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Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
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Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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2
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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3
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Grúz P, Sugiyama KI, Honma M, Nohmi T. Purification and interactions of the MucA' and MucB proteins constituting the DNA polymerase RI. Genes Environ 2019; 41:10. [PMID: 31061684 PMCID: PMC6495647 DOI: 10.1186/s41021-019-0125-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background The MucA' and MucB proteins comprise the core of DNA polymerase RI which is a strong mutator utilized in mutagenicity assays such as the standard Ames test. A close relative DNA polymerase V, composed of the homologous UmuD' and UmuC proteins, is considered to be an ortholog of the mammalian DNA polymerase η. The catalytic subunits of these polymerases belong to the Y-family which specializes in the translesion DNA synthesis across various DNA adducts to rescue stalled chromosomal replication at the expense of mutations. Based on genetic evidence, DNA polymerase RI possesses the greatest ability to induce various types of mutations among all so far characterized members of the Y-superfamily. The exceptionally high mutagenic potential of MucA'B has been taken advantage of in numerous bacterial mutagenicity assays incorporating the conjugative plasmid pKM101 carrying the mucAB operon such as the Ames Test. Results We established new procedures for the purification of MucB protein as well as its accessory protein MucA' using the refolding techniques. The purified MucA' protein behaved as a molecular dimer which was fully stable in solution. The soluble monomeric form of MucB protein was obtained after refolding on a gel-filtration column and remained stable in a nondenaturing buffer containing protein aggregation inhibitors. Using the surface plasmon resonance technique, we demonstrated that the purified MucA' and MucB proteins interacted and that MucB protein preferentially bound to single-stranded DNA. In addition, we revealed that MucB protein interacted with the β-subunit of DNA polymerase III holoenzyme of E. coli. Conclusion The MucA' and MucB proteins can be isolated from inclusion bodies and solubilized in vitro. The refolded MucB protein interacts with its MucA' partner as well as with DNA what suggests it retains biological activity. The interaction of MucB with the processivity subunit of DNA polymerase III may imply the role of the subunit as an accessory protein to MucB during the translesion DNA synthesis.
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Affiliation(s)
- Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501 Japan
| | - Kei-Ichi Sugiyama
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501 Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501 Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501 Japan
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4
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Yalim‐Camci I, Balcik‐Ercin P, Cetin M, Odabas G, Tokay N, Sayan AE, Yagci T. ETS1 is coexpressed with ZEB2 and mediates ZEB2‐induced epithelial‐mesenchymal transition in human tumors. Mol Carcinog 2019; 58:1068-1081. [DOI: 10.1002/mc.22994] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Irem Yalim‐Camci
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Pelin Balcik‐Ercin
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Metin Cetin
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Gorkem Odabas
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - A. Emre Sayan
- Cancer Sciences Unit and Cancer Research UK CentreUniversity of Southampton, Southampton General HospitalSouthampton UK
| | - Tamer Yagci
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
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5
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Rodgers JJ, McClure R, Epis MR, Cohen RJ, Leedman PJ, Harvey JM, Thomas MA, Bentel JM. ETS1 induces transforming growth factor β signaling and promotes epithelial-to-mesenchymal transition in prostate cancer cells. J Cell Biochem 2018; 120:848-860. [PMID: 30161276 DOI: 10.1002/jcb.27446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/16/2018] [Indexed: 02/01/2023]
Abstract
Expression of the transcriptional regulator, E26 transformation-specific 1 (ETS1), is elevated in human prostate cancers, and this is associated with more aggressive tumor behavior and a rapid progression to castrate-resistant disease. Multiple ETS1 isoforms with distinct biological activities have been characterized and in 44 matched nonmalignant and malignant human prostate specimens, messenger RNAs for two ETS1 isoforms, ETS1p51 and ETS1p42, were detected, with ETS1p51 levels significantly lower in prostate tumor compared to matched nonmalignant prostate tissues. In contrast, ETS1p51 protein, the only ETS1 isoform detected, was expressed at significantly higher levels in malignant prostate. Analysis of epithelial-to-mesenchymal transition (EMT)-associated genes regulated following overexpression of ETS1p51 in the LNCaP prostate cancer cell line predicted promotion of transforming growth factor β (TGFβ) signaling and of EMT. ETS1p51 overexpression upregulated cellular levels of the EMT transcriptional regulators, ZEB1 and SNAIL1, resulted in reduced expression of the mesenchymal marker vimentin with concomitantly elevated levels of claudin 1, an epithelial tight junction protein, and increased prostate cancer cell migration and invasion. ETS1p51-induced activation of the pro-EMT TGFβ signaling pathway that was predicted in polymerase chain reaction arrays was verified by demonstration of elevated SMAD2 phosphorylation following ETS1p51 overexpression. Attenuation of ETS1p51 effects on prostate cancer cell migration and invasion by inhibition of TGFβ pathway signaling indicated that ETS1p51 effects were in part mediated by induction of TGFβ signaling. Thus, overexpression of ETS1p51, the predominant ETS1 isoform expressed in prostate tumors, promotes an EMT program in prostate cancer cells in part via activation of TGFβ signaling, potentially accounting for the poor prognosis of ETS1-overexpressing prostate tumors.
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Affiliation(s)
- Jamie J Rodgers
- Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Western Australia, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Robert McClure
- Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Michael R Epis
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | - Ronald J Cohen
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia.,Uropath, West Leederville, Western Australia, Australia
| | - Peter J Leedman
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,Centre for Medical Research and Medical School, University of Western Australia, Crawley, Western Australia, Australia
| | - Jennet M Harvey
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia.,Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Crawley, Western Australia, Australia
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- Australian Prostate Cancer BioResource (APCB), Brisbane, Queensland, Australia
| | - Marc A Thomas
- Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Western Australia, Australia.,Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Crawley, Western Australia, Australia
| | - Jacqueline M Bentel
- Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Western Australia, Australia.,Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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6
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Wu J, Wang H, Zhu A, Long F. Adsorption Kinetics of Single-Stranded DNA on Functional Silica Surfaces and Its Influence Factors: An Evanescent-Wave Biosensor Study. ACS OMEGA 2018; 3:5605-5614. [PMID: 30023924 PMCID: PMC6044497 DOI: 10.1021/acsomega.7b02063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
Thorough understandings on the real-time kinetics involved in DNA adsorption on a solid surface is essential in various fields, such as in DNA hybridization studies, DNA extraction and purification, DNA-based biosensing, and gene-based medicine discovery. Herein, the real-time properties of single-stranded DNA (ssDNA) adsorption onto functional silica surfaces under various conditions were investigated using an evanescent wave optical biosensing platform. Results demonstrated that the driving force and adsorption mechanism of DNA were closely related to the kind of functional groups on the silica surfaces. The main driving forces of DNA adsorption onto hydroxyl- and protein-modified solid surfaces were the hydrophobic interaction, hydrogen bonding, and the interaction between DNA phosphate and functional groups on the silica surface, which strengthened with increased ionic strength. However, the electrostatic attraction between the negative charge of DNA and positive charge of the amino silica surface was likely the most important factor influencing DNA adsorption onto the amino surface. This influence can be reduced by increasing the ionic strength. Although low-ionic-strength Mg2+ provided a greater adsorption efficiency than high-ionic-strength Na+, the balance of ssDNA adsorption onto hydroxyl- and ovalbumin (OVA)-modified silica surfaces was achieved faster in the presence of Na+ than in the presence of Mg2+. DNA adsorption was also influenced significantly by pH, and the hydroxyl- and OVA-modified surfaces exhibited the strongest adsorption at pH 3.0, whereas DNA adsorption onto the amino surface increased with increased pH. DNA adsorption onto various functional surfaces could be perfectly fitted by second-order Langmuir models, indicating that the process was a single-molecular-layer adsorption.
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7
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Li ZL, Abe H, Ueki K, Kumagai K, Araki R, Otsuki Y. Identification of c-Jun as bcl-2 Transcription Factor in Human Uterine Endometrium. J Histochem Cytochem 2016; 51:1601-9. [PMID: 14623928 DOI: 10.1177/002215540305101204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We describe the application of the biomolecular interaction (BIA) technique to detection of the interaction between protein (e.g., c-Jun) and DNA (e.g., two AP-1 motifs from bcl-2 promoter), compared with immunohistochemistry (IHC) of c-Jun. The specific binding assay for the interaction of c-Jun and activating protein-1 (AP-1) motifs was performed using a Biacore 2000 system. Intense immunoreactivity of c-Jun in glandular cells of the human uterine endometrium was observed in the proliferative phase, while c-Jun in stromal cells was expressed throughout the menstrual cycle. In contrast to the IHC of c-Jun, the specific binding of c-Jun to two separate AP-1 motifs in the bcl-2 promoter region was detected only in nuclear extracts of glandular cells, but not in stromal cells, during the proliferative phase. These results indicate that, while transmitting various signals, c-Jun enhances the transcription level of bcl-2, which in turn keeps glandular cells alive and proliferating in normal human endometrium during the proliferative phase. Moreover, the method involving real-time biomolecular interactions such as DNA-protein binding is novel for the study of transcription factors when combined with IHC.
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Affiliation(s)
- Z L Li
- Department of Anatomy, Osaka Medical College, Osaka, Japan
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8
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Pantoja-Uceda D, Neira JL, Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI, Santoro J. Dissecting the Binding between Glutamine Synthetase and Its Two Natively Unfolded Protein Inhibitors. Biochemistry 2016; 55:3370-82. [DOI: 10.1021/acs.biochem.6b00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - José L. Neira
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto
de Biocomputación y Física de Sistemas Complejos (BIFI),
Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena Saelices
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Rocío Robles-Rengel
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Francisco J. Florencio
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Jorge Santoro
- Instituto
de Química Física Rocasolano (IQFR), CSIC, 28006 Madrid, Spain
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9
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Dittmer J. The role of the transcription factor Ets1 in carcinoma. Semin Cancer Biol 2015; 35:20-38. [PMID: 26392377 DOI: 10.1016/j.semcancer.2015.09.010] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 12/12/2022]
Abstract
Ets1 belongs to the large family of the ETS domain family of transcription factors and is involved in cancer progression. In most carcinomas, Ets1 expression is linked to poor survival. In breast cancer, Ets1 is primarily expressed in the triple-negative subtype, which is associated with unfavorable prognosis. Ets1 contributes to the acquisition of cancer cell invasiveness, to EMT (epithelial-to-mesenchymal transition), to the development of drug resistance and neo-angiogenesis. The aim of this review is to summarize the current knowledge on the functions of Ets1 in carcinoma progression and on the mechanisms that regulate Ets1 activity in cancer.
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Affiliation(s)
- Jürgen Dittmer
- Clinic for Gynecology, Martin Luther University Halle-Wittenberg, Germany.
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10
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Findlay VJ, LaRue AC, Turner DP, Watson PM, Watson DK. Understanding the role of ETS-mediated gene regulation in complex biological processes. Adv Cancer Res 2014; 119:1-61. [PMID: 23870508 DOI: 10.1016/b978-0-12-407190-2.00001-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ets factors are members of one of the largest families of evolutionarily conserved transcription factors, regulating critical functions in normal cell homeostasis, which when perturbed contribute to tumor progression. The well-documented alterations in ETS factor expression and function during cancer progression result in pleiotropic effects manifested by the downstream effect on their target genes. Multiple ETS factors bind to the same regulatory sites present on target genes, suggesting redundant or competitive functions. The anti- and prometastatic signatures obtained by examining specific ETS regulatory networks will significantly improve our ability to accurately predict tumor progression and advance our understanding of gene regulation in cancer. Coordination of multiple ETS gene functions also mediates interactions between tumor and stromal cells and thus contributes to the cancer phenotype. As such, these new insights may provide a novel view of the ETS gene family as well as a focal point for studying the complex biological control involved in tumor progression. One of the goals of molecular biology is to elucidate the mechanisms that contribute to the development and progression of cancer. Such an understanding of the molecular basis of cancer will provide new possibilities for: (1) earlier detection, as well as better diagnosis and staging of disease; (2) detection of minimal residual disease recurrences and evaluation of response to therapy; (3) prevention; and (4) novel treatment strategies. Increased understanding of ETS-regulated biological pathways will directly impact these areas.
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Affiliation(s)
- Victoria J Findlay
- Department of Pathology and Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
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11
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Wojcechowskyj JA, Didigu CA, Lee JY, Parrish NF, Sinha R, Hahn BH, Bushman FD, Jensen ST, Seeholzer SH, Doms RW. Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry. Cell Host Microbe 2013; 13:613-623. [PMID: 23684312 PMCID: PMC4104530 DOI: 10.1016/j.chom.2013.04.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/11/2013] [Accepted: 04/22/2013] [Indexed: 12/30/2022]
Abstract
Receptor engagement by HIV-1 during host cell entry activates signaling pathways that can reprogram the cell for optimal viral replication. To obtain a global view of the signaling events induced during HIV-1 entry, we conducted a quantitative phosphoproteomics screen of primary human CD4(+) T cells after infection with an HIV-1 strain that engages the receptors CD4 and CXCR4. We quantified 1,757 phosphorylation sites with high stringency. The abundance of 239 phosphorylation sites from 175 genes, including several proteins in pathways known to be impacted by HIV-receptor binding, changed significantly within a minute after HIV-1 exposure. Several previously uncharacterized HIV-1 host factors were also identified and confirmed through RNAi depletion studies. Surprisingly, five serine/arginine-rich (SR) proteins involved in messenger RNA splicing, including the splicing factor SRm300 (SRRM2), were differentially phosophorylated. Mechanistic studies with SRRM2 suggest that HIV-1 modulates host cell alternative splicing machinery during entry in order to facilitate virus replication and release.
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Affiliation(s)
- Jason A Wojcechowskyj
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Chuka A Didigu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Jessica Y Lee
- Protein and Proteomics Core, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Nicholas F Parrish
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rohini Sinha
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shane T Jensen
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven H Seeholzer
- Protein and Proteomics Core, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Robert W Doms
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA.
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12
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Review of Ets1 structure, function, and roles in immunity. Cell Mol Life Sci 2013; 70:3375-90. [PMID: 23288305 DOI: 10.1007/s00018-012-1243-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 11/20/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Abstract
The Ets1 transcription factor is a member of the Ets gene family and is highly conserved throughout evolution. Ets1 is known to regulate a number of important biological processes in normal cells and in tumors. In particular, Ets1 has been associated with regulation of immune cell function and with an aggressive behavior in tumors that express it at high levels. Here we review and summarize the general features of Ets1 and describe its roles in immunity and autoimmunity, with a focus on its roles in B lymphocytes. We also review evidence that suggests that Ets1 may play a role in malignant transformation of hematopoietic malignancies including B cell malignancies.
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13
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Ultrasensitive quantum dots-based DNA detection and hybridization kinetics analysis with evanescent wave biosensing platform. Biosens Bioelectron 2011; 26:2390-5. [DOI: 10.1016/j.bios.2010.10.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Revised: 10/10/2010] [Accepted: 10/11/2010] [Indexed: 11/19/2022]
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14
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Caspase cleavage of Ets-1 p51 generates fragments with transcriptional dominant-negative function. Biochem J 2010; 426:229-41. [PMID: 20001963 DOI: 10.1042/bj20090877] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ets-1 is a transcription factor that plays an important role in various physiological and pathological processes, such as development, angiogenesis, apoptosis and tumour invasion. In the present study, we have demonstrated that Ets-1 p51, but not the spliced variant Ets-1 p42, is processed in a caspase-dependent manner in Jurkat T-leukaemia cells undergoing apoptosis, resulting in three C-terminal fragments Cp20, Cp17 and Cp14 and a N-terminal fragment, Np36. In vitro cleavage of Ets-1 p51 by caspase 3 produces fragments consistent with those observed in cells undergoing apoptosis. These fragments are generated by cleavage at three sites located in the exon VII-encoded region of Ets-1 p51. This region is absent from the Ets-1 p42 isoform, which therefore cannot be cleaved by caspases. In Ets-1 p51, cleavage generates C-terminal fragments containing the DNA-binding domain, but lacking the transactivation domain. The Cp17 fragment, the major cleavage product generated during apoptosis, is devoid of transcriptional activity and inhibits Ets-1 p51-mediated transactivation of target genes by competing with Ets-1 p51 for binding to Ets-binding sites present in the target promoters. In the present study, we have demonstrated that caspase cleavage of Ets-1 within the exon VII-encoded region leads to specific down-regulation of the Ets-1 p51 isoform during apoptosis. Furthermore, our results establish that caspase cleavage generates a stable C-terminal fragment that acts as a natural dominant-negative form of the full-length Ets-1 p51 protein.
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15
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Leprivier G, Baillat D, Begue A, Hartmann B, Aumercier M. Ets-1 p51 and p42 isoforms differentially modulate Stromelysin-1 promoter according to induced DNA bend orientation. Nucleic Acids Res 2009; 37:4341-52. [PMID: 19465391 PMCID: PMC2715226 DOI: 10.1093/nar/gkp307] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Stromelysin-1 gene promoter contains a palindrome of two Ets-binding sites (EBS) that bind the p51 and p42 isoforms of the human Ets-1-transcription factor. A previous study established that full gene transactivation is associated with a ternary complex consisting of two p51 bound to the two EBS on the promoter. p42, only able to bind one of the two EBS, induces only very weak activity. Here, we investigate the mechanism by which the Stromelysin-1 promoter discriminates between p51 and p42. The differential stoichiometry of the two Ets-1 isoforms arises from the Stromelysin-1 EBS palindrome. The ternary complex requires the presence of two inhibitory domains flanking the DNA-binding domain and the ability to form an intramolecular autoinhibition module. Most importantly, the p51-ternary and the p42-binary complexes induce DNA curvatures with opposite orientations. These results establish that differential DNA bending, via p51 and p42 differential binding, is correlated with the Stromelysin-1 promoter activation process.
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Affiliation(s)
- Gabriel Leprivier
- CNRS UMR 8161, Institut de Biologie de Lille, Université de Lille 1 and Lille 2, IFR 142, BP 447, 59021 Lille Cedex, France
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16
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Laitem C, Leprivier G, Choul-Li S, Begue A, Monte D, Larsimont D, Dumont P, Duterque-Coquillaud M, Aumercier M. Ets-1 p27: a novel Ets-1 isoform with dominant-negative effects on the transcriptional properties and the subcellular localization of Ets-1 p51. Oncogene 2009; 28:2087-99. [PMID: 19377509 DOI: 10.1038/onc.2009.72] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The transcription factor Ets-1 is implicated in various physiological processes and invasive pathologies. We identified a novel variant of ets-1, ets-1Delta(III-VI), resulting from the alternative splicing of exons III to VI. This variant encodes a 27 kDa isoform, named Ets-1 p27. Ets-1 p27 lacks the threonine-38 residue, the Pointed domain and the transactivation domain, all of which are required for the transactivation of Ets-1 target genes. Both inhibitory domains surrounding the DNA-binding domain are conserved, suggesting that Ets-1 p27, like the full-length Ets-1 p51 isoform, is autoinhibited for DNA binding. We showed that Ets-1 p27 binds DNA in the same way as Ets-1 p51 does and that it acts both at a transcriptional and a subcellular localization level, thereby constituting a dual-acting dominant negative of Ets-1 p51. Ets-1 p27 blocks Ets-1 p51-mediated transactivation of target genes and induces the translocation of Ets-1 p51 from the nucleus to the cytoplasm. Furthermore, Ets-1 p27 overexpression represses the tumor properties of MDA-MB-231 mammary carcinoma cells in correlation with the known implication of Ets-1 in various cellular mechanisms. Thus the dual-acting dominant-negative function of Ets-1 p27 gives to the Ets-1 p27/Ets-1 p51 ratio a determining effect on cell fate.
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Affiliation(s)
- C Laitem
- CNRS Unité Mixte de Recherche 8161, Institut de Biologie de Lille, Institut Pasteur de Lille, Universités de Lille 1 and Lille 2, IFR 142, Lille, France
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17
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De Crescenzo G, Boucher C, Durocher Y, Jolicoeur M. Kinetic Characterization by Surface Plasmon Resonance-Based Biosensors: Principle and Emerging Trends. Cell Mol Bioeng 2008. [DOI: 10.1007/s12195-008-0035-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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18
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Shiota M, Izumi H, Miyamoto N, Onitsuka T, Kashiwagi E, Kidani A, Hirano G, Takahashi M, Ono M, Kuwano M, Naito S, Sasaguri Y, Kohno K. Ets regulates peroxiredoxin1 and 5 expressions through their interaction with the high-mobility group protein B1. Cancer Sci 2008; 99:1950-9. [PMID: 19016754 PMCID: PMC11159958 DOI: 10.1111/j.1349-7006.2008.00912.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 06/02/2008] [Accepted: 06/08/2008] [Indexed: 01/12/2023] Open
Abstract
Peroxiredoxins (Prdxs) are thiol-specific antioxidant proteins that are highly expressed in human cancer cells. Prdxs have been shown to be involved in tumor cell proliferation under conditions of microenvironmental stress such as hypoxia. We hypothesized that Prdxs could be categorized into two groups, stress-inducible and non-inducible ones. In this study, we analyzed the promoter activity and expression levels of five Prdx family members in human cancer cells. We found that both Prdx1 and Prdx5 are inducible after treatment with hydrogen peroxide or hypoxia, but that Prdx2, Prdx3, and Prdx4 are not or are only marginally inducible. We also found that Ets transcription factors are the key activators for stress-inducible expression. High-mobility group protein HMGB1 was shown to function as a coactivator through direct interactions with Ets transcription factors. The DNA binding of Ets transcription factors was significantly enhanced by HMGB1. Silencing of Ets1, Ets2, Prdx1, and Prdx5 expression sensitized cells to oxidative stress. These data indicate that transcription of Prdx genes mediated by Ets/HMG proteins might protect cells from oxidative stress.
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Affiliation(s)
- Masaki Shiota
- Department of Molecular Biology, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan
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19
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Abstract
We describe the formation of protein-DNA contacts in the two-state route for DNA sequence recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes in the transition state and constitutes the bottleneck of complex formation. Although a few nonspecific ionic interactions are formed at this early stage, they mainly play a stabilizing role in the final consolidated complex. The interface is fairly plastic in the transition state, likely because of a high level of hydration. The overall picture of this two-state route largely agrees with a smooth energy landscape for binding that speeds up DNA recognition. This "direct" two-state route differs from the parallel multistep pathway described for this system, which involves nonspecific contacts and at least two intermediate species that must involve substantial conformational rearrangement in either or both macromolecules.
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20
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De Crescenzo G, Woodward L, Srinivasan B. Online optimization of surface plasmon resonance‐based biosensor experiments for improved throughput and confidence. J Mol Recognit 2008; 21:256-66. [DOI: 10.1002/jmr.894] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Shultzaberger RK, Roberts LR, Lyakhov IG, Sidorov IA, Stephen AG, Fisher RJ, Schneider TD. Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res 2007; 35:5275-83. [PMID: 17617646 PMCID: PMC2018646 DOI: 10.1093/nar/gkm471] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 05/26/2007] [Accepted: 05/29/2007] [Indexed: 11/20/2022] Open
Abstract
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy, are unknown. However, the on-rate could be independent of the sequence since a protein is likely to bind once it is near a site. To test this, we used surface plasmon resonance and electromobility shift assays to determine the kinetics for binding of the Fis protein to a range of naturally occurring binding sites. We observed that the logarithm of the off-rate is indeed proportional to the individual information of the binding sites, as predicted. However, the on-rate is also related to the information, but to a lesser degree. We suggest that the on-rate is mostly determined by DNA bending, which in turn is determined by the sequence information. Finally, we observed a break in the binding curve around zero bits of information. The break is expected from information theory because it represents the coding demarcation between specific and nonspecific binding.
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Affiliation(s)
- Ryan K. Shultzaberger
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Lindsey R. Roberts
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Ilya G. Lyakhov
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Igor A. Sidorov
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Andrew G. Stephen
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Robert J. Fisher
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Thomas D. Schneider
- National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
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22
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Di Primo C, Lebars I. Determination of refractive index increment ratios for protein-nucleic acid complexes by surface plasmon resonance. Anal Biochem 2007; 368:148-55. [PMID: 17659251 DOI: 10.1016/j.ab.2007.06.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 06/12/2007] [Accepted: 06/13/2007] [Indexed: 12/11/2022]
Abstract
Three nucleic acid-protein complexes of 1:1 stoichiometry were analyzed by surface plasmon resonance on a Biacore biosensor to test whether or not proteins and nucleic acids yielded similar refractive index increments on binding. The expected maximum response in resonance units, (RU(exp))(max), and the observed one, (RU(obs))(max), on saturation of immobilized targets by interacting partners were compared to determine the ratio of (deltan/deltaC)(protein) to (deltan/deltaC)(nucleic acid), where n is the refractive index at the surface and C is the concentration of one partner. Our results suggest that proteins and nucleic acids behave similarly and that the discrepancy between the expected and observed maximum responses for such complexes reflects inaccurate evaluation of the binding responses. Therefore, no correction of the instrument response is required for protein and nucleic acid interaction studies on a Biacore biosensor.
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Affiliation(s)
- Carmelo Di Primo
- INSERM U869, Institut Européen de Chimie et Biologie, Pessac F-33607, France.
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23
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Higuchi T, Bartel FO, Masuya M, Deguchi T, Henderson KW, Li R, Muise-Helmericks RC, Kern MJ, Watson DK, Spyropoulos DD. Thymomegaly, microsplenia, and defective homeostatic proliferation of peripheral lymphocytes in p51-Ets1 isoform-specific null mice. Mol Cell Biol 2007; 27:3353-66. [PMID: 17339335 PMCID: PMC1899970 DOI: 10.1128/mcb.01871-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ets1 is a member of the Ets transcription factor family. Alternative splicing of exon VII results in two naturally occurring protein isoforms: full-length Ets1 (p51-Ets1) and Ets1(DeltaVII) (p42-Ets1). These isoforms bear key distinctions regarding protein-protein interactions, DNA binding kinetics, and transcriptional target specificity. Disruption of both Ets1 isoforms in mice results in the loss of detectable NK and NKT cell activity and defects in B and T lymphocytes. We generated mice that express only the Ets1(DeltaVII) isoform. Ets1(DeltaVII) homozygous mice express no p51-Ets1 and elevated levels of the p42-Ets1 protein relative to the wild type and display increased perinatal lethality, thymomegaly, and peripheral lymphopenia. Proliferation was increased in both the thymus and the spleen, while apoptosis was decreased in the thymus and increased in the spleen of homozygotes. Significant elevations of CD8(+) and CD8(+)CD4(+) thymocytes were observed. Lymphoid cell (CD19(+), CD4(+), and CD8(+)) reductions were predominantly responsible for diminished spleen cellularity, with fewer memory cells and a failure of homeostatic proliferation to maintain peripheral lymphocytes. Collectively, the Ets1(DeltaVII) mutants demonstrate lymphocyte maturation defects associated with misregulation of p16(Ink4a), p27(Kip1), and CD44. Thus, a balance in the differential regulation of Ets1 isoforms represents a potential mechanism in the control of lymphoid maturation and homeostasis.
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Affiliation(s)
- Tsukasa Higuchi
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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24
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Winzor DJ, Jackson CM. Interpretation of the temperature dependence of equilibrium and rate constants. J Mol Recognit 2006; 19:389-407. [PMID: 16897812 DOI: 10.1002/jmr.799] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The objective of this review is to draw attention to potential pitfalls in attempts to glean mechanistic information from the magnitudes of standard enthalpies and entropies derived from the temperature dependence of equilibrium and rate constants for protein interactions. Problems arise because the minimalist model that suffices to describe the energy differences between initial and final states usually comprises a set of linked equilibria, each of which is characterized by its own energetics. For example, because the overall standard enthalpy is a composite of those individual values, a positive magnitude for DeltaH(o) can still arise despite all reactions within the subset being characterized by negative enthalpy changes: designation of the reaction as being entropy driven is thus equivocal. An experimenter must always bear in mind the fact that any mechanistic interpretation of the magnitudes of thermodynamic parameters refers to the reaction model rather than the experimental system. For the same reason there is little point in subjecting the temperature dependence of rate constants for protein interactions to transition-state analysis. If comparisons with reported values of standard enthalpy and entropy of activation are needed, they are readily calculated from the empirical Arrhenius parameters.
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Affiliation(s)
- Donald J Winzor
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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25
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Winzor DJ, Jackson CM. Interpretation of the temperature dependence of rate constants in biosensor studies. Anal Biochem 2005; 337:289-93. [PMID: 15691509 DOI: 10.1016/j.ab.2004.10.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Indexed: 10/26/2022]
Abstract
A comparison is made between Arrhenius and transition-state analyses of the temperature dependence of rate constants reported in four published biosensor studies. Although the Eyring transition-state theory seemingly affords a more definitive solution to the problem of characterizing the activation energetics, the analysis is equivocal because of inherent assumptions about reaction mechanism and the magnitude of the transmission coefficient. In view of those uncertainties it is suggested that a preferable course of action entails reversion to the empirical Arrhenius analysis with regard to the energy of activation and a preexponential factor. The former is essentially equivalent to the enthalpy of activation, whereas the magnitude of the latter indicates directly the extent of disparity between the frequency of product formation and the universal frequency factor (temperature multiplied by the ratio of the Boltzmann and Planck constants) and hence the likelihood of a more complicated kinetic mechanism than that encompassed by the Eyring transition-state theory.
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Affiliation(s)
- Donald J Winzor
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Qld. 4072, Australia.
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26
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Pei H, Li C, Adereth Y, Hsu T, Watson DK, Li R. Caspase-1 is a direct target gene of ETS1 and plays a role in ETS1-induced apoptosis. Cancer Res 2005; 65:7205-13. [PMID: 16103071 PMCID: PMC2265436 DOI: 10.1158/0008-5472.can-04-3566] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ETS1, the founding member of Ets transcriptional factor family, plays an important role in cell proliferation, differentiation, lymphoid cell development, transformation, angiogenesis, and apoptosis. Previous work has shown that ETS1 represses tumorigenicity of colon carcinoma cells in vivo, and that the p42-ETS1 protein bypasses a defect in apoptosis in colon carcinoma cells through the up-regulation of caspase-1 expression. In this report, we show that expression of p42-ETS1 inhibits tumorigenicity of colon cancer DLD-1 cells through induction of apoptosis in vivo. In support of the hypothesis that caspase-1 might be a target involved in the sensitization of DLD-1 cells to Fas-induced apoptosis by ETS1, overexpression of caspase-1 bypasses Fas-induced apoptosis in these cells as well. Furthermore, ETS1-mediated apoptosis was observed in MOP8 cells, a transformed mouse NIH3T3 cell line. To determine whether ETS1 activates the transcription of caspase-1, luciferase reporters driven by the wild-type and mutant caspase-1 promoters were generated. Both p51-ETS1 and p42-ETS1 transactivated the caspase-1 transcription and a functional Ets binding site is identified in the caspase-1 promoter. Wild-type caspase-1 promoter (pGL3-ICE) was strongly transactivated by ETS1 and this transactivation was dramatically diminished by the mutation of the potential Ets binding site (-525 bp). In addition, electrophoretic mobility shift assay and chromatin immunoprecipitation assay showed complex formation between this binding site and ETS1 proteins. Taken together, ETS1 transcriptionally induces the expression of caspase-1; as such, the regulatory control of caspase-1 expression by ETS1 may underlie the apoptotic susceptibility modulated by ETS1 in specific tumor cells.
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Affiliation(s)
- Huiping Pei
- Department of Pathology and Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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27
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Special-Purpose Modifications and Immobilized Functional Nucleic Acids for Biomolecular Interactions. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b136673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Mannelli I, Minunni M, Tombelli S, Wang R, Michela Spiriti M, Mascini M. Direct immobilisation of DNA probes for the development of affinity biosensors. Bioelectrochemistry 2005; 66:129-38. [PMID: 15833713 DOI: 10.1016/j.bioelechem.2004.04.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 04/07/2004] [Accepted: 04/13/2004] [Indexed: 11/21/2022]
Abstract
An immobilisation procedure based on the direct coupling of thiolated probes (Probe-C6-SH) to bare gold sensor surfaces has been compared with a reference immobilisation method, based on the coupling of biotinylated probes onto a streptavidin-coated dextran-modified surface. The instrumentations used were a quartz crystal microbalance (QCM) and the optical instruments Biacore X and Spreeta based on surface plasmon resonance (SPR). The performances of the DNA-based sensors resulting from direct coupling of thiolated DNA probes onto electrodes of quartz crystals or gold SPR-chips have been studied in terms of the main analytical parameters, i.e. selectivity, sensitivity, reproducibility, etc. In particular, the two immobilisation approaches have been applied to the analysis of oligonucleotides, DNA amplified by polymerase chain reaction (PCR) and genomic DNA enzymatically digested.
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Affiliation(s)
- Ilaria Mannelli
- Dipartimento di Chimica, Università degli Studi di Firenze, Polo Scientifico, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
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29
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Gaidamakov SA, Gorshkova II, Schuck P, Steinbach PJ, Yamada H, Crouch RJ, Cerritelli SM. Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain. Nucleic Acids Res 2005; 33:2166-75. [PMID: 15831789 PMCID: PMC1079969 DOI: 10.1093/nar/gki510] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 03/25/2005] [Accepted: 03/25/2005] [Indexed: 11/14/2022] Open
Abstract
Ribonucleases H have mostly been implicated in eliminating short RNA primers used for initiation of lagging strand DNA synthesis. Escherichia coli RNase HI cleaves these RNA-DNA hybrids in a distributive manner. We report here that eukaryotic RNases H1 have evolved to be processive enzymes by attaching a duplex RNA-binding domain to the RNase H region. Highly conserved amino acids of the duplex RNA-binding domain are required for processivity and nucleic acid binding, which leads to dimerization of the protein. The need for a processive enzyme underscores the importance in eukaryotic cells of processing long hybrids, most of which remain to be identified. However, long RNA-DNA hybrids formed during immunoglobulin class-switch recombination are potential targets for RNase H1 in the nucleus. In mitochondria, where RNase H1 is essential for DNA formation during embryogenesis, long hybrids may be involved in DNA replication.
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Affiliation(s)
- Sergei A. Gaidamakov
- Laboratory of Molecular Genetics, National Institute of Child Health and Human DevelopmentBethesda, MD 20892, USA
| | - Inna I. Gorshkova
- Laboratory of Molecular Genetics, National Institute of Child Health and Human DevelopmentBethesda, MD 20892, USA
- Protein Biophysics Resource, Division of Bioengineering and Physical Science, Office of Research Services, Office of the DirectorBethesda, MD 20892, USA
| | - Peter Schuck
- Protein Biophysics Resource, Division of Bioengineering and Physical Science, Office of Research Services, Office of the DirectorBethesda, MD 20892, USA
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Department of Health and Human ServicesBethesda, MD 20892, USA
| | - Hirofumi Yamada
- Laboratory of Molecular Genetics, National Institute of Child Health and Human DevelopmentBethesda, MD 20892, USA
| | - Robert J. Crouch
- Laboratory of Molecular Genetics, National Institute of Child Health and Human DevelopmentBethesda, MD 20892, USA
| | - Susana M. Cerritelli
- Laboratory of Molecular Genetics, National Institute of Child Health and Human DevelopmentBethesda, MD 20892, USA
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30
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Brecht M, Sewald K, Schiene K, Keen G, Fricke M, Sauer M, Niehaus K. The use of surface plasmon resonance (SPR) and fluorescence resonance energy transfer (FRET) to monitor the interaction of the plant G-proteins Ms-Rac1 and Ms-Rac4 with GTP. J Biotechnol 2005; 112:151-64. [PMID: 15288950 DOI: 10.1016/j.jbiotec.2004.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 03/19/2004] [Accepted: 04/01/2004] [Indexed: 10/26/2022]
Abstract
Using an RT-PCR approach a cDNA clone, designated Ms-Rac4 and putatively coding for a small GTPase was isolated from Medicago sativa. Ms-Rac4 and the earlier described Ms-Rac1 [Mol. Gen. Genet. 263 (2000) 761] belong to the class of GTP-binding Rho of plants (Rop) proteins. At the amino acid level they display all conserved regions that are common to GTP-binding proteins. Phylogenetically both are located in the group Ia, but within this group they are well-separated. Computed structure models of both proteins revealed a high degree of structural conservation. Particularly the switch I and switch II region are 100% conserved between Ms-Rac1 and Ms-Rac4 and highly conserved as compared to other Rac-like G-proteins. Both GTPases differ in structure within the fourth loop and the fourth helix. GTP-binding properties of the heterologously expressed Ms-Rac1 and Ms-Rac4 was shown by fluorescence resonance energy transfer (FRET) using mantGTP and by surface plasmon resonance (SPR). By this method the specificity of the G-protein/GTP interaction was shown and the inhibitory effect of GTP, EDTA and Mg(2+) on the Ms-Rac1 and Ms-Rac4 binding to immobilized GTP was characterized. Ms-Rac1 and Ms-Rac4 exhibited the same affinity to GTP and are similarly affected by GTP, EDTA and Mg(2+). Thus, the predicted structural differences do not result in different GTP-binding properties of Ms-Rac1 and Ms-Rac4.
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Affiliation(s)
- Martina Brecht
- Faculty of Biology, Genetics, University of Bielefeld, D-33501 Bielefeld, Germany
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31
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Lee GM, Donaldson LW, Pufall MA, Kang HS, Pot I, Graves BJ, McIntosh LP. The structural and dynamic basis of Ets-1 DNA binding autoinhibition. J Biol Chem 2004; 280:7088-99. [PMID: 15591056 DOI: 10.1074/jbc.m410722200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor Ets-1 is regulated by the allosteric coupling of DNA binding with the unfolding of an alpha-helix (HI-1) within an autoinhibitory module. To understand the structural and dynamic basis for this autoinhibition, we have used NMR spectroscopy to characterize Ets-1DeltaN301, a partially inhibited fragment of Ets-1. The NMR-derived Ets-1DeltaN301 structure reveals that the autoinhibitory module is formed predominantly by the hydrophobic packing of helices from the N-terminal (HI-1, HI-2) and C-terminal (H4, H5) inhibitory sequences, along with H1 of the intervening DNA binding ETS domain. The intramolecular interactions made by HI-1 in Ets-1DeltaN301 are similar to the intermolecular contacts observed in the crystal structure of an Ets-1DeltaN300 dimer, confirming that the latter represents a domain-swapped species. (15)N relaxation studies demonstrate that the backbone of the N-terminal inhibitory sequence is mobile on the nanosecond-picosecond and millisecond-microsecond time scales. Furthermore, hydrogen exchange measurements reveal that amide protons in helices HI-1 and HI-2 exchange with water at rates only approximately 15- and approximately 75-fold slower, respectively, than predicted for an unfolded polypeptide. These findings indicate that inhibitory helices are only marginally stable even in the absence of DNA. The energetic coupling of DNA binding with the facile unfolding of the labile HI-1 provides a mechanism for modulating Ets-1 DNA binding activity via protein partnerships, post-translational modifications, or mutations. Ets-1 autoinhibition illustrates how conformational equilibria within structural domains can regulate macromolecular interactions.
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Affiliation(s)
- Gregory M Lee
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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32
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Tsoi PY, Yang M. Surface plasmon resonance study of the molecular recognition between polymerase and DNA containing various mismatches and conformational changes of DNA-protein complexes. Biosens Bioelectron 2004; 19:1209-18. [PMID: 15046752 DOI: 10.1016/j.bios.2003.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2003] [Revised: 11/11/2003] [Accepted: 11/13/2003] [Indexed: 11/18/2022]
Abstract
Although surface plasmon resonance (SPR) biosensor technique has been used to study protein-protein interactions and to detect conformational changes of proteins, it has not been shown whether the SPR biosensor can be used to study a complex kinetic system such as the protein-DNA binding, which sometimes involves several binding steps as well as dynamic conformational changes of the complexes. In this study, we have used SPR biosensor and T7 polymerase as the model system to study the interactions of the polymerase with a series of DNA template-primer duplexes containing different number of mismatches and GC contents at various positions near the primer 3'-end. In general, the binding constants measured by the SPR are several magnitudes smaller than those determined in solution, indicating the limitation of the surface-based technique for measuring solution-based interactions. However, the distinct polymerase binding profiles obtained for DNA duplexes differed by as low as a single mismatch suggest that the SPR data can be used for relative comparison purpose among a set of experiments carried out under identical conditions. The successful fitting of the binding profiles using the established translocation model also demonstrated that SPR can be used to monitor conformational changes, as well as to derive relative kinetic values, within a complicated DNA-protein interaction system. The results also demonstrated that SPR biosensor may be used as a sensitive technique for studying molecular recognition events, such as single-base discrimination involved in protein-DNA interactions.
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Affiliation(s)
- Pui Yan Tsoi
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
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Mönke G, Altschmied L, Tewes A, Reidt W, Mock HP, Bäumlein H, Conrad U. Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA. PLANTA 2004; 219:158-66. [PMID: 14767767 DOI: 10.1007/s00425-004-1206-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Accepted: 12/03/2003] [Indexed: 05/20/2023]
Abstract
In Arabidopsis thaliana (L.) Heynh. the seed-specific transcription factors ABI3 and FUS3 have key regulatory functions during the development of mature seeds. The highly conserved RY motif [DNA motif CATGCA(TG)], present in many seed-specific promoters, is an essential target of both regulators. Here we show that, in vitro, the full-length ABI3 protein, as well as FUS3 protein, is able to bind to RY-DNA and that the B3 domains of both transcription factors are necessary and sufficient for the specific interaction with the RY element. Flanking sequences of the RY motif modulate the binding, but the presence of an RY sequence alone allows the specific interaction of ABI3 and FUS3 with the target in vitro. Transcriptional activity of ABI3 and FUS3, measured by transient promoter activation, requires the B3 DNA-binding domain and an activation domain. In addition to the known N-terminal-located activation domain, a second transcription activation domain was found in the B1 region of ABI3.
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Affiliation(s)
- Gudrun Mönke
- Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben, Corrensstr.3, 6466 Gatersleben, Germany
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Lionneton F, Lelièvre E, Baillat D, Stehelin D, Soncin F. Characterization and functional analysis of the p42Ets-1 variant of the mouse Ets-1 transcription factor. Oncogene 2004; 22:9156-64. [PMID: 14668797 DOI: 10.1038/sj.onc.1207241] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have identified the mouse exon VII splice variant of the Ets-1 transcription factor. The variant is expressed in all cell lines which express ets-1, at lower levels, it is also expressed in the mouse embryo in vivo. The corresponding protein, p42Ets-1, is a transcription factor as it is able to bind to specific DNA sequences and to transactivate a bona fide ETS reporter vector. A comparison of optimal DNA-binding sites shows that p42Ets-1 binds to more various DNA sequences than p51Ets-1; p42Ets-1 recognizes the same optimal consensus sequence as p51Ets-1, but also many variations of it, mainly at base -1, which is located just prior to the GGAA/T core sequence. The binding differences were quantified by surface plasmon resonance analyses and the protein region responsible for the differences in DNA sequence recognition located in the Val280-Glu302 fragment, which is encoded by exon VII. The specific DNA-binding properties of each isoform translates into clear differences in activity, p42Ets-1 transactivates the natural VE-cadherin gene promoter through both ETS-binding site (EBS)2 and EBS4 whereas p51Ets-1 is mainly active on EBS4. Altogether, our data suggest that p42Ets-1 acts as a distinct transcription factor from p51Ets-1.
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Affiliation(s)
- Frédéric Lionneton
- Institut de Biologie de Lille, CNRS UMR 8526, 1 rue Calmette, 59021 Lille Cedex, France
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35
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Abstract
The Ets1 proto-oncoprotein is a member of the Ets family of transcription factors that share a unique DNA binding domain, the Ets domain. The DNA binding activity of Ets1 is controlled by kinases and transcription factors. Some transcription factors, such as AML-1, regulate Ets1 by targeting its autoinhibitory module. Others, such as Pax-5, alter Ets1 DNA binding properties. Ets1 harbors two phosphorylation sites, threonine-38 and an array of serines within the exon VII domain. Phosphorylation of threonine-38 by ERK1/2 activates Ets1, whereas phosphorylation of the exon VII domain by CaMKII or MLCK inhibits Ets1 DNA binding activity. Ets1 is expressed by numerous cell types. In haemotopoietic cells, it contributes to the regulation of cellular differentiation. In a variety of other cells, including endothelial cells, vascular smooth muscle cells and epithelial cancer cells, Ets1 promotes invasive behavior. Regulation of MMP1, MMP3, MMP9 and uPA as well as of VEGF and VEGF receptor gene expression has been ascribed to Ets1. In tumors, Ets1 expression is indicative of poorer prognosis.
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Affiliation(s)
- Jürgen Dittmer
- Universität Halle-Wittenberg Universitätsklinik und Poliklinik für Gynäkologie Magdeburger Str, 24 06097 Halle, Saale, Germany.
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Affiliation(s)
- Donald J Winzor
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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Ojennus DD, Lehto SE, Wuttke DS. Electrostatic interactions in the reconstitution of an SH2 domain from constituent peptide fragments. Protein Sci 2003; 12:44-55. [PMID: 12493827 PMCID: PMC2312404 DOI: 10.1110/ps.0227903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fragment complementation has been used to delineate the essential recognition elements for stable folding in Src homology 2 (SH2) domains by using NMR spectroscopy, alanine scanning, and surface plasmon resonance. The unfolded 9-kD and 5-kD peptide fragments formed by limited proteolytic digestion of the N-terminal SH2 domain from the p85alpha subunit of phosphatidylinositol 3'-kinase fold into an active native-like structure on interaction with one another. The corresponding 5-kD fragment of the homologous Src protein, however, was not capable of structurally complementing the p85 9-kD fragment, indicating that fragment complementation among these SH2 domains is sensitive to the sequence differences between the Src and p85 domains. Partial complementation and folding activity could be recovered with hybrid sequences of these SH2 domains. Complete alanine scanning of the 5-kD p85 fragment was used to identify the sequence recognition elements required for complex formation. The alanine substitutions in the p85 5-kD fragment that abolished binding affinity with the cognate 9-kD fragment correlate well with highly conserved residues among SH2 domains that are either integrally involved in core packing or found at the interface between fragments. Surprisingly, however, mutation of a nonconserved surface-exposed aspartic acid to alanine was found to have a significant effect on complementation. A single additional mutation of arginine to aspartic acid allowed for recovery of native structure and increased the thermal stability of the designed Src-p85 chimera by 18 degrees C. This modification appears to relieve an unfavorable surface electrostatic interaction, demonstrating the importance of surface charge interactions in protein stability.
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Affiliation(s)
- Deanna Dahlke Ojennus
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA
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38
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Skillman AG, Maurer KW, Roe DC, Stauber MJ, Eargle D, Ewing TJA, Muscate A, Davioud-Charvet E, Medaglia MV, Fisher RJ, Arnold E, Gao HQ, Buckheit R, Boyer PL, Hughes SH, Kuntz ID, Kenyon GL. A novel mechanism for inhibition of HIV-1 reverse transcriptase. Bioorg Chem 2002; 30:443-58. [PMID: 12642128 DOI: 10.1016/s0045-2068(02)00502-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The human immunodeficiency virus (HIV) epidemic is an important medical problem. Although combination drug regimens have produced dramatic decreases in viral load, current therapies do not provide a cure for HIV infection. We have used structure-based design and combinatorial medicinal chemistry to identify potent and selective HIV-1 reverse transcriptase (RT) inhibitors that may work by a mechanism distinct from that of current HIV drugs. The most potent of these compounds (compound 4, 2-naphthalenesulfonic acid, 4-hydroxy-7-[[[[5-hydroxy-6-[(4-cinnamylphenyl)azo]-7-sulfo-2-naphthalenyl]amino]carbonyl]amino]-3-[(4-cinnamylphenyl)azo], disodium salt) has an IC(50) of 90 nM for inhibition of polymerase chain extension, a K(d) of 40 nM for inhibition of DNA-RT binding, and an IC(50) of 25-100 nM for inhibition of RNaseH cleavage. The parent compound (1) was as effective against 10 nucleoside and non-nucleoside resistant HIV-1 RT mutants as it was against the wild-type enzyme. Compound 4 inhibited HIV-1 RT and murine leukemia virus (MLV) RT, but it did not inhibit T(4) DNA polymerase, T(7) DNA polymerase, or the Klenow fragment at concentrations up to 200 nM. Finally, compound 4 protected cells from HIV-1 infection at a concentration more than 40 times lower than the concentration at which it caused cellular toxicity.
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Affiliation(s)
- A Geoffrey Skillman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 513 Parnassus Ave, Box 0446, San Francisco, CA 94143-0446, USA
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39
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Liu H, Grundström T. Calcium regulation of GM-CSF by calmodulin-dependent kinase II phosphorylation of Ets1. Mol Biol Cell 2002; 13:4497-507. [PMID: 12475968 PMCID: PMC138649 DOI: 10.1091/mbc.e02-03-0149] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The multipotent cytokine granulocyte macrophage-colony stimulating factor (GM-CSF) is involved in particular in the physiological response to infection and in inflammatory responses. GM-CSF is produced by many cell types, including T lymphocytes responding to T-cell receptor activation and mantle zone B lymphocytes. B-cell receptor and T-cell receptor activation generates two major signals: an increase in intracellular Ca(2+) concentration and a protein kinase cascade. Previous studies have shown that the Ca(2+)/calmodulin-dependent phosphatase calcineurin mediates stimulation of GM-CSF transcription in response to Ca(2+). In this study, we show that Ca(2+) signaling also regulates GM-CSF transcription negatively through Ca(2+)/calmodulin-dependent kinase II (CaMK II) phosphorylation of serines in the autoinhibitory domain for DNA binding of the transcription factor Ets1. Wild-type Ets1 negatively affects GM-CSF transcription on Ca(2+) stimulation in the presence of cyclosporin A, which inhibits calcineurin. Conversely, Ets1 with mutated CaMK II target serines showed an increase in transactivation of the GM-CSF promoter/enhancer. Moreover, constitutively active CaMK II inhibited transactivation of GM-CSF by wild-type Ets1 but not by Ets1 with mutated CaMK II sites. Mutation of CaMK II target serines in Ets1 also relieves inhibition of cooperative transactivation of GM-CSF with the Runx1/AML1 transcription factor. In addition, the Ca(2+)-dependent phosphorylation of Ets1 reduces the binding of Ets1 to the GM-CSF promoter in vivo.
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Affiliation(s)
- Hebin Liu
- Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden
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Gambari R. Biospecific interaction analysis: a tool for drug discovery and development. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2002; 1:119-35. [PMID: 12174673 DOI: 10.2165/00129785-200101020-00005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent development of surface plasmon resonance (SPR)-based biosensor technologies for biospecific interaction analysis (BIA) enables the monitoring of a variety of molecular reactions in real-time. The biomolecular interactions occur at the surface of a flow cell of a sensor chip between a ligand immobilized on the surface and an injected analyte. SPR-based BIA offers many advantages over most of the other methodologies available for the study of biomolecular interactions, including full automation, no requirement for labeling, and the availability of a large variety of activated sensor chips that allow immobilization of DNA, RNA, proteins, peptides and cells. The assay is rapid and requires only small quantitities of both ligand and analyte in order to obtain informative results. In addition, the sensor chip can be re-used many times, leading to low running costs. Aside from the analysis of all possible combinations of peptide, protein, DNA and RNA interactions, this technology can also be used for screening of monoclonal antibodies and epitope mapping, analysis of interactions between low molecular weight compounds and proteins or nucleic acids, interactions between cells and ligands, and real-time monitoring of gene expression. Applications of SPR-based BIA in medicine include the molecular diagnosis of viral infections and genetic diseases caused by point mutations. Future perspectives include the combinations of SPR-based BIA with mass spectrometry, the use of biosensors in proteomics, and the application of this technology to design and develop efficient drug delivery systems.
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Affiliation(s)
- R Gambari
- Department of Biochemistry and Molecular Biology, and Biotechnology Center, Ferrara University, Ferrara, Italy.
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41
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Rüfer A, Neuenschwander PF, Sauer B. Analysis of Cre-loxP interaction by surface plasmon resonance: influence of spermidine on cooperativity. Anal Biochem 2002; 308:90-9. [PMID: 12234468 DOI: 10.1016/s0003-2697(02)00247-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To study target site selectivity of one important class of DNA-binding proteins, site-specific DNA recombinases, we developed an automated real-time kinetic assay based on surface plasmon resonance (BIACORE) and formulated a curve-fitting model that takes into account cooperative interactions. Monitoring the interaction between the Cre DNA recombinase and its specific target site loxP by BIACORE, we found that Cre associates with loxP tightly and highly cooperatively. We observed that the cooperative moment of the Cre-loxP interaction is strongly dependent on the concentration of spermidine, a small polyamine influencing DNA conformation. Thus, DNA conformation can have a profound impact on substrate recognition and subsequent recombination.
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Affiliation(s)
- Andreas Rüfer
- Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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42
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Baillat D, Bègue A, Stéhelin D, Aumercier M. ETS-1 transcription factor binds cooperatively to the palindromic head to head ETS-binding sites of the stromelysin-1 promoter by counteracting autoinhibition. J Biol Chem 2002; 277:29386-98. [PMID: 12034715 DOI: 10.1074/jbc.m200088200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stromelysin-1 (matrix metalloproteinase-3) is a member of the matrix metalloproteinase family. Regulation of its gene expression is critical for tissue homeostasis. Patterns of increased co-expression of stromelysin-1 and ETS-1 genes have been observed in pathological processes. Stromelysin-1 promoter is transactivated by ETS proteins through two palindromic head to head ETS-binding sites, an unusual configuration among metalloproteinase promoters. By using surface plasmon resonance, electrophoretic mobility shift assay, and photo-cross-linking, we showed that full-length human ETS-1 (p51) binds cooperatively to the ETS-binding site palindrome of the human stromelysin-1 promoter, with facilitated binding of the second ETS-1 molecule to form an ETS-1.DNA.ETS-1 ternary complex. The study of N-terminal deletion mutants allowed us to conclude that cooperative binding implied autoinhibition counteraction, requiring the 245-330-residue region of the protein that is encoded by exon VII of the gene. This region was deleted in the natural p42 isoform of ETS-1, which was unable to bind cooperatively to the palindrome. Transient transfection experiments showed a good correlation between DNA binding and promoter transactivation for p51. In contrast, p42 showed a poorer transactivation, reinforcing the significance of cooperative binding for full transactivation. It is the first time that ETS-1 was shown to be able to counteract its own autoinhibition.
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Affiliation(s)
- David Baillat
- CNRS Unité Mixte de Recherche 8526, Institut de Biologie de Lille, Institut Pasteur de Lille, B.P. 447, 1 Rue Calmette, 59021 Lille Cedex, France
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43
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Sigmundsson K, Másson G, Rice R, Beauchemin N, Obrink B. Determination of active concentrations and association and dissociation rate constants of interacting biomolecules: an analytical solution to the theory for kinetic and mass transport limitations in biosensor technology and its experimental verification. Biochemistry 2002; 41:8263-76. [PMID: 12081475 DOI: 10.1021/bi020099h] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate determination of kinetic rate constants for interacting biomolecules requires knowledge of the active concentrations of the participating molecules. Also, in other biomedical and clinical applications, sensitive, precise and accurate methods are needed to determine the concentration of biologically active molecules, which frequently constitute only a fraction of the total molecular pool. Here we report a novel development of the approach to determining active concentrations based on surface plasmon resonance (SPR) technology. The method relies on changes in binding rates with varying flow rates under conditions of partial mass transport, and does not require standards of known concentrations, given that the molecular mass of the molecule of interest is known. We introduce an analytical solution to the differential equations describing the formation of a 1:1 bimolecular complex, taking into account both the association and dissociation reactions, under partial mass transport limitations. This solution can be used in global fitting to binding curves obtained at different flow rates. The accuracy, precision, and sensitivity of this approach were determined in experiments involving binding of tyrosine-phosphorylated recombinant proteins to anti-phosphotyrosine antibodies, where the active concentration could be determined independently by in vitro phosphorylation with (33)P. There was an excellent agreement between the active concentrations determined by the analytical SPR-based method and by determination of the level of radioactivity of the phosphorylated protein. The SPR-based method allows determination of protein concentrations at picomolar levels. A procedure for accurate determinations of association and dissociation rate constants, based on the analytical solution of the mass transport and binding theory, is outlined.
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Affiliation(s)
- Kristmundur Sigmundsson
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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44
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Yi S, Bernat B, Pál G, Kossiakoff A, Li WH. Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones. Mol Biol Evol 2002; 19:1083-92. [PMID: 12082127 DOI: 10.1093/oxfordjournals.molbev.a004166] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Primate growth hormone (GH) has evolved rapidly, having undergone approximately 30% amino acid substitutions from the inferred ancestral eutherian sequence. Nevertheless, human growth hormone (hGH) is physiologically effective when administered to nonprimate mammals. In contrast, its functional counterpart, the human growth hormone receptor (hGHR), has evolved species specificity so that it responds only to Old World primate GHs. It has been proposed that this species specificity of the hGHR is largely caused by the Leu --> Arg change at position 43 after a prior His --> Asp change at position 171 of the GH. Sequence analyses supported this hypothesis and revealed that the transitional phase in the GH:GHR coevolution still persists in New World monkeys. For example, although the GH of the squirrel monkey has the His --> Asp substitution at position 171, residue 43 of its GHR is a Leu, the nonprimate residue. If the squirrel monkey truly represents an intermediate stage of GH:GHR coevolution, its GHR should respond to both hGH and nonprimate GH. Also, if the emergence of species specificity was a result of the selection for a more efficient GH:GHR interaction, then changing residue 43 of the squirrel monkey growth hormone receptor (smGHR) to Arg should increase its binding affinity toward higher primate GH. To test these hypotheses, we performed protein-binding assays between the smGHR and both human and rat GHs, using the surface plasmon resonance methodology. Furthermore, the effects of reciprocal mutations at position 43 of human and squirrel monkey GHRs are measured for their binding affinities toward human and squirrel monkey GHs. The results from the binding kinetic assays clearly demonstrate that the smGHR is in the intermediate state of the evolution of species specificity. Interestingly, the altered residue Arg at position 43 of the smGHR does not lead to an increased binding affinity. The implications of these results on the evolution of the GH:GHR interaction and on functional evolution are discussed.
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Affiliation(s)
- Soojin Yi
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.
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45
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Tsoi PY, Yang M. Kinetic study of various binding modes between human DNA polymerase beta and different DNA substrates by surface-plasmon-resonance biosensor. Biochem J 2002; 361:317-25. [PMID: 11772403 PMCID: PMC1222311 DOI: 10.1042/0264-6021:3610317] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The interaction of a series of DNA substrates with human DNA polymerase beta has been studied in real time by using a surface-plasmon-resonance (SPR) biosensor technique. We have prepared the sensor surfaces comprising different DNA targets, including single-stranded DNA, blunt-end double-stranded DNA, gapped DNA and DNA template-primer duplexes containing various mismatches at different positions. The binding and dissociation of polymerase beta at the DNA-modified surfaces was measured in real time, and the kinetics profiles of polymerase-DNA interaction were analysed using various physical models. The results showed that polymerase beta binding to single-stranded DNA (K(A)=1.25 x 10(8) M(-1); where K(A) is the equilibrium affinity constant) was thermodynamically more favourable than to blunt-end DNA duplex (K(A)=7.56x10(7) M(-1)) or gapped DNA (K(A)=8.53x10(7) M(-1)), with a single binding mode on each DNA substrate. However, polymerase beta bound to DNA template-primer duplexes (15 bp with a 35 nt overhang) at two sites, presumably one at the single-strand overhang and the other at the 3'-end of the primer. When the DNA duplex was fully matched, most of the polymerase beta (83%) bound to the template-primer duplex region. The introduction of different numbers of mismatches near the 3'-end of the primer caused the binding affinity and the fraction of polymerase beta bound at the duplex region to decrease 8-58-fold and 15-40%, respectively. On the other hand, the affinity of polymerase beta for the single-strand overhang remained unchanged while the fraction bound to the single-strand region increased by 15-40%. The destabilizing effect of the mismatches was due to both a decrease in the rate of binding and an increase in the rate of dissociation for polymerase beta.
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Affiliation(s)
- Pui Yan Tsoi
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
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46
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Baert JL, Beaudoin C, Coutte L, de Launoit Y. ERM transactivation is up-regulated by the repression of DNA binding after the PKA phosphorylation of a consensus site at the edge of the ETS domain. J Biol Chem 2002; 277:1002-12. [PMID: 11682477 DOI: 10.1074/jbc.m107139200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The final step of the transduction pathway is the activation of gene transcription, which is driven by kinase cascades leading to changes in the activity of many transcription factors. Among these latter, PEA3/E1AF, ER81/ETV1, and ERM, members of the well conserved PEA3 group from the Ets family are involved in these processes. We show here that protein kinase A (PKA) increases the transcriptional activity of human ERM and human ETV1, through a Ser residue situated at the edge of the ETS DNA-binding domain. PKA phosphorylation does not directly affect the ERM transactivation domains but does affect DNA binding activity. Unphosphorylated wild-type ERM bound DNA avidly, whereas after PKA phosphorylation it did so very weakly. Interestingly, S367A mutation significantly reduced the ERM-mediated transcription in the presence of the kinase, and the DNA binding of this mutant, although similar to that of unphosphorylated wild-type protein, was insensitive to PKA treatment. Mutations, which may mimic a phosphorylated serine, converted ERM from an efficient DNA-binding protein to a poor DNA binding one, with inefficiency of PKA phosphorylation. The present data clearly demonstrate a close correlation between the capacity of PKA to increase the transactivation of ERM and the drastic down-regulation of the binding of the ETS domain to the targeted DNA. What we thus demonstrate here is a relatively rare transcription activation mechanism through a decrease in DNA binding, probably by the shift of a non-active form of an Ets protein to a PKA-phosphorylated active one, which should be in a conformation permitting a transactivation domain to be active.
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Affiliation(s)
- Jean-Luc Baert
- UMR 8526 CNRS/Institut Pasteur de Lille, Institut de Biologie de Lille, BP 447, 1 rue Calmette, 59021 Lille Cedex, France
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47
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Davis TM, Wilson WD. Surface plasmon resonance biosensor analysis of RNA-small molecule interactions. Methods Enzymol 2001; 340:22-51. [PMID: 11494851 DOI: 10.1016/s0076-6879(01)40416-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- T M Davis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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48
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Khaleghpour K, Kahvejian A, De Crescenzo G, Roy G, Svitkin YV, Imataka H, O'Connor-McCourt M, Sonenberg N. Dual interactions of the translational repressor Paip2 with poly(A) binding protein. Mol Cell Biol 2001; 21:5200-13. [PMID: 11438674 PMCID: PMC87244 DOI: 10.1128/mcb.21.15.5200-5213.2001] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cap structure and the poly(A) tail of eukaryotic mRNAs act synergistically to enhance translation. This effect is mediated by a direct interaction of eukaryotic initiation factor 4G and poly(A) binding protein (PABP), which brings about circularization of the mRNA. Of the two recently identified PABP-interacting proteins, one, Paip1, stimulates translation, and the other, Paip2, which competes with Paip1 for binding to PABP, represses translation. Here we studied the Paip2-PABP interaction. Biacore data and far-Western analysis revealed that Paip2 contains two binding sites for PABP, one encompassing a 16-amino-acid stretch located in the C terminus and a second encompassing a larger central region. PABP also contains two binding regions for Paip2, one located in the RNA recognition motif (RRM) region and the other in the carboxy-terminal region. A two-to-one stoichiometry for binding of Paip2 to PABP with two independent K(d)s of 0.66 and 74 nM was determined. Thus, our data demonstrate that PABP and Paip2 could form a trimeric complex containing one PABP molecule and two Paip2 molecules. Significantly, only the central Paip2 fragment, which binds with high affinity to the PABP RRM region, inhibits PABP binding to poly(A) RNA and translation.
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Affiliation(s)
- K Khaleghpour
- Department of Biochemistry and McGill Cancer Center, McGill University, Montréal, Québec, Canada H3G 1Y6
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49
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Abstract
The FLAG (Sigma, St. Louis, MO, USA) peptide is a frequently used hydrophilic and immunogenic fusion tag which was specifically designed to facilitate rapid purification by immunoaffinity chromatography. The monoclonal antibody M1 recognizes the free N-terminus of the peptide tag in a calcium dependent manner. Dissociation of the complex can be performed by the addition of chelating agents such as EDTA. This effect can be exploited for immunoaffinity purification of FLAG-tagged fusion proteins. Kinetic information obtained from monitoring interactions in real-time measurement (Biacore 2000) using surface plasmon resonance as detection principle did not show any difference for association and dissociation rate constants in the presence (k(a) = 3.03 x 10(3) M(-1) k(d) = 1.25 x 10(-3) s(-1)) and in the absence of Ca2+ (k(a) = 3.59 x 10(3) M(-1) s(-1), k(d) = 1.16 x 10(-3) s(-1)). These findings corroborate the reports from Mol. Immunol. 33 (1996) 601-608 describing similar binding analyzed by enzyme-linked immunosorbent assay experiments. These investigations are in contrast to the observations in immunoaffinity chromatography with immobilized anti-FLAG antibody M1.
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Affiliation(s)
- A Einhauer
- Institute of Applied Microbiology, University of Agricultural Sciences, Vienna, Austria
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Khalifa MB, Choulier L, Lortat-Jacob H, Altschuh D, Vernet T. BIACORE data processing: an evaluation of the global fitting procedure. Anal Biochem 2001; 293:194-203. [PMID: 11399032 DOI: 10.1006/abio.2001.5119] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Data from real-time molecular interaction analysis using BIACORE are currently evaluated by numerical integration. We have investigated the ability of two software packages (BIAevaluation 3.0 and CLAMP99) to analyze complex interactions. Three experimental data sets of high quality obtained with BIACORE upgraded and 2000 instruments, representative of simple bimolecular, heterogeneous ligand, and mass-transport-limited interactions, were processed by the global fitting procedure. The two software, which differ mainly in the statistical assessment of the output values, were able to discriminate correctly between various interacting models and provided very close output parameters with satisfactory statistical tests.
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Affiliation(s)
- M B Khalifa
- Laboratoire d'Ingénierie des Macromolécules, Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, Grenoble Cedex 1, 38027, France
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