology and Therapeutics, College of Medicine, Qassim University, Buraidah, Saudi Arabia
- Department of Clinical Pharmacology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mahmoud E. Youssef
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
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Zhou Y, Nakajima R, Shirasawa M, Fikriyanti M, Zhao L, Iwanaga R, Bradford AP, Kurayoshi K, Araki K, Ohtani K. Expanding Roles of the E2F-RB-p53 Pathway in Tumor Suppression. BIOLOGY 2023; 12:1511. [PMID: 38132337 PMCID: PMC10740672 DOI: 10.3390/biology12121511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. The activity of E2F is controlled by the tumor suppressor pRB, which binds to E2F and actively suppresses target gene expression, thereby restraining cell proliferation. Signaling pathways originating from growth stimulative and growth suppressive signals converge on pRB (the RB pathway) to regulate E2F activity. In most cancers, the function of pRB is compromised by oncogenic mutations, and E2F activity is enhanced, thereby facilitating cell proliferation to promote tumorigenesis. Upon such events, E2F activates the Arf tumor suppressor gene, leading to activation of the tumor suppressor p53 to protect cells from tumorigenesis. ARF inactivates MDM2, which facilitates degradation of p53 through proteasome by ubiquitination (the p53 pathway). P53 suppresses tumorigenesis by inducing cellular senescence or apoptosis. Hence, in almost all cancers, the p53 pathway is also disabled. Here we will introduce the canonical functions of the RB-E2F-p53 pathway first and then the non-classical functions of each component, which may be relevant to cancer biology.
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Affiliation(s)
- Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mariana Fikriyanti
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Andrew P. Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama, Fukushima 963-8611, Japan;
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
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Degn K, Beltrame L, Tiberti M, Papaleo E. PDBminer to Find and Annotate Protein Structures for Computational Analysis. J Chem Inf Model 2023; 63:7274-7281. [PMID: 37977136 DOI: 10.1021/acs.jcim.3c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Computational methods relying on protein structure strongly depend on the structure selected for investigation. Typical sources of protein structures include experimental structures available at the Protein Data Bank (PDB) and high-quality in silico model structures, such as those available at the AlphaFold Protein Structure Database. Either option has significant advantages and drawbacks, and exploring the wealth of available structures to identify the most suitable ones for specific applications can be a daunting task. We provide an open-source software package, PDBminer, with the purpose of making structure identification and selection easier, faster, and less error prone. PDBminer searches the AlphaFold Database and the PDB for available structures of interest and provides an up-to-date, quality-ranked table of structures applicable for further use. PDBminer provides an overview of the available protein structures to one or more input proteins, parallelizing the runs if multiple cores are specified. The output table reports the coverage of the protein structures aligned to the UniProt sequence, overcoming numbering differences in PDB structures and providing information regarding model quality, protein complexes, ligands, and nucleic acid chain binding. The PDBminer2coverage and PDBminer2network tools assist in visualizing the results. PDBminer can be applied to overcome the tedious task of choosing a PDB structure without losing the wealth of additional information available in the PDB. Here, we showcase the main functionalities of the package on the p53 tumor suppressor protein. The package is available at http://github.com/ELELAB/PDBminer.
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Affiliation(s)
- Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Ludovica Beltrame
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
- Cancer Structural Biology, Danish Cancer Institute, 2100 Copenhagen, Denmark
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Safieh J, Chazan A, Saleem H, Vyas P, Danin-Poleg Y, Ron D, Haran TE. A molecular mechanism for the "digital" response of p53 to stress. Proc Natl Acad Sci U S A 2023; 120:e2305713120. [PMID: 38015851 PMCID: PMC10710088 DOI: 10.1073/pnas.2305713120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
The tumor suppressor protein p53 accumulates in response to cellular stress and consequently orchestrates the expression of multiple genes in a p53-level and time-dependent manner to overcome stress consequences, for which a molecular mechanism is currently unknown. Previously, we reported that DNA torsional flexibility distinguishes among p53 response elements (REs) and that transactivation at basal p53 levels is correlated with p53 REs flexibility. Here, we calculated the flexibility of ~200 p53 REs. By connecting functional outcomes of p53-target genes' activation to the calculated flexibility of their REs, we show that genes known to belong to pathways that are activated rapidly upon stress contain REs that are significantly more flexible relative to REs of genes known to be involved in pathways that are activated later in the response to stress. The global structural properties of several p53 REs belonging to different pathways were experimentally validated. Additionally, reporter-gene expression driven by flexible p53 REs occurred at lower p53 levels and with faster rates than expression from rigid REs. Furthermore, analysis of published endogenous mRNA levels of p53-target genes as a function of REs' flexibility showed that early versus late genes differ significantly in their flexibility properties of their REs and that highly flexible p53 REs enable high-activation level exclusively to early-response genes. Overall, we demonstrate that DNA flexibility of p53 REs contributes significantly to functional selectivity in the p53 system by facilitating the initial steps of p53-dependent target-genes expression, thereby contributing to survival versus death decisions in the p53 system.
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Affiliation(s)
- Jessy Safieh
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Ariel Chazan
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Hanna Saleem
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Pratik Vyas
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Yael Danin-Poleg
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Dina Ron
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Tali E. Haran
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544064. [PMID: 37333386 PMCID: PMC10274755 DOI: 10.1101/2023.06.07.544064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength (λ D N A P R O ) of the DNA-protein contact potential. For an optimal choice of λ D N A P R O , the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway,Austin TX 78712, USA
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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: 96] [Impact Index Per Article: 96.0] [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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Koulgi S, Achalere A, Sonavane U, Joshi R. Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain. J Chem Inf Model 2022; 62:6449-6461. [PMID: 35614540 DOI: 10.1021/acs.jcim.2c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The transcription factor p53 is one of the most widely studied cancer proteins. Its temperature-sensitive nature suggests reduction in functionality at physiological temperatures. Temperature-induced conformational variations and their impact on its functional ability still remain unexplored. A total of 20.8 μs molecular dynamics simulations of wildtype p53 in the apo and the DNA-bound states have been performed at 300 K and 310 K. Further, Markov State Modeling (MSM) analyses were performed, considering Cα-Cα distances as reaction coordinates. Filtering of these distances based on correlation with the time-independent components (tICs) resulted in 16 and 32 distances for apo and DNA-bound systems, respectively. Individual MSM analyses using these filtered distances were performed for both p53 systems. These Cα-Cα residue pairs belonged to the N-terminal, S6/7 β-turn, loop L2, loop L3, and hydrophobic core residues. At physiological temperatures, apo-p53 exhibits exposure of its hydrophobic core, where the temperature-sensitive hotspot residues were also located. This exposure was the result of the S6/7 β-turn and N-terminal moving apart. In the DNA-bound p53 system, loop L1 attains an open conformation at physiological temperatures, which weakens the DNA binding. It is already known that p53 mutants that lack DNA binding also tend to show similar conformational variations. The S6/7 β-turn along with the already known functionally important loop L2 may pose as regions to be targeted to overcome the loss in binding of temperature-sensitive wildtype p53. Rescue strategies directed toward these temperature-sensitive regions may be useful to recuperate its strong binding at physiological temperatures.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Archana Achalere
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
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Planat M, Amaral MM, Fang F, Chester D, Aschheim R, Irwin K. Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding. Curr Issues Mol Biol 2022; 44:1417-1433. [PMID: 35723353 PMCID: PMC9164029 DOI: 10.3390/cimb44040095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/19/2022] [Accepted: 03/20/2022] [Indexed: 12/24/2022] Open
Abstract
Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain—the motif—may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structures close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated with the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs, such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such DNA syntactical rules and their functional roles. This includes the TATA box in the promoter region of some genes, the single-nucleotide markers (SNP) and the motifs of some genes of ubiquitous roles in transcription and regulation.
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Affiliation(s)
- Michel Planat
- Institut FEMTO-ST CNRS UMR 6174, Université de Bourgogne-Franche-Comté, F-25044 Besançon, France
- Correspondence:
| | - Marcelo M. Amaral
- Quantum Gravity Research, Los Angeles, CA 90290, USA; (M.M.A.); (F.F.); (D.C.); (R.A.); (K.I.)
| | - Fang Fang
- Quantum Gravity Research, Los Angeles, CA 90290, USA; (M.M.A.); (F.F.); (D.C.); (R.A.); (K.I.)
| | - David Chester
- Quantum Gravity Research, Los Angeles, CA 90290, USA; (M.M.A.); (F.F.); (D.C.); (R.A.); (K.I.)
| | - Raymond Aschheim
- Quantum Gravity Research, Los Angeles, CA 90290, USA; (M.M.A.); (F.F.); (D.C.); (R.A.); (K.I.)
| | - Klee Irwin
- Quantum Gravity Research, Los Angeles, CA 90290, USA; (M.M.A.); (F.F.); (D.C.); (R.A.); (K.I.)
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12
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Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations. Protein J 2022; 41:27-43. [PMID: 35099676 DOI: 10.1007/s10930-022-10041-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
p53, a tumor suppressor protein, is essential for preventing cancer development. Enhancing our understanding of the human p53 function and its modifications in carcinogenesis will aid in developing more highly effective strategies for cancer prevention and treatment. In this study, we have modeled five human p53 forms, namely, inactive, distal-active, proximal-active, distal-Arg175His mutant, and proximal-Arg175His mutant forms. These forms have been investigated using Gaussian accelerated molecular dynamics (GaMD) simulations in OPC water model at physiological temperature and pH. Our observations, obtained throughout [Formula: see text] of production run, are in good agreement with the relevant results in the classical molecular dynamics (MD) studies. Therefore, GaMD method is more economic and efficient method than the classical MD method for studying biomolecular systems. The featured dynamics of the five human p53-DBD forms include noticeable conformational changes of L1 and [Formula: see text]-[Formula: see text] loops as well as [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] turns. We have identified two clusters that represent two distinct conformational states in each p53-DBD form. The free-energy profiles of these clusters demonstrate the flexibility of the protein to undergo a conformational transition between the two clusters. We have predicted two out of seven possible druggability pockets on the clusters of the Arg175His forms. These two druggability pockets are near the mutation site and are expected to be actual pockets, which will be helpful for the compound clinical progression studies.
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13
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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: 32] [Impact Index Per Article: 10.7] [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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14
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Senitzki A, Safieh J, Sharma V, Golovenko D, Danin-Poleg Y, Inga A, Haran TE. The complex architecture of p53 binding sites. Nucleic Acids Res 2021; 49:1364-1382. [PMID: 33444431 PMCID: PMC7897521 DOI: 10.1093/nar/gkaa1283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Sequence-specific protein-DNA interactions are at the heart of the response of the tumor-suppressor p53 to numerous physiological and stress-related signals. Large variability has been previously reported in p53 binding to and transactivating from p53 response elements (REs) due, at least in part, to changes in direct (base) and indirect (shape) readouts of p53 REs. Here, we dissect p53 REs to decipher the mechanism by which p53 optimizes this highly regulated variable level of interaction with its DNA binding sites. We show that hemi-specific binding is more prevalent in p53 REs than previously envisioned. We reveal that sequences flanking the REs modulate p53 binding and activity and show that these effects extend to 4–5 bp from the REs. Moreover, we show here that the arrangement of p53 half-sites within its REs, relative to transcription direction, has been fine-tuned by selection pressure to optimize and regulate the response levels from p53 REs. This directionality in the REs arrangement is at least partly encoded in the structural properties of the REs. Furthermore, we show here that in the p21-5′ RE the orientation of the half-sites is such that the effect of the flanking sequences is minimized and we discuss its advantages.
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Affiliation(s)
- Alon Senitzki
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Jessy Safieh
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Vasundhara Sharma
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, TN, Italy
| | - Dmitrij Golovenko
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Yael Danin-Poleg
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, TN, Italy
| | - Tali E Haran
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel
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15
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Farkas M, Hashimoto H, Bi Y, Davuluri RV, Resnick-Silverman L, Manfredi JJ, Debler EW, McMahon SB. Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates. Nat Commun 2021; 12:484. [PMID: 33473123 PMCID: PMC7817693 DOI: 10.1038/s41467-020-20783-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/15/2020] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor p53 integrates stress response pathways by selectively engaging one of several potential transcriptomes, thereby triggering cell fate decisions (e.g., cell cycle arrest, apoptosis). Foundational to this process is the binding of tetrameric p53 to 20-bp response elements (REs) in the genome (RRRCWWGYYYN0-13RRRCWWGYYY). In general, REs at cell cycle arrest targets (e.g. p21) are of higher affinity than those at apoptosis targets (e.g., BAX). However, the RE sequence code underlying selectivity remains undeciphered. Here, we identify molecular mechanisms mediating p53 binding to high- and low-affinity REs by showing that key determinants of the code are embedded in the DNA shape. We further demonstrate that differences in minor/major groove widths, encoded by G/C or A/T bp content at positions 3, 8, 13, and 18 in the RE, determine distinct p53 DNA-binding modes by inducing different Arg248 and Lys120 conformations and interactions. The predictive capacity of this code was confirmed in vivo using genome editing at the BAX RE to interconvert the DNA-binding modes, transcription pattern, and cell fate outcome.
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Affiliation(s)
- Marina Farkas
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hideharu Hashimoto
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yingtao Bi
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ramana V Davuluri
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | | | - Erik W Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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16
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Shi T, Dansen TB. Reactive Oxygen Species Induced p53 Activation: DNA Damage, Redox Signaling, or Both? Antioxid Redox Signal 2020; 33:839-859. [PMID: 32151151 DOI: 10.1089/ars.2020.8074] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Significance: The p53 tumor suppressor has been dubbed the "guardian of genome" because of its various roles in the response to DNA damage such as DNA damage repair, cell cycle arrest, senescence, and apoptosis, all of which are in place to prevent mutations from being passed on down the lineage. Recent Advances: Reactive oxygen species (ROS), for instance hydrogen peroxide derived from mitochondrial respiration, have long been regarded mainly as a major source of cellular damage to DNA and other macromolecules. Critical Issues: More recently, ROS have been shown to also play important physiological roles as second messengers in so-called redox signaling. It is, therefore, not clear whether the observed activation of p53 by ROS is mediated through the DNA damage response, redox signaling, or both. In this review, we will discuss the similarities and differences between p53 activation in response to DNA damage and redox signaling in terms of upstream signaling and downstream transcriptional program activation. Future Directions: Understanding whether and how DNA damage and redox signaling-dependent p53 activation can be dissected could be useful to develop anti-cancer therapeutic p53-reactivation strategies that do not depend on the induction of DNA damage and the resulting additional mutational load.
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Affiliation(s)
- Tao Shi
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tobias B Dansen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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17
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Yang J, Bashkenova N, Zang R, Huang X, Wang J. The roles of TET family proteins in development and stem cells. Development 2020; 147:147/2/dev183129. [PMID: 31941705 DOI: 10.1242/dev.183129] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ten-eleven translocation (TET) methylcytosine dioxygenases are enzymes that catalyze the demethylation of 5-methylcytosine on DNA. Through global and site-specific demethylation, they regulate cell fate decisions during development and in embryonic stem cells by maintaining pluripotency or by regulating differentiation. In this Primer, we provide an updated overview of TET functions in development and stem cells. We discuss the catalytic and non-catalytic activities of TETs, and their roles as epigenetic regulators of both DNA and RNA hydroxymethylation, highlighting how TET proteins function in regulating gene expression at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nazym Bashkenova
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ruge Zang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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18
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Siddiqui NA, Mothana RA, Al-Said MS, Parvez MK, Alam P, Tabish Rehman M, Ali M, Alajmi MF, Al-Dosari MS, Al-Rehaily AJ, Nasr FA, Khalid JM. Cell proliferation activity delineated by molecular docking of four new compounds isolated from the aerial parts of Suaeda monoica Forssk. ex. J.F. Gmel. Saudi Pharm J 2019; 28:172-186. [PMID: 32042256 PMCID: PMC7000348 DOI: 10.1016/j.jsps.2019.11.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/29/2019] [Indexed: 11/17/2022] Open
Abstract
Using different chromatographic methods, four new compounds were isolated from the aerial parts of Suaeda monoica (Chenopodiaceae) along with 2-hydroxy-1-naphthoic acid (SCM-3). The structures of the new compounds were established as 6'-hydroxy-10'-geranilanyl naphtha-1-oate (SMC-1), 4,4,8β,10β-Tetramethyl-9β-isobutanyl decalin-13-ol-13-O-β-D-xylopyranoside (SCM-2), 6'-(2-hydroxynaphthalen-3-yl) hexanoic acid (SCM-4) and 1'-(2-Methoxy-3-naphthyl)-4'-(2''-methylbenzoyl)-n-butane (SMC-5) by IR, EIMS and NMR (1 & 2D) analyses. All compounds (50 μg/mL) were tested for cell proliferative potential on cultured human liver cell HepG2 cells by MTT assay. The results revealed a marked cell proliferative potential of all compounds (1.42-1.48 fold) as compared to untreated control. The results of molecular docking and binding with specific proteins such as PTEN (Phosphatase and Tensin homolog) and p53 also justify the cell proliferative potential of the isolated compounds. Glide program with Schrodinger suit 2018 was used to evaluate the binding between SMC compounds and proteins (PTEN and p53). The binding affinity of all compounds was in order of 104-105 M-1 towards both PTEN and p53. All the SMC compounds have been found to bind at the active site of PTEN, thereby may prevent the binding of phosphatidylinositiol 3,4,5-triphosphate (PI3P). In the locked position, PTEN would not be able to hydrolyze PI3P and hence the PI3P regulated signaling pathway remains active. Similarly, SMC molecules were found to interact with the amino acid residues (Ser99, Thr170, Gly199, and Asp224) which are critically involved in the formation of tetrameric p53. The blockage of p53 to attain its active conformation thus may prevent the recruitment of p53 on DNA and hence may promote cell proliferation.
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Affiliation(s)
- Nasir A. Siddiqui
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Corresponding author at: Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. BOX 2457, Riyadh 11451, Saudi Arabia.
| | - Mansour S. Al-Said
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K. Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Perwez Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - M. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohd. Ali
- Department of Pharmacognosy & Phytochemistry, Faculty of Pharmacy, Jamia Hamdard, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed S. Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Adnan J. Al-Rehaily
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fahd A. Nasr
- Medicinal Aromatic, and Poisonous Plants Research Center, Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Jamal M. Khalid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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19
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Huang Y, Liu N, Liu J, Liu Y, Zhang C, Long S, Luo G, Zhang L, Zhang Y. Mutant p53 drives cancer chemotherapy resistance due to loss of function on activating transcription of PUMA. Cell Cycle 2019; 18:3442-3455. [PMID: 31726940 DOI: 10.1080/15384101.2019.1688951] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
P53 is a critical tumor suppressor gene, activating p53 and its downstream targets to induce apoptosis is a promising way for cancer therapy. However, more than 50% of cancer patients have p53 mutations, which may cause cancer therapy resistance, and the underline mechanism is poorly understood. Here, we found that cell viability decrease and apoptosis induced by p53-dependent traditional drugs in colon cancer cells were eliminated in p53 mutant cells. Mutant p53 did not up-regulate the expression of its direct downstream targets PUMA and p21, due to the inhibition of PUMA transcription. Furthermore, mutant p53 could not bind to the promoter of PUMA to activate its transcription like WT p53 did, while overexpressed WT p53 rescued PUMA-induced subsequent apoptosis. In conclusion, our findings demonstrate mutant p53 may cause chemo-resistance of tumor because of inactivating PUMA transcription, which prompts some new insights for clinical therapy of cancer patients with mutant p53.Abbreviations: CRC: Colorectal cancer; CDKs: Cyclin-dependent kinases; PUMA: p53 up-regulated modulator of apoptosis; PDGF: the platelet-derived growth factor; WT p53: wild-type p53 protein; mutp53: mutant p53 proteins; BAX: Bcl-2-associated X protein; NOXA: Phorbol-12-myristate-13-acetate-induced protein 1.
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Affiliation(s)
- Yuan Huang
- College of Biology, Hunan University, Changsha, China
| | - Nannan Liu
- College of Biology, Hunan University, Changsha, China
| | - Jing Liu
- College of Biology, Hunan University, Changsha, China
| | - Yeying Liu
- College of Biology, Hunan University, Changsha, China
| | - Chuchu Zhang
- College of Biology, Hunan University, Changsha, China
| | - Shuaiyu Long
- College of Biology, Hunan University, Changsha, China
| | - Guang Luo
- College of Biology, Hunan University, Changsha, China
| | - Lingling Zhang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yingjie Zhang
- College of Biology, Hunan University, Changsha, China.,Shenzhen Institute, Hunan University, Shenzhen, China
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20
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Chen S, Wu J, Zhong S, Li Y, Zhang P, Ma J, Ren J, Tan Y, Wang Y, Au KF, Siebold C, Bond GL, Chen Z, Lu M, Jones EY, Lu X. iASPP mediates p53 selectivity through a modular mechanism fine-tuning DNA recognition. Proc Natl Acad Sci U S A 2019; 116:17470-17479. [PMID: 31395738 PMCID: PMC6717262 DOI: 10.1073/pnas.1909393116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The most frequently mutated protein in human cancer is p53, a transcription factor (TF) that regulates myriad genes instrumental in diverse cellular outcomes including growth arrest and cell death. Cell context-dependent p53 modulation is critical for this life-or-death balance, yet remains incompletely understood. Here we identify sequence signatures enriched in genomic p53-binding sites modulated by the transcription cofactor iASPP. Moreover, our p53-iASPP crystal structure reveals that iASPP displaces the p53 L1 loop-which mediates sequence-specific interactions with the signature-corresponding base-without perturbing other DNA-recognizing modules of the p53 DNA-binding domain. A TF commonly uses multiple structural modules to recognize its cognate DNA, and thus this mechanism of a cofactor fine-tuning TF-DNA interactions through targeting a particular module is likely widespread. Previously, all tumor suppressors and oncoproteins that associate with the p53 DNA-binding domain-except the oncogenic E6 from human papillomaviruses (HPVs)-structurally cluster at the DNA-binding site of p53, complicating drug design. By contrast, iASPP inhibits p53 through a distinct surface overlapping the E6 footprint, opening prospects for p53-targeting precision medicine to improve cancer therapy.
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Affiliation(s)
- Shuo Chen
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jiale Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shan Zhong
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Yuntong Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ping Zhang
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jingyi Ma
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jingshan Ren
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Yun Tan
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yunhao Wang
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Kin Fai Au
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Gareth L Bond
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - Min Lu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Xin Lu
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom;
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21
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Konc J, Skrlj B, Erzen N, Kunej T, Janezic D. GenProBiS: web server for mapping of sequence variants to protein binding sites. Nucleic Acids Res 2019; 45:W253-W259. [PMID: 28498966 PMCID: PMC5570222 DOI: 10.1093/nar/gkx420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/02/2017] [Indexed: 02/02/2023] Open
Abstract
Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites. The concept of a protein–compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org.
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Affiliation(s)
- Janez Konc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, 6000 Koper, Slovenia
| | - Blaz Skrlj
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Nika Erzen
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Tanja Kunej
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Dusanka Janezic
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, 6000 Koper, Slovenia
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22
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Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. MOLECULAR PLANT 2019; 12:743-763. [PMID: 30447332 DOI: 10.1016/j.molp.2018.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.
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Affiliation(s)
- Xuelei Lai
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
| | - Arnaud Stigliani
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Gilles Vachon
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cristel Carles
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cezary Smaczniak
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chloe Zubieta
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - François Parcy
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
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23
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Omar SI, Tuszynski J. The molecular mechanism of action of methylene quinuclidinone and its effects on the structure of p53 mutants. Oncotarget 2018; 9:37137-37156. [PMID: 30647850 PMCID: PMC6324685 DOI: 10.18632/oncotarget.26440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/26/2018] [Indexed: 11/25/2022] Open
Abstract
One of the most important tumor suppressor proteins in eukaryotic cells is the transcription factor called p53. The importance of this protein in cells comes from the fact that it regulates a wide variety of cellular processes including the cell cycle, metabolism, DNA repair, senescence and apoptosis. In cancer cells, p53 is a major target as the most mutated protein, which has led to the search for potential activators of the mutant protein. Currently, the only mutated-p53 activator in clinical trials is a small molecule called APR-246. There is evidence that the active metabolite of APR-246 binds covalently to mutant p53 and restores its wild-type (wt) activity. In this work, we created atomistic in silico models of the wt, mutant and drugged mutant p53 proteins each in complex with DNA. Using molecular dynamics simulations we generated equilibrated models of the complexes. Detailed analysis revealed that the binding of the APR-246 active metabolite to the mutant proteins alters their interaction with DNA. In particular, the binding of the molecule at loop L1 of the protein allows the loop to anchor the protein to DNA similarly to wt p53. Several important p53-DNA interactions lost due to mutation were also restored in the drugged mutants. These findings, not only provide a possible mechanism of action of this drug, but also criteria to use in virtual screening campaigns for other p53 activators.
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Affiliation(s)
- Sara Ibrahim Omar
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jack Tuszynski
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Department of Physics, Faculty of Science, University of Alberta, Edmonton, Alberta, Canada.,Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
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24
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Omar SI, Lepre MG, Morbiducci U, Deriu MA, Tuszynski JA. Virtual screening using covalent docking to find activators for G245S mutant p53. PLoS One 2018; 13:e0200769. [PMID: 30192754 PMCID: PMC6128461 DOI: 10.1371/journal.pone.0200769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/01/2018] [Indexed: 11/19/2022] Open
Abstract
TP53 is the most mutated gene in all cancers. The mutant protein also accumulates in cells. The high frequency of p53 mutations makes the protein a promising target for anti-cancer therapy. Only a few molecules have been found, using in vitro screening, to reactivate the mutant protein. APR-246 is currently the most successful mutant p53 activator, which reactivates the transcriptional activity of p53 by covalently binding to C124 of the protein. We have recently created in silico models of G245S-mp53 in its apo and DNA-bound forms. In this paper we further report on our in silico screening for potential activators of G245S-mp53. We filtered the ZINC15 database (13 million compounds) to only include drug-like molecules with moderate to standard reactivity. Our filtered database of 130,000 compounds was screened using the DOCKTITE protocol in the Molecular Operating Environment software. We performed covalent docking at C124 of G245S-mp53 to identify potential activators of the mutant protein. The docked compounds were ranked using a consensus scoring approach. We also used ADMET Predictor™ to predict pharmacokinetics and the possible toxicities of the compounds. Our screening procedure has identified compounds, mostly thiosemicarbazones and halo-carbonyls, with the best potential as G245S-mp53 activators, which are described in this work. Based on its binding scores and ADMET risk score, compound 2 is likely to have the best potential as a G245S-mp53 activator compared to the other top hits.
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Affiliation(s)
- Sara Ibrahim Omar
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marco Gaetano Lepre
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Marco Agostino Deriu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, Switzerland
| | - Jack A. Tuszynski
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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25
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Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E. DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinformatics 2018; 33:3661-3663. [PMID: 29036596 DOI: 10.1093/bioinformatics/btx495] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/01/2017] [Indexed: 01/06/2023] Open
Abstract
Summary Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. Availability and implementation The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. Contact delphi@clemson.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lin Li
- Department of Physics, Clemson University, Clemson, SC 29631, USA
| | - Zhe Jia
- Department of Physics, Clemson University, Clemson, SC 29631, USA
| | - Yunhui Peng
- Department of Physics, Clemson University, Clemson, SC 29631, USA
| | | | - Lexuan Sun
- Department of Physics, Clemson University, Clemson, SC 29631, USA
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29631, USA
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26
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New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins. Structure 2018; 26:1237-1250.e6. [PMID: 30057026 DOI: 10.1016/j.str.2018.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/03/2018] [Accepted: 06/20/2018] [Indexed: 01/01/2023]
Abstract
The tumor suppressor p53 acts as a transcription factor recognizing diverse DNA response elements (REs). Previous structural studies of p53-DNA complexes revealed non-canonical Hoogsteen geometry of A/T base pairs at conserved CATG motifs leading to changes in DNA shape and its interface with p53. To study the effects of DNA shape on binding characteristics, we designed REs with modified base pairs "locked" into either Hoogsteen or Watson-Crick form. Here we present crystal structures of these complexes and their thermodynamic and kinetic parameters, demonstrating that complexes with Hoogsteen base pairs are stabilized relative to those with all-Watson-Crick base pairs. CATG motifs are abundant in p53REs such as GADD45 and p53R2 related to cell-cycle arrest and DNA repair. The high-resolution structures of these complexes validate their propensity to adopt the unique Hoogsteen-induced structure, thus providing insights into the functional role of DNA shape and broadening the mechanisms that contribute to DNA recognition by proteins.
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27
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Stiewe T, Haran TE. How mutations shape p53 interactions with the genome to promote tumorigenesis and drug resistance. Drug Resist Updat 2018; 38:27-43. [PMID: 29857816 DOI: 10.1016/j.drup.2018.05.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
Abstract
The tumor suppressive transcription factor p53 regulates a wide array of cellular processes that confer upon cells an essential protection against cancer development. Wild-type p53 regulates gene expression by directly binding to DNA in a sequence-specific manner. p53 missense mutations are the most common mutations in malignant cells and can be regarded as synonymous with anticancer drug resistance and poor prognosis. The current review provides an overview of how the extraordinary variety of more than 2000 different mutant p53 proteins, known as the p53 mutome, affect the interaction of p53 with DNA. We discuss how the classification of p53 mutations to loss of function (LOF), gain of function (GOF), and dominant-negative (DN) inhibition of a remaining wild-type allele, hides a complex p53 mutation spectrum that depends on the distinctive nature of each mutant protein, requiring different therapeutic strategies for each mutant p53 protein. We propose to regard the different mutant p53 categories as continuous variables, that may not be independent of each other. In particular, we suggest here to consider GOF mutations as a special subset of LOF mutations, especially when mutant p53 binds to DNA through cooperation with other transcription factors, and we present a model for GOF mechanism that consolidates many observations on the GOF phenomenon. We review how novel mutant p53 targeting approaches aim to restore a wild-type-like DNA interaction and to overcome resistance to cancer therapy.
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Affiliation(s)
- Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35037 Marburg, Germany.
| | - Tali E Haran
- Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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28
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Li J, Sagendorf JM, Chiu TP, Pasi M, Perez A, Rohs R. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic Acids Res 2018; 45:12877-12887. [PMID: 29165643 PMCID: PMC5728407 DOI: 10.1093/nar/gkx1145] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022] Open
Abstract
Uncovering the mechanisms that affect the binding specificity of transcription factors (TFs) is critical for understanding the principles of gene regulation. Although sequence-based models have been used successfully to predict TF binding specificities, we found that including DNA shape information in these models improved their accuracy and interpretability. Previously, we developed a method for modeling DNA binding specificities based on DNA shape features extracted from Monte Carlo (MC) simulations. Prediction accuracies of our models, however, have not yet been compared to accuracies of models incorporating DNA shape information extracted from X-ray crystallography (XRC) data or Molecular Dynamics (MD) simulations. Here, we integrated DNA shape information extracted from MC or MD simulations and XRC data into predictive models of TF binding and compared their performance. Models that incorporated structural information consistently showed improved performance over sequence-based models regardless of data source. Furthermore, we derived and validated nine additional DNA shape features beyond our original set of four features. The expanded repertoire of 13 distinct DNA shape features, including six intra-base pair and six inter-base pair parameters and minor groove width, is available in our R/Bioconductor package DNAshapeR and enables a comprehensive structural description of the double helix on a genome-wide scale.
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Affiliation(s)
- Jinsen Li
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Jared M Sagendorf
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Tsu-Pei Chiu
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Marco Pasi
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alberto Perez
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Remo Rohs
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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29
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Manzetti S. Bonding of Butylparaben, Bis(2-ethylhexyl)-phthalate, and Perfluorooctanesulfonic Acid to DNA: Comparison with Benzo[a]pyrene Shows Low Probability for Strong Noncovalent DNA Intercalation. Chem Res Toxicol 2017; 31:22-36. [PMID: 29185724 DOI: 10.1021/acs.chemrestox.7b00265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Parabens, phthalates, and perfluorinated compounds are pollutant compounds used in cosmetics, plastics, and fire-fighting foams. All three compounds have been studied over several years for toxicity mechanism; however, a clear view of their ability to bind to DNA has not been supplied empirically. In this work, a simulation study is done to reveal the interaction of three of these pollutants, bis(2-ethylhexyl)-phthalate (DEHP), butylparaben (BPRB), and the protonated form of perfluorooctanesulfonic acid (PFOS(H)), with DNA. The results show that the DEHP, PFOS(H), and BPRB bind with a probability of 1/5 to DNA, with respective bonding energies -23.96 kJ/mol (PFOS(H)), -94.92 kJ/mol (BPRB), and -216.52 kJ/mol (DEHP). The positive control, benzo[a]pyrene diol epoxide (BAP), which is known for its notorious DNA intercalation, binds at a rate of 3/5 simulations, with bonding energies of -6544.52, -7034.66, and -7578.67 kJ/mol. The results are compared to empirical studies and conclusively show that all these pollutants can interfere with transcription and DNA related mechanisms by forming noncovalent interactions with DNA. The results show also that these pollutants are unlikely to undergo strong noncovalent intercalation to DNA, such as BAP, and do not possess the frontier orbital profiles to undergo adduct formation. After many years of research and several unanswered questions on the action of these pollutants on DNA, a calculation on their properties hence to the DNA confirms that there is a low probability for these to undergo a strong intercalation with DNA. Literature shows however that the pollutants are strongly interfering with the protein machinery and receptors on the cell surface and are therefore still priority pollutants for ecotoxicity research.
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Affiliation(s)
- Sergio Manzetti
- Department of Cellular and Molecular Biology, Computational Ecotoxicity Group, Uppsala University , Husargatan 3, SE-75124 Uppsala, Sweden.,Fjordforsk AS, Midtun 155, 6894 Vangsnes, Norway
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30
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Schneider B, Božíková P, Čech P, Svozil D, Černý J. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes (Basel) 2017; 8:E278. [PMID: 29057824 PMCID: PMC5664128 DOI: 10.3390/genes8100278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/06/2017] [Accepted: 10/13/2017] [Indexed: 01/21/2023] Open
Abstract
We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
| | - Paulína Božíková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
| | - Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic.
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
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31
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White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal 2017; 10:10/495/eaam9931. [PMID: 28874603 DOI: 10.1126/scisignal.aam9931] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intracellular pH (pHi) of most cancers is constitutively higher than that of normal cells and enhances proliferation and cell survival. We found that increased pHi enabled the tumorigenic behaviors caused by somatic arginine-to-histidine mutations, which are frequent in cancer and confer pH sensing not seen with wild-type proteins. Experimentally raising the pHi increased the activity of R776H mutant epidermal growth factor receptor (EGFR-R776H), thereby increasing proliferation and causing transformation in fibroblasts. An Arg-to-Gly mutation did not confer these effects. Molecular dynamics simulations of EGFR suggested that decreased protonation of His776 at high pH causes conformational changes in the αC helix that may stabilize the active form of the kinase. An Arg-to-His, but not Arg-to-Lys, mutation in the transcription factor p53 (p53-R273H) decreased its transcriptional activity and attenuated the DNA damage response in fibroblasts and breast cancer cells with high pHi. Lowering pHi attenuated the tumorigenic effects of both EGFR-R776H and p53-R273H. Our data suggest that some somatic mutations may confer a fitness advantage to the higher pHi of cancer cells.
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Affiliation(s)
- Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicolas B Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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32
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Lepre MG, Omar SI, Grasso G, Morbiducci U, Deriu MA, Tuszynski JA. Insights into the Effect of the G245S Single Point Mutation on the Structure of p53 and the Binding of the Protein to DNA. Molecules 2017; 22:E1358. [PMID: 28813011 PMCID: PMC6152093 DOI: 10.3390/molecules22081358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/13/2017] [Accepted: 08/13/2017] [Indexed: 12/20/2022] Open
Abstract
The transcription factor p53 is a potent tumor suppressor dubbed as the "guardian of the genome" because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be a structural hotspot mutation. To understand the behaviors and differences between the wild-type and mutant, both a dimer of the wild type p53 (wt-p53) and its G245S mutant (G245S-mp53), complexed with DNA, were simulated using molecular dynamics for more than 1 μs. wt-p53 and G245S-mp53 apo monomers were simulated for 1 μs as well. Conformational analyses and binding energy evaluations performed underline important differences and therefore provide insights to understand the G245S-mp53 loss of function. Our results indicate that the G245S mutation destabilizes several structural regions in the protein that are crucial for DNA binding when found in its apo form and highlight differences in the mutant-DNA complex structure compared to the wt protein. These findings not only provide means that can be applied to other p53 mutants but also serve as structural basis for further studies aimed at the development of cancer therapies based on restoring the function of p53.
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Affiliation(s)
- Marco Gaetano Lepre
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
| | - Sara Ibrahim Omar
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | - Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
| | - Marco Agostino Deriu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Jack A Tuszynski
- Department of Oncology, Department of Physics, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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33
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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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Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
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35
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Sukhbaatar N, Bachmayr-Heyda A, Auer K, Aust S, Deycmar S, Horvat R, Pils D. Two different, mutually exclusively distributed, TP53 mutations in ovarian and peritoneal tumor tissues of a serous ovarian cancer patient: indicative for tumor origin? Cold Spring Harb Mol Case Stud 2017; 3:a001461. [PMID: 28679689 PMCID: PMC5495036 DOI: 10.1101/mcs.a001461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/31/2017] [Indexed: 12/13/2022] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is characterized by a TP53 mutation rate of up to 96.7% and associated with a more aggressive tumor biology. The origin of HGSOC is thought to arise either from fallopian tube secretory cells or the ovarian surface epithelium/inclusion cysts, the former with more evidence. Peritoneal tumor spread is heterogeneous, either excessive in the peritoneum (with miliary appearance) or more confined to the ovaries with only few (bigger and exophytically growing) peritoneal implants. Using RNA sequencing and DNA digital droplet polymerase chain reaction (PCR), we identified two different functional TP53 mutations in one HGSOC patient: one exclusively in the ovarian tumor mass and the other exclusively in ascites tumor cells, peritoneal tumor masses, and a lymph node metastasis. In blood, both mutations could be detected, the one from the peritoneal tumors with much higher frequency, presumably because of the higher tumor load. We conclude that this mutually exclusive distribution of two different TP53 mutations in different tumor tissues indicates the development of two independent carcinomas in the peritoneal cavity, probably one originating from a precancerous lesion in the fallopian tube and the other from the ovaries. In addition, in the patient's ascites CD45 and EpCAM, double-positive cells were found-proliferating but testing negative for the above-mentioned TP53 mutations. This mutually exclusive distribution of two TP53 mutations is probably further evidence that HGSOC can originate either from the fallopian tube or (more seldom) the ovaries, the former more prone for excessive peritoneal tumor spread.
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Affiliation(s)
- Nyamdelger Sukhbaatar
- Department of Obstetrics and Gynecology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Anna Bachmayr-Heyda
- Department of Obstetrics and Gynecology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Katharina Auer
- Department of Obstetrics and Gynecology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Stefanie Aust
- Department of Obstetrics and Gynecology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Simon Deycmar
- Department of Obstetrics and Gynecology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Reinhard Horvat
- Department of Pathology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Dietmar Pils
- Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems (CeMSIIS), Medical University of Vienna, A-1090 Vienna, Austria
- Department of Surgery, Medical University of Vienna, A-1090 Vienna, Austria
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36
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Leng F. Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. Biophys Rev 2017; 8:123-133. [PMID: 28510217 DOI: 10.1007/s12551-016-0239-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/27/2016] [Indexed: 12/18/2022] Open
Abstract
Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (-) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop. These constrained (-) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.
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Affiliation(s)
- Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.
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37
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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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38
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Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode. J Mol Biol 2016; 428:3013-25. [DOI: 10.1016/j.jmb.2016.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/09/2016] [Accepted: 06/14/2016] [Indexed: 01/20/2023]
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39
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Leng F. Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. Biophys Rev 2016; 8:197-207. [PMID: 28510223 DOI: 10.1007/s12551-016-0204-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022] Open
Abstract
Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (-) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop. These constrained (-) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.
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Affiliation(s)
- Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.
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40
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dos Santos HG, Nunez-Castilla J, Siltberg-Liberles J. Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One 2016; 11:e0151961. [PMID: 27003913 PMCID: PMC4803236 DOI: 10.1371/journal.pone.0151961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Conformational and functional flexibility promote protein evolvability. High evolvability allows related proteins to functionally diverge and perhaps to neostructuralize. p53 is a multifunctional protein frequently referred to as the Guardian of the Genome–a hub for e.g. incoming and outgoing signals in apoptosis and DNA repair. p53 has been found to be structurally disordered, an extreme form of conformational flexibility. Here, p53, and its paralogs p63 and p73, were studied for further insights into the evolutionary dynamics of structural disorder, secondary structure, and phosphorylation. This study is focused on the post gene duplication phase for the p53 family in vertebrates, but also visits the origin of the protein family and the early domain loss and gain events. Functional divergence, measured by rapid evolutionary dynamics of protein domains, structural properties, and phosphorylation propensity, is inferred across vertebrate p53 proteins, in p63 and p73 from fish, and between the three paralogs. In particular, structurally disordered regions are redistributed among paralogs, but within clades redistribution of structural disorder also appears to be an ongoing process. Despite its deemed importance as the Guardian of the Genome, p53 is indeed a protein with high evolvability as seen not only in rearranged structural disorder, but also in fluctuating domain sequence signatures among lineages.
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Affiliation(s)
- Helena G. dos Santos
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
| | - Janelle Nunez-Castilla
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
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41
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Al-Zyoud WA, Hynson RMG, Ganuelas LA, Coster ACF, Duff AP, Baker MAB, Stewart AG, Giannoulatou E, Ho JWK, Gaus K, Liu D, Lee LK, Böcking T. Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Res 2016; 44:1411-20. [PMID: 26681693 PMCID: PMC4756830 DOI: 10.1093/nar/gkv1466] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022] Open
Abstract
Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR-DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR-DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites/genetics
- Chromatography, Gel
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon/genetics
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Multimerization
- Protein Structure, Tertiary
- Scattering, Small Angle
- Sequence Homology, Nucleic Acid
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
- X-Ray Diffraction
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Affiliation(s)
- Walid A Al-Zyoud
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Robert M G Hynson
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Lorraine A Ganuelas
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Adelle C F Coster
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Matthew A B Baker
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Alastair G Stewart
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Eleni Giannoulatou
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Joshua W K Ho
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Katharina Gaus
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Lawrence K Lee
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
| | - Till Böcking
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
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42
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Zhang X, Xu CX, Di Felice R, Sponer J, Islam B, Stadlbauer P, Ding Y, Mao L, Mao ZW, Qin PZ. Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. Biochemistry 2015; 55:360-72. [PMID: 26678746 DOI: 10.1021/acs.biochem.5b01189] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Guanine-rich oligonucleotides can form a unique G-quadruplex (GQ) structure with stacking units of four guanine bases organized in a plane through Hoogsteen bonding. GQ structures have been detected in vivo and shown to exert their roles in maintaining genome integrity and regulating gene expression. Understanding GQ conformation is important for understanding its inherent biological role and for devising strategies to control and manipulate functions based on targeting GQ. Although a number of biophysical methods have been used to investigate structure and dynamics of GQs, our understanding is far from complete. As such, this work explores the use of the site-directed spin labeling technique, complemented by molecular dynamics simulations, for investigating GQ conformations. A nucleotide-independent nitroxide label (R5), which has been previously applied for probing conformations of noncoding RNA and DNA duplexes, is attached to multiple sites in a 22-nucleotide DNA strand derived from the human telomeric sequence (hTel-22) that is known to form GQ. The R5 labels are shown to minimally impact GQ folding, and inter-R5 distances measured using double electron-electron resonance spectroscopy are shown to adequately distinguish the different topological conformations of hTel-22 and report variations in their occupancies in response to changes of the environment variables such as salt, crowding agent, and small molecule ligand. The work demonstrates that the R5 label is able to probe GQ conformation and establishes the base for using R5 to study more complex sequences, such as those that may potentially form multimeric GQs in long telomeric repeats.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Cui-Xia Xu
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China
| | - Rosa Di Felice
- Department of Physics and Astronomy, University of Southern California , Los Angeles, California 90089, United States.,Center S3, CNR institute of Nanoscience , Modena, Italy
| | - Jiri Sponer
- Central European Institute of Technology (CEITEC), Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Barira Islam
- Central European Institute of Technology (CEITEC), Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Yuan Ding
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Lingling Mao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China
| | - Zong-Wan Mao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China
| | - Peter Z Qin
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
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43
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p53 dynamics upon response element recognition explored by molecular simulations. Sci Rep 2015; 5:17107. [PMID: 26596470 PMCID: PMC4656996 DOI: 10.1038/srep17107] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/26/2015] [Indexed: 01/25/2023] Open
Abstract
p53 is a representative transcription factor that activates multiple target genes. To realize stimulus-dependent specificities, p53 has to recognize targets with structural variety, of which molecular mechanisms are largely unknown. Here, we conducted a series of long-time scale (totally more than 100-ms) coarse-grained molecular dynamics simulations, uncovering structure and dynamics of full-length p53 tetramer that recognizes its response element (RE). We obtained structures of a full-length p53 tetramer that binds to the RE, which is strikingly different from the structure of p53 at search. These structures are not only consistent with previous low-resolution or partial structural information, but also give access to previously unreachable detail, such as the preferential distribution of intrinsically disordered regions, the contacts between core domains, the DNA bending, and the connectivity of linker regions. We also explored how the RE variation affects the structure of the p53-RE complex. Further analysis of simulation trajectories revealed how p53 finds out the RE and how post-translational modifications affect the search mechanism.
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44
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Significant Differences in the Development of Acquired Resistance to the MDM2 Inhibitor SAR405838 between In Vitro and In Vivo Drug Treatment. PLoS One 2015; 10:e0128807. [PMID: 26070072 PMCID: PMC4466389 DOI: 10.1371/journal.pone.0128807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/30/2015] [Indexed: 01/27/2023] Open
Abstract
SAR405838 is a potent and specific MDM2 inhibitor currently being evaluated in Phase I clinical trials for the treatment of human cancer. Using the SJSA-1 osteosarcoma cell line which harbors an amplified MDM2 gene and wild-type p53, we have investigated the acquired resistance mechanisms both in vitro and in vivo to SAR405838. Treatment of SJSA-1 cells with SAR405838 in vitro leads to dose-dependent cell growth inhibition, cell cycle arrest and robust apoptosis. However, prolonged treatment of SJSA-1 cells in vitro with SAR405838 results in profound acquired resistance to the drug. Analysis of in vitro-derived resistant cell lines showed that p53 is mutated in the DNA binding domain and can no longer be activated by SAR405838. Treatment of the parental SJSA-1 xenograft tumors with SAR405838 in mice yields rapid tumor regression but the tumors eventually regrow. Culturing the regrown tumors established a number of sublines, which showed only modest (3–5 times) loss of sensitivity to SAR405838 in vitro. Sequencing of the p53 showed that it retains its wild-type status in these in vivo sublines, with the exception of one subline, which harbors a single heterozygous C176F p53 mutation. Using xenograft models of two in vivo derived sublines, which has either wild-type p53 or p53 containing a single heterozygous C176F mutation, we showed that while SAR405838 effectively achieves partial tumor regression in these models, it no longer induces complete tumor regression and tumors resume growth once the treatment is stopped. Harvesting and culturing tumors obtained from a prolonged treatment with SAR405838 in mice established additional in vivo sublines, which all contain a single heterozygous C176F mutation with no additional p53 mutation detected. Interestingly, SAR405838 can still effectively activate p53 in all sublines containing a single heterozygous C176F mutation, with a moderately reduced potency as compared to that in the parental cell line. Consistently, SAR405838 is 3–5 times less effective in all the in vivo derived sublines containing a single heterozygous C176F p53 mutation than in the SJSA-1 parental cell line in assays of cell growth and apoptosis. Computational modeling suggested that a p53 tetramer containing two wild-type p53 molecules and two C176F mutated molecules can maintain the structural stability and interactions with DNA by formation of additional hydrophobic and cation-π interactions which compensate for the loss of sulphur-zinc coordination. Our data thus show that SJSA-1 tumor cells acquire very different levels of resistance in vitro and in vivo to the MDM2 inhibitor SAR405838. Our present study may have a significant implication for the investigation of resistant mechanisms for other classes of anticancer drugs.
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FUSE Binding Protein 1 Facilitates Persistent Hepatitis C Virus Replication in Hepatoma Cells by Regulating Tumor Suppressor p53. J Virol 2015; 89:7905-21. [PMID: 25995247 DOI: 10.1128/jvi.00729-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/14/2015] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) is a leading cause of chronic hepatitis C (CHC), liver cirrhosis, and hepatocellular carcinoma (HCC). Immunohistochemistry of archived HCC tumors showed abundant FBP1 expression in HCC tumors with the CHC background. Oncomine data analysis of normal versus HCC tumors with the CHC background indicated a 4-fold increase in FBP1 expression with a concomitant 2.5-fold decrease in the expression of p53. We found that FBP1 promotes HCV replication by inhibiting p53 and regulating BCCIP and TCTP, which are positive and negative regulators of p53, respectively. The severe inhibition of HCV replication in FBP1-knockdown Huh7.5 cells was restored to a normal level by downregulation of either p53 or BCCIP. Although p53 in Huh7.5 cells is transcriptionally inactive as a result of Y220C mutation, we found that the activation and DNA binding ability of Y220C p53 were strongly suppressed by FBP1 but significantly activated upon knockdown of FBP1. Transient expression of FBP1 in FBP1 knockdown cells fully restored the control phenotype in which the DNA binding ability of p53 was strongly suppressed. Using electrophoretic mobility shift assay (EMSA) and isothermal titration calorimetry (ITC), we found no significant difference in in vitro target DNA binding affinity of recombinant wild-type p53 and its Y220C mutant p53. However, in the presence of recombinant FBP1, the DNA binding ability of p53 is strongly inhibited. We confirmed that FBP1 downregulates BCCIP, p21, and p53 and upregulates TCTP under radiation-induced stress. Since FBP1 is overexpressed in most HCC tumors with an HCV background, it may have a role in promoting persistent virus infection and tumorigenesis. IMPORTANCE It is our novel finding that FUSE binding protein 1 (FBP1) strongly inhibits the function of tumor suppressor p53 and is an essential host cell factor required for HCV replication. Oncomine data analysis of a large number of samples has revealed that overexpression of FBP1 in most HCC tumors with chronic hepatitis C is significantly linked with the decreased expression level of p53. The most significant finding is that FBP1 not only physically interacts with p53 and interferes with its binding to the target DNA but also functions as a negative regulator of p53 under cellular stress. FBP1 is barely detectable in normal differentiated cells; its overexpression in HCC tumors with the CHC background suggests that FBP1 has an important role in promoting HCV infection and HCC tumors by suppressing p53.
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Comoglio F, Schlumpf T, Schmid V, Rohs R, Beisel C, Paro R. High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep 2015; 11:821-34. [PMID: 25921534 DOI: 10.1016/j.celrep.2015.03.070] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/09/2015] [Accepted: 03/29/2015] [Indexed: 11/16/2022] Open
Abstract
At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, the genetic and chromatin features defining metazoan replication start sites remain largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and suggest that they transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence motifs, mark and predict origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship among DNA topology, chromatin, transcription, and replication initiation across metazoa.
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Affiliation(s)
- Federico Comoglio
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tommy Schlumpf
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Virginia Schmid
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A 2015; 112:4654-9. [PMID: 25775564 DOI: 10.1073/pnas.1422023112] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
DNA binding specificities of transcription factors (TFs) are a key component of gene regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs to their genomic target sites are poorly understood. A better understanding of TF-DNA binding requires the ability to quantitatively model TF binding to accessible DNA as its basic step, before additional in vivo components can be considered. Traditionally, these models were built based on nucleotide sequence. Here, we integrated 3D DNA shape information derived with a high-throughput approach into the modeling of TF binding specificities. Using support vector regression, we trained quantitative models of TF binding specificity based on protein binding microarray (PBM) data for 68 mammalian TFs. The evaluation of our models included cross-validation on specific PBM array designs, testing across different PBM array designs, and using PBM-trained models to predict relative binding affinities derived from in vitro selection combined with deep sequencing (SELEX-seq). Our results showed that shape-augmented models compared favorably to sequence-based models. Although both k-mer and DNA shape features can encode interdependencies between nucleotide positions of the binding site, using DNA shape features reduced the dimensionality of the feature space. In addition, analyzing the feature weights of DNA shape-augmented models uncovered TF family-specific structural readout mechanisms that were not revealed by the DNA sequence. As such, this work combines knowledge from structural biology and genomics, and suggests a new path toward understanding TF binding and genome function.
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48
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Schaefer K, Geil WM, Sweredoski MJ, Moradian A, Hess S, Barton JK. Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain. Biochemistry 2015; 54:932-41. [PMID: 25584637 PMCID: PMC4310631 DOI: 10.1021/bi501424v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/19/2014] [Indexed: 11/29/2022]
Abstract
Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were (13)C2D2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward (13)C2D2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.
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Affiliation(s)
- Kathryn
N. Schaefer
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Wendy M. Geil
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Michael J. Sweredoski
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Annie Moradian
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Sonja Hess
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
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49
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Tangprasertchai NS, Zhang X, Ding Y, Tham K, Rohs R, Haworth IS, Qin PZ. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. Methods Enzymol 2015; 564:427-53. [PMID: 26477260 PMCID: PMC4641853 DOI: 10.1016/bs.mie.2015.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.
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Affiliation(s)
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Kenneth Tham
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ian S. Haworth
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA,Corresponding author:
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50
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Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SFA, Wells AD, Chen L. DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions. Nucleic Acids Res 2015; 43:1268-82. [PMID: 25567984 PMCID: PMC4333414 DOI: 10.1093/nar/gku1373] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 12/12/2022] Open
Abstract
FOXP3 is a lineage-specific transcription factor that is required for regulatory T cell development and function. In this study, we determined the crystal structure of the FOXP3 forkhead domain bound to DNA. The structure reveals that FOXP3 can form a stable domain-swapped dimer to bridge DNA in the absence of cofactors, suggesting that FOXP3 may play a role in long-range gene interactions. To test this hypothesis, we used circular chromosome conformation capture coupled with high throughput sequencing (4C-seq) to analyze FOXP3-dependent genomic contacts around a known FOXP3-bound locus, Ptpn22. Our studies reveal that FOXP3 induces significant changes in the chromatin contacts between the Ptpn22 locus and other Foxp3-regulated genes, reflecting a mechanism by which FOXP3 reorganizes the genome architecture to coordinate the expression of its target genes. Our results suggest that FOXP3 mediates long-range chromatin interactions as part of its mechanisms to regulate specific gene expression in regulatory T cells.
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Affiliation(s)
- Yongheng Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chunxia Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Chun-Chi Liu
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew E Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | | | - Lee E Edsall
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Xianghong Jasmine Zhou
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Struan F A Grant
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Lin Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
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