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Pan W, Biswas T, Shahabi S, Suryajaya W, Vasquez A, Du Q, Ghosh G, Wang VYF. Phosphorylation-induced flexibility of proto-oncogenic Bcl3 regulates transcriptional activation by NF-κB p52 homodimer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.601400. [PMID: 38979190 PMCID: PMC11230411 DOI: 10.1101/2024.06.30.601400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The overexpression of proto-oncogene Bcl3 is observed in various cancers. Bcl3 is extensively phosphorylated and associates with homodimers of NF-κB p50 and p52 to regulate transcription. Through cellular and biochemical assays, we observed that phospho-mimetic Glu substitution at Ser366 in addition to previously studied Ser33, 114 and 446 is necessary to switch Bcl3 from an IκB-like inhibitor to a transcriptional activator. To study interactive features of p52 and Bcl3, and phosphorylation- mediated changes in Bcl3 that regulate DNA-binding by p52, we performed HDX-MS of both Bcl3 and p52 within various complexes. Nature of interactions within Bcl3:(p52:p52) complex in presence and absence of DNA, differential flexibility of Bcl3, and allosteric changes in Bcl3 upon phospho-modifications revealed why a facile accommodation of DNA requires phosphorylation. The inhibitory nature of unphosphorylated Bcl3 on DNA binding by p52:p52 also relieved by a C-terminal deletion of Bcl3. Overall, this study revealed mechanistic bases of how Bcl3 phosphorylation regulates transcriptional potential of NF-κB and intricate cell physiology, a dysregulation of which can lead to cancers.
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Hasegawa Y, Asada S. DNA-dependent protein kinase catalytic subunit binds to the transactivation domain 1 of NF-κB p65. Biochem Biophys Rep 2023; 35:101538. [PMID: 37674974 PMCID: PMC10477060 DOI: 10.1016/j.bbrep.2023.101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Nuclear factor-kappa B (NF-κB) is a transcriptional factor that binds to the ∼10-base-pair κB motif on target genes and acts as an inflammatory regulator. Since dysregulation of NF-κB is thought to be related to various diseases, it would be very important to elucidate its post-translational modifications and binding partners in detail and to deeply understand mechanisms of the NF-κB dysregulation. NF-κB p65 is known to interact with the basic transcription factor TFIID subunit hTAFII31/TAF9 through the ФXXФФ (Ф, hydrophobic amino acid; X, any amino acid) motif in a similar fashion to p53. MDM2 is known to inhibit p53 from binding to hTAFII31/TAF9 by masking p53's ФXXФФ motif. Here, as can be rationalized from this observation, we searched for novel nuclear proteins that interact with the transactivation domain 1 (TA1) of NF-κB p65 containing a ФXXФФ motif. We prepared a GST-tagged polypeptide, GST-p65532-550, from Phe532-Ser550 of the TA1 domain and found various U937 cell nuclear proteins that bound to GST-p65532-550. The largest bound protein the size of ∼400 kDa was subjected to mass spectrometric analysis and found to be DNA-dependent protein kinase catalytic subunit (DNA-PKcs). An immunoprecipitation experiment with an antibody against p65 and nuclear extracts from TNF-α-treated A549 cells suggested that NF-κB p65 indeed binds to DNA-PKcs in human cells. Furthermore, binding assays with a series of His-tagged DNA-PKcs fragments suggested that DNA-PKcs can bind to NF-κB p65 through the interaction of the TA1 domain with the region 541-750 in the N-HEAT domain or the region 2485-2576 in the M-HEAT domain.
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Affiliation(s)
- Yuta Hasegawa
- Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akiha-ku, Niigata, Niigata, 956-8603, Japan
| | - Shinichi Asada
- Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akiha-ku, Niigata, Niigata, 956-8603, Japan
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3
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Biswas D, Somkuwar BG, Borah JC, Varadwaj PK, Gupta S, Khan ZA, Mondal G, Chattoraj A, Deb L. Phytochemical mediated modulation of COX-3 and NFκB for the management and treatment of arthritis. Sci Rep 2023; 13:13612. [PMID: 37604838 PMCID: PMC10442333 DOI: 10.1038/s41598-023-37729-2] [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: 08/25/2022] [Accepted: 06/27/2023] [Indexed: 08/23/2023] Open
Abstract
In this study, we investigated whether zerumbone (ZBN), ellagic acid (ELA) and quercetin (QCT), the plant-derived components, can modulate the role of COX-3 or cytokines liable in arthritic disorder. Initially, the effect of ZBN, ELA, and QCT on inflammatory process was investigated using in-vitro models. In-silico docking and molecular dynamics study of these molecules with respective targets also corroborate with in-vitro studies. Further, the in-vivo anti-arthritic potential of these molecules in Complete Freund's adjuvant (CFA)-induced arthritic rats was confirmed. CFA increases in TNF-α and IL-1β levels in the arthritic control animals were significantly (***p < 0.001) attenuated in the ZBN- and ELA-treated animals. CFA-induced attenuation in IL-10 levels recovered under treatment. Moreover, ELA attenuated CFA-induced upregulation of COX-3 and ZBN downregulated CFA-triggered NFκB expression in arthritic animals. The bonding patterns of zerumbone in the catalytic sites of targets provide a useful hint in designing and developing suitable derivatives that can be used as a potential drug. To our best knowledge, the first time we are reporting the role of COX-3 in the treatment of arthritic disorders which could provide a novel therapeutic approach for the treatment of inflammatory disorders.
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Affiliation(s)
- Dipak Biswas
- Natural Product Chemistry and Pharmacology Programme, Medicinal Plants and Horticulture Resources Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Bharat Gopalrao Somkuwar
- Bioinformatics and Bioresources Database Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Jagat Chandra Borah
- Natural Product Chemistry and Pharmacology Programme, Medicinal Plants and Horticulture Resources Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
- Institute of Advanced Study in Science and Technology, (An Autonomous Institute Under Department of Science & Technology, Govt. of India) Vigyan Path, Paschim Boragaon Garchuk, Guwahati, 781035, Assam, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Devghat, Jhalwa, Allahabad, 211015, Uttar Pradesh, India
| | - Saurabh Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Devghat, Jhalwa, Allahabad, 211015, Uttar Pradesh, India
| | - Zeeshan Ahmad Khan
- Biological Rhythm Laboratory, Animal Resources Programme, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Gopinath Mondal
- Biological Rhythm Laboratory, Animal Resources Programme, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Asamanja Chattoraj
- Biological Rhythm Laboratory, Animal Resources Programme, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
- Department of Animal Science, Kazi Nazrul University, Paschim Bardhaman, Asansol, 71330, West Bengal, India
| | - Lokesh Deb
- Natural Product Chemistry and Pharmacology Programme, Medicinal Plants and Horticulture Resources Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India.
- Institute of Bioresources and Sustainable Development-Regional Centre, Sikkim (Department of Biotechnology, Government of India), 5th Mile, Near Metro Point, Tadong, Gangtok, 737102, Sikkim, India.
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Olajide M, Abdul-Hammed M, Bello IA, Adedotun IO, Afolabi TI. Identification of potential inhibitors of thymidylate synthase (TS) (PDB ID: 6QXH) and nuclear factor kappa-B (NF–κB) (PDB ID: 1A3Q) from Capsicum annuum (bell pepper) towards the development of new therapeutic drugs against colorectal cancer (CRC). PHYSICAL SCIENCES REVIEWS 2023. [DOI: 10.1515/psr-2022-0281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Abstract
Colorectal cancer is the third most deadly cancer globally. Drug resistance and attendant side effects make the available standard anti-colorectal cancer drugs against target receptors inefficient. Phytochemicals from medicinal plants are safer, cheaper, effective, and heal diseases from the cellular level. This study is aimed at identifying potential inhibitors of thymidylate synthase (TS) and nuclear factor kappa-B (NF–κB) target receptors from Capsicum annuum towards the development of new therapeutic drugs against colorectal cancer via in silico approach. One hundred and fifty (150) ligands previously reported from Capsicum annuum were downloaded from the PubChem database and were subjected to chemo-informatics analyses such as ADMET, drug-likeness, oral bioavailability, bioactivity, and PASS prediction to ascertain their therapeutic and safety profile before docking. The ligands that passed the analyses were docked against TS and NF–κB in duplicate using a creditable docking tool (PyRx). Raltitrexed and emetine were used as the standard drug inhibitors for TS and NF–κB, respectively. The results obtained from this study showed that feruloyl-beta-D-glucose (8.45 kcal/mol), 5-O-caffeoylquinic acid (−8.40 kcal/mol), 5-O-caffeoylquinic acid methyl ester (−7.89 kcal/mol), feruloyl hexoside (−7.40 kcal/mol), O-glucopyranoside (−7.55 kcal/mol), and quercetin (−7.00 kcal/mol) shared the same binding pocket with TS while feruloyl-beta-D-glucose (−7.00 kcal/mol), chlorogenic acid (−6.90 kcal/mol), 5-O-caffeoylquinic acid (−6.90 kcal/mol) and feruloyl hexoside (−6.50 kcal/mol) shared the same pocket with NF–κB. These compounds were selected as best hits due to their excellent inhibitory efficiency and chemoinformatic profiles. Thus, the compounds may function as prospective lead compounds for developing a new anti-colorectal cancer drug.
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Affiliation(s)
- Monsurat Olajide
- Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Along Ogbomoso Ilorin Expressway, Ladoke Akintola University Of Technology , Ogbomoso , Oyo , 210214 , Nigeria
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Ogbomoso , Oyo State , Nigeria
- Department of Chemical Sciences , Crescent University Abeokuta , Abeokuta , Ogun State , Nigeria
| | - Misbaudeen Abdul-Hammed
- Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Along Ogbomoso Ilorin Expressway, Ladoke Akintola University Of Technology , Ogbomoso , Oyo , 210214 , Nigeria
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Ogbomoso , Oyo State , Nigeria
| | - Isah Adewale Bello
- Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Along Ogbomoso Ilorin Expressway, Ladoke Akintola University Of Technology , Ogbomoso , Oyo , 210214 , Nigeria
| | - Ibrahim Olaide Adedotun
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Ogbomoso , Oyo State , Nigeria
| | - Tolulope Irapada Afolabi
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry , Ladoke Akintola University of Technology, Faculty of Pure and Applied Science , Ogbomoso , Oyo State , Nigeria
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5
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Deka K, Li Y. Transcriptional Regulation during Aberrant Activation of NF-κB Signalling in Cancer. Cells 2023; 12:cells12050788. [PMID: 36899924 PMCID: PMC10001244 DOI: 10.3390/cells12050788] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/16/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The NF-κB signalling pathway is a major signalling cascade involved in the regulation of inflammation and innate immunity. It is also increasingly recognised as a crucial player in many steps of cancer initiation and progression. The five members of the NF-κB family of transcription factors are activated through two major signalling pathways, the canonical and non-canonical pathways. The canonical NF-κB pathway is prevalently activated in various human malignancies as well as inflammation-related disease conditions. Meanwhile, the significance of non-canonical NF-κB pathway in disease pathogenesis is also increasingly recognized in recent studies. In this review, we discuss the double-edged role of the NF-κB pathway in inflammation and cancer, which depends on the severity and extent of the inflammatory response. We also discuss the intrinsic factors, including selected driver mutations, and extrinsic factors, such as tumour microenvironment and epigenetic modifiers, driving aberrant activation of NF-κB in multiple cancer types. We further provide insights into the importance of the interaction of NF-κB pathway components with various macromolecules to its role in transcriptional regulation in cancer. Finally, we provide a perspective on the potential role of aberrant NF-κB activation in altering the chromatin landscape to support oncogenic development.
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Affiliation(s)
- Kamalakshi Deka
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore 138673, Singapore
- Correspondence: ; Tel.: +65-6316-2947
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6
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Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VYF. Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. eLife 2023; 12:e86258. [PMID: 36779700 PMCID: PMC9991059 DOI: 10.7554/elife.86258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023] Open
Abstract
The mammalian NF-κB p52:p52 homodimer together with its cofactor Bcl3 activates transcription of κB sites with a central G/C base pair (bp), while it is inactive toward κB sites with a central A/T bp. To understand the molecular basis for this unique property of p52, we have determined the crystal structures of recombinant human p52 protein in complex with a P-selectin(PSel)-κB DNA (5'-GGGGTGACCCC-3') (central bp is underlined) and variants changing the central bp to A/T or swapping the flanking bp. The structures reveal a nearly two-fold widened minor groove in the central region of the DNA as compared to all other currently available NF-κB-DNA complex structures, which have a central A/T bp. Microsecond molecular dynamics (MD) simulations of free DNAs and p52 bound complexes reveal that free DNAs exhibit distinct preferred conformations, and p52:p52 homodimer induces the least amount of DNA conformational changes when bound to the more transcriptionally active natural G/C-centric PSel-κB, but adopts closed conformation when bound to the mutant A/T and swap DNAs due to their narrowed minor grooves. Our binding assays further demonstrate that the fast kinetics favored by entropy is correlated with higher transcriptional activity. Overall, our studies have revealed a novel conformation for κB DNA in complex with NF-κB and pinpoint the importance of binding kinetics, dictated by DNA conformational and dynamic states, in controlling transcriptional activation for NF-κB.
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Affiliation(s)
- Wenfei Pan
- Faculty of Health Sciences, University of MacauTaipaChina
| | | | - Tianjie Li
- Department of Physics, Chinese University of Hong KongShatinHong Kong
| | - Yi Wang
- Department of Physics, Chinese University of Hong KongShatinHong Kong
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of MacauTaipaChina
- MoE Frontiers Science Center for Precision Oncology, University of MacauTaipaMacao
- Cancer Centre, Faculty of Health Sciences, University of MacauTaipaChina
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7
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Bello SO, Yunusa A, Adamu AA, Imam MU, Bello MB, Shuaibu A, Igumbor EU, Habib ZG, Popoola MA, Ochu CL, Bello AY, Deeni YY, Okoye I. Innovative, rapid, high-throughput method for drug repurposing in a pandemic-A case study of SARS-CoV-2 and COVID-19. Front Pharmacol 2023; 14:1130828. [PMID: 36937851 PMCID: PMC10014809 DOI: 10.3389/fphar.2023.1130828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Several efforts to repurpose drugs for COVID-19 treatment have largely either failed to identify a suitable agent or agents identified did not translate to clinical use. Reasons that have been suggested to explain the failures include use of inappropriate doses, that are not clinically achievable, in the screening experiments, and the use of inappropriate pre-clinical laboratory surrogates to predict efficacy. In this study, we used an innovative algorithm, that incorporates dissemination and implementation considerations, to identify potential drugs for COVID-19 using iterative computational and wet laboratory methods. The drugs were screened at doses that are known to be achievable in humans. Furthermore, inhibition of viral induced cytopathic effect (CPE) was used as the laboratory surrogate to predict efficacy. Erythromycin, pyridoxine, folic acid and retapamulin were found to inhibit SARS-CoV-2 induced CPE in Vero cells at concentrations that are clinically achievable. Additional studies may be required to further characterize the inhibitions of CPE and the possible mechanisms.
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Affiliation(s)
- Shaibu Oricha Bello
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- *Correspondence: Shaibu Oricha Bello,
| | - Abdulmajeed Yunusa
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Adamu Ahmed Adamu
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Medical Biochemistry, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of veterinary Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abdulmalik Shuaibu
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of veterinary Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Ehimario Uche Igumbor
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - Zaiyad Garba Habib
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Department of Medicine, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Mustapha Ayodele Popoola
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
| | - Chinwe Lucia Ochu
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Nigerian Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Aishatu Yahaya Bello
- Department of Clinical pharmacy and Pharmacy Practice, Faculty of Pharmaceutical sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Yusuf Yahaya Deeni
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Department of Microbiology and Biotechnology, Federal University of Dutse, Dutse, Nigeria
- Centre for Environmental and Public Health Research and Development, Kano, Nigeria
| | - Ifeoma Okoye
- University of Nigeria Centre for Clinical Trials, University of Nigeria Teaching Hospital, Enugu, Ituku Ozalla, Nigeria
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Bernal GM, Wu L, Voce DJ, Weichselbaum RR, Yamini B. p52 signaling promotes cellular senescence. Cell Biosci 2022; 12:43. [PMID: 35379326 PMCID: PMC8981737 DOI: 10.1186/s13578-022-00779-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/27/2022] [Indexed: 11/24/2022] Open
Abstract
Background Nuclear factor-κB is a multi-subunit transcription factor that plays a central role in cellular senescence. We previously reported that an increase in the p52 subunit is seen in senescent cells and aged tissue. In the current work, we examined the mechanism by which p52 is activated and whether the increase in p52 promotes senescence. Results Using both primary mouse embryonic fibroblasts (MEFs) and WI-38 human lung fibroblasts, we examined cells after serial passage and following prolonged culture. An increase in p52 was found in the nucleus relative to pre-senescent cells. The increase in p52 protein was not reflected by an increase in NFKB2 mRNA or by an increase in the abundance of upstream activating kinases, IKKα and NIK. To examine whether p52 promotes senescence, we over-expressed mature p52 in primary MEFs. Significantly more senescence was seen compared to control, a finding not seen with p52 mutated at critical DNA binding residues. In addition, blocking p52 nuclear translocation with the peptide inhibitor, SN52, decreased β-galactosidase (β-gal) formation. Subsequent filtration studies demonstrated that proteins in conditioned media (CM) were necessary for the increase in p52 and mass spectrometry identified S100A4 and cyclophilin A (CYPA) as potential factors in CM necessary for induction of p52. The requirement of these proteins in CM for induction of p52 was confirmed using depletion and supplementation studies. In addition, we found that activation of STAT3 signaling was required for the increase in p52. Finally, genome wide ChIP-sequencing analysis confirmed that there is an increase in p52 chromatin enrichment with senescence and identified several downstream factors whose expression is regulated by increased p52 binding. Conclusions These results demonstrate that p52 nuclear translocation is increased in senescent cells by factors in conditioned media and that mature p52 induces cellular senescence. The data are consistent with the prior observation that p52 is elevated in aged tissue and support the hypothesis that p52 contributes to organismal aging. Supplementary information The online version contains supplementary material available at 10.1186/s13578-022-00779-6.
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Pal A, Chakrabarti P, Dey S. ProDFace: A web-tool for the dissection of protein-DNA interfaces. Front Mol Biosci 2022; 9:978310. [PMID: 36148013 PMCID: PMC9486321 DOI: 10.3389/fmolb.2022.978310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
Protein-DNA interactions play a crucial role in gene expression and regulation. Identifying the DNA binding surface of proteins has long been a challenge–in comparison to protein-protein interactions, limited progress has been made in the development of efficient DNA binding site prediction and protein-DNA docking methods. Here we present ProDFace, a web tool that characterizes the binding region of a protein-DNA complex based on amino acid propensity, hydrogen bond (HB) donor capacity (number of solvent accessible HB donor groups), sequence conservation at the interface core and rim region, and geometry. The program takes as input the structure of a protein-DNA complex in PDB (Protein Data Bank) format, and outputs various physicochemical and geometric parameters of the interface, as well as conservation of the interface residues in the protein component. Values are provided for the whole interface, and after dissecting it into core and rim regions. Details of water mediated HBs between protein and DNA, potential HB donor groups present at the binding surface of protein, and conserved interface residues are also provided as downloadable text files. These parameters can be useful in evaluating and validating protein-DNA docking solutions, structures derived from simulation as well as solutions from the available prediction tools, and facilitate the development of more efficient prediction methods. The web-tool is freely available at structbioinfo.iitj.ac.in/resources/bioinfo/pd_interface.
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Affiliation(s)
- Arumay Pal
- School of Bioengineering, Vellore Institute of Technology, Bhopal, India
| | | | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, India
- *Correspondence: Sucharita Dey,
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10
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Pan W, Deng L, Wang H, Wang VYF. Atypical IκB Bcl3 enhances the generation of the NF-κB p52 homodimer. Front Cell Dev Biol 2022; 10:930619. [PMID: 35990614 PMCID: PMC9389042 DOI: 10.3389/fcell.2022.930619] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
The NF-κB family of dimeric transcription factors regulate diverse biological functions. Their cellular expression profiles differ, which lead to different concentrations in different cell/tissue types. Although the activation mechanisms of different NF-κB dimers have been widely investigated, there is limited information on specific NF-κB dimers’ formation. The NF-κB p52:p52 homodimer regulates an important subset of target genes in cancer cells; however, the molecular mechanism of the generation of this specific homodimer remains unclear. Our study has revealed that the atypical IκB protein, Bcl3, plays an essential role in enhancing the p52:p52 homodimer population which is a unique mechanism to p52 within the NF-κB family. p52 was shown to heterodimerize with four other NF-κB subunits (RelA, RelB, cRel, and p50); all heterodimers, except p52:p50, are significantly more stable than the p52:p52 homodimer. Bcl3 is able to compete with all other NF-κB subunits in cells for efficient p52:p52 homodimer formation which consequently leads to the upregulation of target genes that are involved in cell proliferation, migration, and inflammation, which explain why aberrant activation of Bcl3 and p52 leads to cancer.
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Affiliation(s)
- Wenfei Pan
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Macau SAR, China
| | - Limei Deng
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Macau SAR, China
| | - Haitao Wang
- Thoracic Surgery Branch, Clinical Research, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Macau SAR, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Macau SAR, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida da Universidade, Macau SAR, China
- *Correspondence: Vivien Ya-Fan Wang,
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11
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Erdogan F, Qadree AK, Radu TB, Orlova A, de Araujo ED, Israelian J, Valent P, Mustjoki SM, Herling M, Moriggl R, Gunning PT. Structural and mutational analysis of member-specific STAT functions. Biochim Biophys Acta Gen Subj 2022; 1866:130058. [PMID: 34774983 DOI: 10.1016/j.bbagen.2021.130058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The STAT family of transcription factors control gene expression in response to signals from various stimulus. They display functions in diseases ranging from autoimmunity and chronic inflammatory disease to cancer and infectious disease. SCOPE OF REVIEW This work uses an approach informed by structural data to explore how domain-specific structural variations, post-translational modifications, and the cancer genome mutational landscape dictate STAT member-specific activities. MAJOR CONCLUSIONS We illustrated the structure-function relationship of STAT proteins and highlighted their effect on member-specific activity. We correlated disease-linked STAT mutations to the structure and cancer genome mutational landscape and proposed rational drug targeting approaches of oncogenic STAT pathway addiction. GENERAL SIGNIFICANCE Hyper-activated STATs and their variants are associated with multiple diseases and are considered high value oncology targets. A full understanding of the molecular basis of member-specific STAT-mediated signaling and the strategies to selectively target them requires examination of the difference in their structures and sequences.
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Affiliation(s)
- Fettah Erdogan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada
| | - Abdul K Qadree
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada
| | - Tudor B Radu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Canada
| | - Johan Israelian
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Satu M Mustjoki
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Marco Herling
- Department of Hematology, Cellular Therapy, and Hemostaseology, University of Leipzig, Leipzig, Germany
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada.
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12
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Ghosh G, Wang VYF. Origin of the Functional Distinctiveness of NF-κB/p52. Front Cell Dev Biol 2021; 9:764164. [PMID: 34888310 PMCID: PMC8650618 DOI: 10.3389/fcell.2021.764164] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
The transcription regulators of the NF-κB family have emerged as a critical factor affecting the function of various adult tissues. The NF-κB family transcription factors are homo- and heterodimers made up of five monomers (p50, p52, RelA, cRel and RelB). The family is distinguished by sequence homology in their DNA binding and dimerization domains, which enables them to bind similar DNA response elements and participate in similar biological programs through transcriptional activation and repression of hundreds of genes. Even though the family members are closely related in terms of sequence and function, they all display distinct activities. In this review, we discuss the sequence characteristics, protein and DNA interactions, and pathogenic involvement of one member of family, NF-κB/p52, relative to that of other members. We pinpoint the small sequence variations within the conserved region that are mostly responsible for its distinct functional properties.
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Affiliation(s)
- Gourisankar Ghosh
- Department of Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
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13
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Rauch DA, Harding JC, Ratner L, Wickline SA, Pan H. Targeting NF-κB with Nanotherapy in a Mouse Model of Adult T-Cell Leukemia/Lymphoma. NANOMATERIALS 2021; 11:nano11061582. [PMID: 34208564 PMCID: PMC8234599 DOI: 10.3390/nano11061582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022]
Abstract
Adult T-cell leukemia/lymphoma (ATLL) is an aggressive, clonal malignancy of mature T cells caused by human T-cell leukemia virus type 1. Although it is a rare tumor type, it serves as an excellent model of a virus driven process that transforms cells and engenders a highly malignant tumor that is extraordinarily difficult to treat. The viral transcriptional transactivator (Tax) in the HTLV-1 genome directly promotes tumorigenesis, and Tax-induced oncogenesis depends on its ability to constitutively activate NF-κB signaling. Accordingly, we developed and evaluated a nano-delivery system that simultaneously inhibits both canonical (p65) and noncanonical (p100) NF-κB signaling pathways locally in tumors after systemic administration. Our results demonstrate that siRNA is delivered rapidly to ATLL tumors after either i.p. or i.v. injection. The siRNA treatment significantly reduced both p65 and p100 mRNA and protein expression. Anti-NF-κB nanotherapy significantly inhibited tumor growth in two distinct tumor models in mice: a spontaneous Tax-driven tumor model, and a Tax tumor cell transplant model. Moreover, siRNA nanotherapy sensitized late-stage ATLL tumors to the conventional chemotherapeutic agent etoposide, indicating a pleiotropic benefit for localized siRNA nanotherapeutics.
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Affiliation(s)
- Daniel A. Rauch
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA; (J.C.H.); (L.R.)
- Correspondence: (D.A.R.); (H.P.); Tel.: +1-314-747-0506 (D.A.R.); +1-813-396-9755 (H.P.)
| | - John C. Harding
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA; (J.C.H.); (L.R.)
| | - Lee Ratner
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA; (J.C.H.); (L.R.)
| | - Samuel A. Wickline
- USF Health Heart Institute, University of South Florida, Tampa, FL 33602, USA;
| | - Hua Pan
- USF Health Heart Institute, University of South Florida, Tampa, FL 33602, USA;
- Correspondence: (D.A.R.); (H.P.); Tel.: +1-314-747-0506 (D.A.R.); +1-813-396-9755 (H.P.)
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14
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Bhaskar BV, Rammohan A, Babu TM, Zheng GY, Chen W, Rajendra W, Zyryanov GV, Gu W. Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies. Sci Rep 2021; 11:12150. [PMID: 34108504 PMCID: PMC8190100 DOI: 10.1038/s41598-021-90287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023] Open
Abstract
Dietary compounds play an important role in the prevention and treatment of many cancers, although their specific molecular mechanism is not yet known. In the present study, thirty dietary agents were analyzed on nine drug targets through in silico studies. However, nine dietary scaffolds, such as silibinin, flavopiridol, oleandrin, ursolic acid, α-boswellic acid, β-boswellic acid, triterpenoid, guggulsterone, and oleanolic acid potentially bound to the cavity of PI3K-α, PKC-η, H-Ras, and Ras with the highest binding energy. Particularly, the compounds silibinin and flavopiridol have been shown to have broad spectrum anticancer activity. Interestingly, flavopiridol was embedded in the pockets of PI3K-α and PKC-η as bound crystal inhibitors in two different conformations and showed significant interactions with ATP binding pocket residues. However, complex-based pharmacophore modeling achieved two vital pharmacophoric features namely, two H-bond acceptors for PI3K-α, while three are hydrophobic, one cat-donor and one H-bond donor and acceptor for PKC-η, respectively. The database screening with the ChemBridge core library explored potential hits on a valid pharmacophore query. Therefore, to optimize perspective lead compounds from the hits, which were subjected to various constraints such as docking, MM/GBVI, Lipinski rule of five, ADMET and toxicity properties. Henceforth, the top ligands were sorted out and examined for vital interactions with key residues, arguably the top three promising lead compounds for PI3K-α, while seven for PKC-η, exhibiting binding energy from - 11.5 to - 8.5 kcal mol-1. Therefore, these scaffolds could be helpful in the development of novel class of effective anticancer agents.
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Affiliation(s)
- Baki Vijaya Bhaskar
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China.
| | - Aluru Rammohan
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Ekaterinburg, 620002, Russia
| | | | - Gui Yu Zheng
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China
| | - Weibin Chen
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China
| | - Wudayagiri Rajendra
- Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, 517502, India
| | - Grigory V Zyryanov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Ekaterinburg, 620002, Russia
| | - Wei Gu
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China.
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15
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Raza T, Dhaka N, Joseph D, Dadhwal P, Kakita VMR, Atreya HS, Mukherjee SP. Insights into the NF-κB-DNA Interaction through NMR Spectroscopy. ACS OMEGA 2021; 6:12877-12886. [PMID: 34056439 PMCID: PMC8154232 DOI: 10.1021/acsomega.1c01299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Transcription factors bind specifically to their target elements in the genome, eliciting specific gene expression programs. The nuclear factor-κB (NF-κB) system is a family of proteins comprising inducible transcription activators, which play a critical role in inflammation and cancer. The NF-κB members function as dimers with each monomeric unit binding the κB-DNA. Despite the available structures of the various NF-κB dimers in complex with the DNA, the structural features of these dimers in the nucleic acid-free form are not well-characterized. Using solution NMR spectroscopy, we characterize the structural features of 73.1 kDa p50 subunit of the NF-κB homodimer in the DNA-free form and compare it with the κB DNA-bound form of the protein. The study further reveals that in the nucleic acid-free form, the two constituent domains of p50, the N-terminal and the dimerization domains, are structurally independent of each other. However, in a complex with the κB DNA, both the domains of p50 act as a single unit. The study also provides insights into the mechanism of κB DNA recognition by the p50 subunit of NF-κB.
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Affiliation(s)
- Tahseen Raza
- Department
of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee, Uttarakhand 247667, India
| | - Nitin Dhaka
- Department
of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee, Uttarakhand 247667, India
| | - David Joseph
- NMR
Research Centre, Indian Institute of Science
Bengaluru, Bengaluru, Karnataka 560012, India
| | - Prikshat Dadhwal
- Department
of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee, Uttarakhand 247667, India
| | - Veera Mohana Rao Kakita
- UM-DAE-Centre
for Excellence in Basic Sciences, University
of Mumbai, Kalina Campus, Mumbai, Maharashtra 400098, India
| | - Hanudatta S. Atreya
- NMR
Research Centre, Indian Institute of Science
Bengaluru, Bengaluru, Karnataka 560012, India
| | - Sulakshana P. Mukherjee
- Department
of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee, Uttarakhand 247667, India
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16
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Timucin AC. Structure based peptide design, molecular dynamics and MM-PBSA studies for targeting C terminal dimerization of NFAT5 DNA binding domain. J Mol Graph Model 2020; 103:107804. [PMID: 33248341 DOI: 10.1016/j.jmgm.2020.107804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 11/27/2022]
Abstract
NFAT5 as a transcription factor with an established role in osmotic stress response, has also been revealed to be active under numerous settings, including pathological conditions such as diabetic microvascular complications, chronic arthritis and cancer. Despite these links, current strategies for downregulating NFAT5 activity only relies on indirect modulators, not directly targeting NFAT5, itself. With this study, through using a computational approach, an original peptide was explored to directly target C terminal dimerization of NFAT5 RHR, located in its DNA binding domain. At first, homodimeric NFAT5 RHR bound to its consensus DNA was used for prediction of a preliminary peptide sequence. Possible amino acid replacements for this preliminary peptide were predicted for optimization, which was followed by addition of a cell penetrating peptide sequence. These attempts yielded a small peptide library, which was further investigated for peptide affinities towards C terminal of NFAT5 RHR through molecular docking, 50 ns and 250 ns molecular dynamics simulations, followed by estimation of MM-PBSA based relative binding free energies. Results indicated that after receiving mutations on the preliminary peptide sequence for optimization, a unique peptide could target C terminal dimerization region of NFAT5 RHR through using its cell penetrating peptide sequence. In conclusion, this is the first study presenting computational evidence on identification of a novel peptide capable of directly targeting NFAT5 dimerization. Besides, future implications of these observations were also discussed in terms of methodology and possible applications.
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Affiliation(s)
- Ahmet Can Timucin
- Department of Chemical Engineering, Faculty of Natural Sciences and Engineering, Üsküdar University, Turkey; Neuropsychopharmacology Application and Research Center (NPARC), Üsküdar University, Turkey.
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17
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Mulero MC, Wang VYF, Huxford T, Ghosh G. Genome reading by the NF-κB transcription factors. Nucleic Acids Res 2019; 47:9967-9989. [PMID: 31501881 PMCID: PMC6821244 DOI: 10.1093/nar/gkz739] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5'-GGGRNNNYCC-3' (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal structures of NF-κB in complex with diverse κB DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-κB dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-κB might overcome these obstacles. In this review, we first highlight structural features of NF-κB:DNA complexes and how distinctive features of NF-κB proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-κB dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-κB to selectively bind κB sites in vivo.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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18
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Mulero MC, Huxford T, Ghosh G. NF-κB, IκB, and IKK: Integral Components of Immune System Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:207-226. [PMID: 31628658 DOI: 10.1007/978-981-13-9367-9_10] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The NF-κB (Nuclear Factor kappa B) transcription factor plays crucial roles in the regulation of numerous biological processes including development of the immune system, inflammation, and innate and adaptive immune responses. Control over the immune cell functions of NF-κB results from signaling through one of two different routes: the canonical and noncanonical NF-κB signaling pathways. Present at the end of both pathways are the proteins NF-κB, IκB, and the IκB kinase (IKK). These proteins work together to deliver the myriad outcomes that influence context-dependent transcriptional control in immune cells. In the present chapter, we review the structural information available on NF-κB, IκB, and IKK, the critical terminal components of the NF-κB signaling, in relation to their physiological function.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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19
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Xu X, Li Y, Bharath SR, Ozturk MB, Bowler MW, Loo BZL, Tergaonkar V, Song H. Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1. Nat Commun 2018; 9:3183. [PMID: 30093619 PMCID: PMC6085347 DOI: 10.1038/s41467-018-05644-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Transcriptional factors ETS1/2 and p52 synergize downstream of non-canonical NF-κB signaling to drive reactivation of the −146C>T mutant TERT promoter in multiple cancer types, but the mechanism underlying this cooperativity remains unknown. Here we report the crystal structure of a ternary p52/ETS1/−146C>T TERT promoter complex. While p52 needs to associate with consensus κB sites on the DNA to function during non-canonical NF-κB signaling, we show that p52 can activate the −146C>T TERT promoter without binding DNA. Instead, p52 interacts with ETS1 to form a heterotetramer, counteracting autoinhibition of ETS1. Analogous to observations with the GABPA/GABPB heterotetramer, the native flanking ETS motifs are required for sustained activation of the −146C>T TERT promoter by the p52/ETS1 heterotetramer. These observations provide a unifying mechanism for transcriptional activation by GABP and ETS1, and suggest that genome-wide targets of non-canonical NF-κB signaling are not limited to those driven by consensus κB sequences. Incessant telomere synthesis in cancer cells depends on specific mutations in the TERT promoter, enabling its activation by transcription factors ETS1 and p52. Here, the authors elucidate the structural basis for p52/ETS1 binding to mutant TERT, suggesting a general mechanism for TERT reactivation in cancer.
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Affiliation(s)
- Xueyong Xu
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Yinghui Li
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Mert Burak Ozturk
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, France.,Unit of Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, France
| | - Bryan Zong Lin Loo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore. .,Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, 5001, SA, Australia.
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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20
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Chen B, Zhu Y, Ye S, Zhang R. Structure of the DNA-binding domain of human myelin-gene regulatory factor reveals its potential protein-DNA recognition mode. J Struct Biol 2018; 203:170-178. [PMID: 29729323 DOI: 10.1016/j.jsb.2018.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 04/04/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
Abstract
Myelin-gene regulatory factor (MYRF) is a membrane-bound transcription factors, which is responsible for the differentiation of oligodendrocytes and myelination of central nervous system. Followed by a self-cleavage by the intramolecular chaperone auto-processing (ICA) domain, DNA-binding domain (DBD) of MYRF is released from the endoplasmic reticulum (ER) and was then translocated to the nucleus to regulate gene expression. In present work, we have solved the crystal structure of the human MYRF-DBD to 1.85-Å resolution. It exhibits a typical s-type Ig-fold and packs as symmetric trimeric form in the crystal via hydrogen-bond networks in three regions. Accordingly, we identified a couple of key residues on MYRF-DBD, which might play important roles in DNA-binding, in particular Arg521 on its C-terminal tail. The R521A mutant of DBD showed only 17% affinity to dsDNA targets compared to wild-type DBD. Then we built a plausible protein-DNA binding model of MYRF-DBD, which will help to elucidate its mechanism in DNA-binding and transcriptional regulation.
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Affiliation(s)
- Baohua Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Sheng Ye
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.
| | - Rongguang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China.
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21
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Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J 2018; 37:63-74. [PMID: 29054852 PMCID: PMC5753038 DOI: 10.15252/embj.201797833] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/11/2017] [Accepted: 09/22/2017] [Indexed: 01/07/2023] Open
Abstract
DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA This active site can accommodate and excise N3-methylcytosine (3mC) and N1-methyladenine (1mA), which are also repaired by AlkB-catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Kori T Lay
- Department of Chemistry, University of California, Davis, CA, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, CA, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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22
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Cramer P. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday. J Mol Biol 2017; 429:2603-2610. [PMID: 28501586 DOI: 10.1016/j.jmb.2017.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 10/19/2022]
Abstract
Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective.
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Affiliation(s)
- Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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Structure determination of transient transcription complexes. Biochem Soc Trans 2017; 44:1177-82. [PMID: 27528766 DOI: 10.1042/bst20160079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 11/17/2022]
Abstract
The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects.
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Cookson VJ, Waite SL, Heath PR, Hurd PJ, Gandhi SV, Chapman NR. Binding loci of RelA-containing nuclear factor-kappaB dimers in promoter regions of PHM1-31 myometrial smooth muscle cells. Mol Hum Reprod 2015; 21:865-83. [DOI: 10.1093/molehr/gav051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/03/2015] [Indexed: 12/15/2022] Open
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25
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Fatima A, Abdul ABH, Abdullah R, Karjiban RA, Lee VS. Binding mode analysis of zerumbone to key signal proteins in the tumor necrosis factor pathway. Int J Mol Sci 2015; 16:2747-66. [PMID: 25629232 PMCID: PMC4346863 DOI: 10.3390/ijms16022747] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/07/2015] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the second most common cancer among women worldwide. Several signaling pathways have been implicated as causative and progression agents. The tumor necrosis factor (TNF) α protein plays a dual role in promoting and inhibiting cancer depending largely on the pathway initiated by the binding of the protein to its receptor. Zerumbone, an active constituent of Zingiber zerumbet, Smith, is known to act on the tumor necrosis factor pathway upregulating tumour necrosis factor related apoptosis inducing ligand (TRAIL) death receptors and inducing apoptosis in cancer cells. Zerumbone is a sesquiterpene that is able to penetrate into the hydrophobic pockets of proteins to exert its inhibiting activity with several proteins. We found a good binding with the tumor necrosis factor, kinase κB (IKKβ) and the Nuclear factor κB (NF-κB) component proteins along the TNF pathway. Our results suggest that zerumbone can exert its apoptotic activities by inhibiting the cytoplasmic proteins. It inhibits the IKKβ kinase that activates the NF-κB and also binds to the NF-κB complex in the TNF pathway. Blocking both proteins can lead to inhibition of cell proliferating proteins to be downregulated and possibly ultimate induction of apoptosis.
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Affiliation(s)
- Ayesha Fatima
- UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Ahmad Bustamam Hj Abdul
- UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Rasedee Abdullah
- UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Roghayeh Abedi Karjiban
- Department of Chemistry, Faculty of Science, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University Malaya, Petaling Jaya, 50603 Selangor, Malaysia.
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26
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Yang G, Wright CJ, Hinson MD, Fernando AP, Sengupta S, Biswas C, La P, Dennery PA. Oxidative stress and inflammation modulate Rev-erbα signaling in the neonatal lung and affect circadian rhythmicity. Antioxid Redox Signal 2014; 21:17-32. [PMID: 24252172 PMCID: PMC4048579 DOI: 10.1089/ars.2013.5539] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS The response to oxidative stress and inflammation varies with diurnal rhythms. Nevertheless, it is not known whether circadian genes are regulated by these stimuli. We evaluated whether Rev-erbα, a key circadian gene, was regulated by oxidative stress and/or inflammation in vitro and in a mouse model. RESULTS A unique sequence consisting of overlapping AP-1 and nuclear factor kappa B (NFκB) consensus sequences was identified on the mouse Rev-erbα promoter. This sequence mediates Rev-erbα promoter activity and transcription in response to oxidative stress and inflammation. This region serves as an NrF2 platform both to receive oxidative stress signals and to activate Rev-erbα, as well as an NFκB-binding site to repress Rev-erbα with inflammatory stimuli. The amplitude of the rhythmicity of Rev-erbα was altered by pre-exposure to hyperoxia or disruption of NFκB in a cell culture model of circadian simulation. Oxidative stress overcame the inhibitory effect of NFκB binding on Rev-erbα transcription. This was confirmed in neonatal mice exposed to hyperoxia, where hyperoxia-induced lung Rev-erbα transcription was further increased with NFκB disruption. Interestingly, this effect was not observed in similarly exposed adult mice. INNOVATION These data provide novel mechanistic insights into how key circadian genes are regulated by oxidative stress and inflammation in the neonatal lung. CONCLUSION Rev-erbα transcription and circadian oscillation are susceptible to oxidative stress and inflammation in the neonate. Due to Rev-erbα's role in cellular metabolism, this could contribute to lung cellular function and injury from inflammation and oxidative stress.
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Affiliation(s)
- Guang Yang
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Clyde J. Wright
- Department of Pediatrics, University of Colorado, Aurora, Colorado
| | - Maurice D. Hinson
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Amal P. Fernando
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Shaon Sengupta
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chhanda Biswas
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ping La
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Phyllis A. Dennery
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
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27
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Kasparkova J, Thibault T, Kostrhunova H, Stepankova J, Vojtiskova M, Muchova T, Midoux P, Malinge JM, Brabec V. Different affinity of nuclear factor-kappa B proteins to DNA modified by antitumor cisplatin and its clinically ineffective trans isomer. FEBS J 2014; 281:1393-1408. [PMID: 24418212 DOI: 10.1111/febs.12711] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/06/2013] [Accepted: 12/13/2013] [Indexed: 01/06/2023]
Abstract
Nuclear factor-kappa B (NF-кB) comprises a family of protein transcription factors that have a regulatory function in numerous cellular processes and are implicated in the cancer cell response to antineoplastic drugs, including cisplatin. We characterized the effects of DNA adducts of cisplatin and ineffective transplatin on the affinity of NF-кB proteins to their consensus DNA sequence (кB site). Although the кB site-NF-κB protein interaction was significantly perturbed by DNA adducts of cisplatin, transplatin adducts were markedly less effective both in cell-free media and in cellulo using a decoy strategy derivatized-approach. Moreover, NF-κB inhibitor JSH-23 [4-methyl-N¹-(3-phenylpropyl)benzene-1,2-diamine] augmented cisplatin cytotoxicity in ovarian cancer cells and the data showed strong synergy with JSH-23 for cisplatin. The distinctive structural features of DNA adducts of the two platinum complexes suggest a unique role for conformational distortions induced in DNA by the adducts of cisplatin with respect to inhibition of the binding of NF-кB to the platinated кB sites. Because thousands of κB sites are present in the DNA, the mechanisms underlying the antitumor efficiency of cisplatin in some tumor cells may involve downstream processes after inhibition of the binding of NF-κB to κB site(s) by DNA adducts of cisplatin, including enhanced programmed cell death in response to drug treatment.
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Affiliation(s)
- Jana Kasparkova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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28
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Lone IN, Shukla MS, Charles Richard JL, Peshev ZY, Dimitrov S, Angelov D. Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1. PLoS Genet 2013; 9:e1003830. [PMID: 24086160 PMCID: PMC3784511 DOI: 10.1371/journal.pgen.1003830] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/12/2013] [Indexed: 01/29/2023] Open
Abstract
NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility shift assay to investigate the binding of NF-κB to nucleosomal templates. We show that NF-κB p50 homodimer is able to bind to its recognition sequence, when it is localized at the edge of the core particle, but not when the recognition sequence is at the interior of the nucleosome. Remodeling of the nucleosome by the chromatin remodeling machine RSC was not sufficient to allow binding of NF-κB to its recognition sequence located in the vicinity of the nucleosome dyad, but RSC-induced histone octamer sliding allowed clearly detectable binding of NF-κB with the slid particle. Importantly, nucleosome dilution-driven removal of H2A–H2B dimer led to complete accessibility of the site located close to the dyad to NF-κB. Finally, we found that NF-κB was able to displace histone H1 and prevent its binding to nucleosome. These data provide important insight on the role of chromatin structure in the regulation of transcription of NF-κB dependent genes. In eukaryotes DNA is hierarchically packaged into chromatin by histones. The fundamental subunit of chromatin is the nucleosome. The packaging of DNA into nucleosomes not only restricts DNA accessibility for regulatory proteins but also provides opportunities to regulate DNA based processes. Accessibility of transcription factor NF-κB to their recognition sequences embedded in nucleosomes is highly controversial. On one hand in vivo studies have suggested that packaging of DNA into chromatin plays an important role in regulating the expression of NF-κB dependent genes, and on the other hand some in vitro studies reported that NF-κB can bind by itself to its recognition sequences embedded in the nucleosome. In this study, we show that NF-κB can specifically bind to its recognition sequences placed at the end of the nucleosome but not when placed inside the nucleosome core. We then demonstrate that disruption of nucleosome is necessary for the productive binding of NF-κB. Finally, we show that the presence of histone H1 does not affect the specific binding of NF-κB to its cognate sequence, when its binding region overlaps with the binding site of NF-κB. We propose that histone eviction is needed for NF-κB to bind specifically to its recognition sequence embedded in the nucleosome.
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Affiliation(s)
- Imtiaz Nisar Lone
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Manu Shubhdarshan Shukla
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- Université Joseph Fourier - Grenoble 1, INSERM Institut Albert Bonniot, U823, Site Santé-BP 170, Grenoble, France
| | - John Lalith Charles Richard
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- Université Joseph Fourier - Grenoble 1, INSERM Institut Albert Bonniot, U823, Site Santé-BP 170, Grenoble, France
| | - Zahary Yordanov Peshev
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- Institute of Electronics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stefan Dimitrov
- Université Joseph Fourier - Grenoble 1, INSERM Institut Albert Bonniot, U823, Site Santé-BP 170, Grenoble, France
- * E-mail: (SD); (DA)
| | - Dimitar Angelov
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (SD); (DA)
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29
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The transcriptional specificity of NF-κB dimers is coded within the κB DNA response elements. Cell Rep 2012; 2:824-39. [PMID: 23063365 PMCID: PMC4167904 DOI: 10.1016/j.celrep.2012.08.042] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/08/2012] [Accepted: 08/21/2012] [Indexed: 11/30/2022] Open
Abstract
Nuclear factor κB (NF-κB) regulates gene expression by binding to specific DNA elements, known collectively as κB sites, that are contained within the promoters/enhancers of target genes. We found that the identity of the central base pair (bp) of κB sites profoundly affects the transcriptional activity of NF-κB dimers. RelA dimers prefer an A/T bp at this position for optimal transcriptional activation (A/T-centric) and discriminate against G/C-centric κB sites. The p52 homodimer, in contrast, activates transcription from G/C-centric κB sites in complex with Bcl3 but represses transcription from the A/T-centric sites. The p52:Bcl3 complex binds to these two classes of κB sites in distinct modes, permitting the recruitment of coactivator, corepressor, or both coactivator and corepressor complexes in promoters that contain G/C-, A/T-, or both G/C- and A/T-centric sites. Therefore, through sensing of bp differences within κB sites, NF-κB dimers modulate biological programs by activating, repressing, and altering the expression of effector genes.
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30
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Abstract
The signaling module that specifies nuclear factor-κΒ (NF-κB) activation is a three-component system: NF-κB, inhibitor of NF-κΒ (IκΒ), and IκΒ kinase complex (IKK). IKK receives upstream signals from the surface or inside the cell and converts itself into a catalytically active form, leading to the destruction of IκB in the inhibited IκB:NF-κB complex, leaving active NF-κB free to regulate target genes. Hidden within this simple module are family members that all can undergo various modifications resulting in expansion of functional spectrum. Three-dimensional structures representing all three components are now available. These structures have allowed us to interpret cellular observations in molecular terms and at the same time helped us to bring forward new concepts focused towards understanding the specificity in the NF-κB activation pathway.
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Affiliation(s)
- Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92903, USA.
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31
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Mrinal N, Tomar A, Nagaraju J. Role of sequence encoded κB DNA geometry in gene regulation by Dorsal. Nucleic Acids Res 2011; 39:9574-91. [PMID: 21890896 PMCID: PMC3239199 DOI: 10.1093/nar/gkr672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Many proteins of the Rel family can act as both transcriptional activators and repressors. However, mechanism that discerns the ‘activator/repressor’ functions of Rel-proteins such as Dorsal (Drosophila homologue of mammalian NFκB) is not understood. Using genomic, biophysical and biochemical approaches, we demonstrate that the underlying principle of this functional specificity lies in the ‘sequence-encoded structure’ of the κB-DNA. We show that Dorsal-binding motifs exist in distinct activator and repressor conformations. Molecular dynamics of DNA-Dorsal complexes revealed that repressor κB-motifs typically have A-tract and flexible conformation that facilitates interaction with co-repressors. Deformable structure of repressor motifs, is due to changes in the hydrogen bonding in A:T pair in the ‘A-tract’ core. The sixth nucleotide in the nonameric κB-motif, ‘A’ (A6) in the repressor motifs and ‘T’ (T6) in the activator motifs, is critical to confer this functional specificity as A6 → T6 mutation transformed flexible repressor conformation into a rigid activator conformation. These results highlight that ‘sequence encoded κB DNA-geometry’ regulates gene expression by exerting allosteric effect on binding of Rel proteins which in turn regulates interaction with co-regulators. Further, we identified and characterized putative repressor motifs in Dl-target genes, which can potentially aid in functional annotation of Dorsal gene regulatory network.
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Affiliation(s)
- Nirotpal Mrinal
- Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500001, India.
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32
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Abstract
NF-κBs are a family of transcription factors that control a number of essential cellular functions including immune responses, cell proliferation and antiapoptosis. NF-κB activities are tightly regulated through upstream signaling molecules and downstream feedback loops. In this review, structural discoveries in the NF-κB pathway are presented. With the structure information, the following questions may be addressed: (1) How do NF-κBs activate their target genes? (2) How do IκBs inhibit NF-κB activities in the steady state? (3) How do upstream signaling molecules activate the NF-κB pathway? and (4) How do the feedback loops shut down the NF-κB pathway to avoid constitutive NF-κB activation?
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Affiliation(s)
- Chao Zheng
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
| | - Qian Yin
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
| | - Hao Wu
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
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33
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Huxford T, Ghosh G. A structural guide to proteins of the NF-kappaB signaling module. Cold Spring Harb Perspect Biol 2010; 1:a000075. [PMID: 20066103 DOI: 10.1101/cshperspect.a000075] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The prosurvival transcription factor NF-kappaB specifically binds promoter DNA to activate target gene expression. NF-kappaB is regulated through interactions with IkappaB inhibitor proteins. Active proteolysis of these IkappaB proteins is, in turn, under the control of the IkappaB kinase complex (IKK). Together, these three molecules form the NF-kappaB signaling module. Studies aimed at characterizing the molecular mechanisms of NF-kappaB, IkappaB, and IKK in terms of their three-dimensional structures have lead to a greater understanding of this vital transcription factor system.
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Affiliation(s)
- Tom Huxford
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, USA
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34
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The Skp2 promoter integrates signaling through the NF-kappaB, p53, and Akt/GSK3beta pathways to regulate autophagy and apoptosis. Mol Cell 2010; 38:524-38. [PMID: 20513428 DOI: 10.1016/j.molcel.2010.03.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 09/21/2009] [Accepted: 03/17/2010] [Indexed: 01/04/2023]
Abstract
NF-kappaB and p53 are important regulators of the cellular response to stress. Here, we identify the Skp2 gene as being both an NF-kappaB and p53 target after DNA damage. However, Skp2 expression can be either induced or repressed in a manner requiring both the p52 NF-kappaB subunit and p53, with subsequent effects on autophagy, apoptosis, and p53 function. This process is regulated by the Akt(PKB)/GSK3beta pathway. When Akt is active, GSK3beta is repressed, allowing p52 and p53 to cooperatively induce Skp2 expression. However, if Akt is inactive, GSK3beta phosphorylates p52 at Ser 222. This modification disrupts p52 homodimer/Bcl-3 complexes and facilitates transcriptional repression by p52/-c-Rel. The Skp2 promoter therefore integrates signaling through the NF-kappaB, p53, and Akt/GSK3beta pathways to regulate cell fate in response to DNA damage.
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35
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Huxford T, Hoffmann A, Ghosh G. Understanding the logic of IκB:NF-κB regulation in structural terms. Curr Top Microbiol Immunol 2010; 349:1-24. [PMID: 20845107 DOI: 10.1007/82_2010_99] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
NF-κB is an inducible transcription factor that controls expression of diverse stress response genes. The entire mammalian NF-κB family is generated from a small cadre of five gene products that assemble with one another in various combinations to form active homo- and heterodimers. The ability of NF-κB to alter target gene expression is regulated at many levels. Chief among these regulatory mechanisms is the noncovalent association in the cell cytoplasm of NF-κB dimers with IκB inhibitor proteins. Removal of IκB leads to accumulation of active NF-κB within the cell nucleus where it binds to specific DNA sequences contained within the promoter regions of target genes and initiates recruitment of general transcription factors and assembly of the basal transcription machinery. Here we provide a detailed description of these fundamental NF-κB regulatory events using as a basis macromolecular structures and experimental data derived from structure-based biochemistry.
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Affiliation(s)
- Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
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36
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NF-kappaB p52:RelB heterodimer recognizes two classes of kappaB sites with two distinct modes. EMBO Rep 2008; 10:152-9. [PMID: 19098713 DOI: 10.1038/embor.2008.227] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 09/19/2008] [Accepted: 11/03/2008] [Indexed: 11/08/2022] Open
Abstract
The X-ray structure of the nuclear factor-kappaB (NF-kappaB) p52:RelB:kappaB DNA complex reveals a new recognition feature not previously seen in other NF-kappaB:kappaB DNA complexes. Arg 125 of RelB is in contact with an additional DNA base pair. Surprisingly, the p52:RelB R125A mutant heterodimer shows defects both in DNA binding and in transcriptional activity only to a subclass of kappaB sites. We found that the Arg 125-sensitive kappaB sites contain more contiguous and centrally located A:T base pairs than do the insensitive sites. A protein-induced kink observed in this complex, which used an AT-rich kappaB site, might allow the DNA contact by Arg 125; such a kink might not be possible in complexes with non-AT-rich kappaB sites. Furthermore, we show that the p52:RelB heterodimer binds to a broader spectrum of kappaB sites when compared with the p50:RelA heterodimer. We suggest that the p52:RelB heterodimer is more adaptable to complement sequence and structural variations in kappaB sites when compared with other NF-kappaB dimers.
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37
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Yamamoto M, Horie R, Takeiri M, Kozawa I, Umezawa K. Inactivation of NF-kappaB components by covalent binding of (-)-dehydroxymethylepoxyquinomicin to specific cysteine residues. J Med Chem 2008; 51:5780-8. [PMID: 18729348 DOI: 10.1021/jm8006245] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, we designed and synthesized a potent NF-kappaB inhibitor, DHMEQ. Although DHMEQ showed potent anti-inflammatory and anticancer activities in animals, its molecular target has not been elucidated. In the present study, its target protein was found to be p65 and other Rel homology proteins. We found that (-)-DHMEQ bound to p65 covalently with a 1:1 stoichiometry by conducting SPR and MALDI-TOF MS analyses. MS analysis of the chymotrypsin-digested peptide suggested the binding of (-)-DHMEQ to a Cys residue. Formation of Cys/(-)-DHMEQ adduct in the protein was supported by chemical synthesis of the adduct. Substitution of specific Cys in p65 and other Rel homology proteins resulted in the loss of (-)-DHMEQ binding. (-)-DHMEQ is the first NF-kappaB inhibitor that was proven to bind to the specific Cys by chemical methodology. These findings may explain the highly selective inhibition of NF-kappaB and the low toxic effect of (-)-DHMEQ in cells and animals.
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Affiliation(s)
- Mizuki Yamamoto
- Center for Chemical Biology, School of Fundamental Science and Technology, Keio University, Yokohama 223-0061, Japan
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38
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Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res 2008; 36:4941-55. [PMID: 18653524 PMCID: PMC2528173 DOI: 10.1093/nar/gkn473] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein···DNA recognition in the ‘κB’ family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-bp DNA encompassing a cognate κB site recognized by the proto-oncogenic ‘c-Rel’ subfamily of NF-κB transcription factors. Simulations of the κB DNA in explicit water were extended to microsecond duration, providing a broad, atomically detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation—including a peculiar state arising at ≈0.7 μs and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally sheared base pair, followed (at ≈1 μs) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the microsecond-scale simulation include implications for a dynamical NF-κB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
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Affiliation(s)
- Cameron Mura
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093-0365, USA.
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39
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Sun PD, Boyington JC. Overview of protein folds in the immune system. ACTA ACUST UNITED AC 2008; Appendix 1:Appendix 1N. [PMID: 18432648 DOI: 10.1002/0471142735.ima01ns44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The rapid advancement of X-ray crystallography and nuclear magnetic resonance techniques in recent years has resulted in the solution of macromolecular structures at an unprecedented rate. This review aims at providing a comprehensive description of structures and folds related to the function of the immune system. Focus is placed on immunologically relevant proteins such as immunoreceptors and major histocompatibility complexes. Information is also provided regarding protein structure data banks.
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Affiliation(s)
- P D Sun
- National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, USA
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40
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Abstract
This overview provides an illustrated, comprehensive survey of some commonly observed protein‐fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web‐based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein‐structure databases, protein‐structure‐classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon‐diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.
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Affiliation(s)
- Peter D Sun
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
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41
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Raza S, Robertson KA, Lacaze PA, Page D, Enright AJ, Ghazal P, Freeman TC. A logic-based diagram of signalling pathways central to macrophage activation. BMC SYSTEMS BIOLOGY 2008; 2:36. [PMID: 18433497 PMCID: PMC2383880 DOI: 10.1186/1752-0509-2-36] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 04/23/2008] [Indexed: 12/19/2022]
Abstract
Background The complex yet flexible cellular response to pathogens is orchestrated by the interaction of multiple signalling and metabolic pathways. The molecular regulation of this response has been studied in great detail but comprehensive and unambiguous diagrams describing these events are generally unavailable. Four key signalling cascades triggered early-on in the innate immune response are the toll-like receptor, interferon, NF-κB and apoptotic pathways, which co-operate to defend cells against a given pathogen. However, these pathways are commonly viewed as separate entities rather than an integrated network of molecular interactions. Results Here we describe the construction of a logically represented pathway diagram which attempts to integrate these four pathways central to innate immunity using a modified version of the Edinburgh Pathway Notation. The pathway map is available in a number of electronic formats and editing is supported by yEd graph editor software. Conclusion The map presents a powerful visual aid for interpreting the available pathway interaction knowledge and underscores the valuable contribution well constructed pathway diagrams make to communicating large amounts of molecular interaction data. Furthermore, we discuss issues with the limitations and scalability of pathways presented in this fashion, explore options for automated layout of large pathway networks and demonstrate how such maps can aid the interpretation of functional studies.
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Affiliation(s)
- Sobia Raza
- Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
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42
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Moorthy AK, Huang DB, Wang VYF, Vu D, Ghosh G. X-ray structure of a NF-kappaB p50/RelB/DNA complex reveals assembly of multiple dimers on tandem kappaB sites. J Mol Biol 2007; 373:723-34. [PMID: 17869269 PMCID: PMC4167888 DOI: 10.1016/j.jmb.2007.08.039] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Revised: 08/15/2007] [Accepted: 08/16/2007] [Indexed: 01/07/2023]
Abstract
We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.
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43
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Angelov D, Charra M, Müller CW, Cadet J, Dimitrov S. Solution Study of the NF-κB p50-DNA Complex by UV Laser Protein-DNA Cross-linking¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0770592ssotnp2.0.co2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Qing G, Qu Z, Xiao G. Endoproteolytic processing of C-terminally truncated NF-kappaB2 precursors at kappaB-containing promoters. Proc Natl Acad Sci U S A 2007; 104:5324-9. [PMID: 17363471 PMCID: PMC1838492 DOI: 10.1073/pnas.0609914104] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The C-terminal, partially truncated forms of the NF-kappaB2/p52 precursor p100, p100DeltaCs, manifest constitutive processing and oncogenic ability, although the responsible mechanisms remain unknown. Here, we report that p100DeltaCs are specifically processed in association with binding to promoter DNA-containing kappaB sites. In the nucleus, p100DeltaCs bind to the kappaB promoter DNA and subsequently recruit the proteasome to form a stable proteasome/p100DeltaC/DNA complex, which mediates the processing of p100DeltaCs. Notably, the processing at the kappaB promoter is initiated by a proteasome-mediated endoproteolytic cleavage at amino acid D(415) of p100DeltaCs, and the processed p52, but not the precursors themselves, is oncogenic by up-regulating a subset of target genes. Our studies demonstrate a different mechanism of p100 processing and also present evidence showing that the proteasome modulates the action of transcription factors at promoter regions through endoproteolysis.
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Affiliation(s)
- Guoliang Qing
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Nelson Biological Laboratories, 604 Allison Road, Piscataway, NJ 08854
| | - Zhaoxia Qu
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Nelson Biological Laboratories, 604 Allison Road, Piscataway, NJ 08854
| | - Gutian Xiao
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Nelson Biological Laboratories, 604 Allison Road, Piscataway, NJ 08854
- *To whom correspondence should be addressed. E-mail:
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45
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Energetics of the protein-DNA-water interaction. BMC STRUCTURAL BIOLOGY 2007; 7:4. [PMID: 17214883 PMCID: PMC1781455 DOI: 10.1186/1472-6807-7-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 01/10/2007] [Indexed: 11/30/2022]
Abstract
Background To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species. Results An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r2 of 0.21 and standard error of ± 1.71 kcal mol-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r2 of 0.56 and standard error of ± 1.28 kcal mol-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts. Conclusion This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel.
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46
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Abstract
Stimulus-induced nuclear factor-kappaB (NF-kappaB) activity, the central mediator of inflammatory responses and immune function, comprises a family of dimeric transcription factors that regulate diverse gene expression programs consisting of hundreds of genes. A family of inhibitor of kappaB (IkappaB) proteins controls NF-kappaB DNA-binding activity and nuclear localization. IkappaB protein metabolism is intricately regulated through stimulus-induced degradation and feedback re-synthesis, which allows for dynamic control of NF-kappaB activity. This network of interactions has been termed the NF-kappaB signaling module. Here, we summarize the current understanding of the molecular structures and biochemical mechanisms that determine NF-kappaB dimer formation and the signal-processing characteristics of the signaling module. We identify NF-kappaB-kappaB site interaction specificities and dynamic control of NF-kappaB activity as mechanisms that generate specificity in transcriptional regulation. We discuss examples of gene regulation that illustrate how these mechanisms may interface with other transcription regulators and promoter-associated events, and how these mechanisms suggest regulatory principles for NF-kappaB-mediated gene activation.
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Affiliation(s)
- A Hoffmann
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92037, USA.
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47
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Meng WS, Bui HH, Haworth IS. Exploiting the Peptide — MHC Water Interface in the Computer-Aided Design of Non-Natural Peptides that Bind to the Class I MHC Molecule HLA-A2. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020008022372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Schumm K, Rocha S, Caamano J, Perkins ND. Regulation of p53 tumour suppressor target gene expression by the p52 NF-kappaB subunit. EMBO J 2006; 25:4820-32. [PMID: 16990795 PMCID: PMC1618099 DOI: 10.1038/sj.emboj.7601343] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 08/17/2006] [Indexed: 11/08/2022] Open
Abstract
The p52/p100 nuclear factor kappa B (NF-kappaB) subunit (NF-kappaB2) is aberrantly expressed in many tumour types and has been implicated as a regulator of cell proliferation. Here, we demonstrate that endogenous p52 is a direct regulator of Cyclin D1 expression. However, stimulation of Cyclin D1 expression alone cannot account for all the cell cycle effects of p52/p100 and we also find that p52 represses expression of the Cyclin-dependent kinase inhibitor p21(WAF/CIP1). Significantly, this latter effect is dependent upon basal levels of the tumour suppressor p53. By contrast, p52 cooperates with p53 to regulate other known p53 target genes such as PUMA, DR5, Gadd45alpha and Chk1. p52 associates directly with these p53-regulated promoters where it regulates coactivator and corepressor binding. Moreover, recruitment of p52 is p53 dependent and does not require p52-DNA-binding activity. These results reveal a complex role for p52 as regulator of cell proliferation and p53 transcriptional activity. Furthermore, they imply that in some cell types, p52 can regulate p53 function and influence p53-regulated decision-making following DNA damage and oncogene activation.
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Affiliation(s)
- Katie Schumm
- College of Life Sciences, Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Sonia Rocha
- College of Life Sciences, Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Jorge Caamano
- Division of Immunity and Infection, Medical Research Council Centre for Immune Regulation, The Medical School, University of Birmingham, Edgbaston, UK
| | - Neil D Perkins
- College of Life Sciences, Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
- College of Life Sciences, Division of Gene Regulation and Expression, University of Dundee, MSI/WTB/JBC Complex, Dow Street, Dundee DD1 5EH, UK. Tel.: +44 1382 385 606; Fax +44 1382 348 072; E-mail:
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Romanenkov AS, Ustyugov AA, Zatsepin TS, Nikulova AA, Kolesnikov IV, Metelev VG, Oretskaya TS, Kubareva EA. Analysis of DNA-protein interactions in complexes of transcription factor NF-kappaB with DNA. BIOCHEMISTRY (MOSCOW) 2006; 70:1212-22. [PMID: 16336179 DOI: 10.1007/s10541-005-0249-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We have applied bioinformatic analysis of X-ray 3D structures of complexes of transcription factor NF-kappaB with DNAs. We determined the number of possible Van der Waals contacts and hydrogen bonds between amino acid residues and nucleotides. Conservative contacts in the NF-kappaB dimer-DNA complex composed of p50 and/or p65 NF-kappaB subunit and DNA sequences like 5 -GGGAMWTTCC-3 were revealed. Based on these results, we propose a novel scheme for interactions between NF-kappaB p50 homodimer and the kappaB region of the immunoglobulin light chain gene enhancer (Ig-kappaB). We applied a chemical cross-linking technique to study the proximity of some Lys and Cys residues of NF-kappaB p50 subunit with certain reactive nucleotides into its recognition site. In all cases, the experimentally determined protein-DNA contacts were in good agreement with the predicted ones.
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Affiliation(s)
- A S Romanenkov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
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50
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Valdez KE, Turzillo AM. Regulation of nuclear factor-kappaB (NF-kappaB) activity and apoptosis by estradiol in bovine granulosa cells. Mol Cell Endocrinol 2005; 243:66-73. [PMID: 16225986 DOI: 10.1016/j.mce.2005.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 08/22/2005] [Accepted: 09/06/2005] [Indexed: 12/19/2022]
Abstract
Although atresia of bovine follicles is associated with apoptosis of granulosa cells, the signals initiating this cell death have not been resolved. NF-kappaB has been implicated as an important regulator of genes controlling apoptosis, and previous studies indicate that estradiol may modulate NF-kappaB activation. We hypothesized that estradiol activates NF-kappaB, and thus, inhibits apoptosis in granulosa cells of dominant follicles. Dominant follicles were collected on Days 4, 6, and 8 of the first follicular wave following ovulation and assayed for NF-kappaB activity. Concentrations of estradiol in follicular fluid decreased on Day 6 compared to Day 4 of the wave. NF-kappaB activity in granulosa cells was lower on Day 8 compared to Days 4 and 6. In vitro, NF-kappaB activity and minimal incidence of apoptosis (<4%), as measured by Annexin V and TUNEL assays, were associated with production of estradiol. However, inhibition of NF-kappaB in vitro led to a suppression of apoptosis. These results indicate that follicular NF-kappaB activation is associated with estradiol production. However, whether NF-kappaB is playing a pro- or anti-apoptotic role in granulosa cells of the dominant bovine follicle remains to be elucidated.
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Affiliation(s)
- Kelli E Valdez
- Department of Physiological Sciences, University of Arizona, Tucson, AZ 85724, USA
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