1
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El Khoury L, El Hage K, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three integrase strand transfer inhibitors are in intensive clinical use, raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). The onset of integrase resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviral nucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs. These show the DTG > EVG > RAL ranking of their inhibitory activities of the intasome to correspond to that of their free energies of binding, ∆Gs, to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, ∆H, the entropy undergoing marginal variations. We sought whether this ranking might be reproduced through quantum chemistry (QC) Density Functional Theory calculations of intermolecular interaction energies between simplified models consisting of sole halobenzene ring and the highly conserved retroviral nucleobases G4 and C16. These calculations showed that binding of EVG has a small preference over DTG, while RAL ranked third. This indicates that additional interactions of the diketoacid parts of the drugs with DNA could be necessary to further enable preferential binding of DTG. The corresponding ∆Etotvalues computed with a polarizable molecular mechanics/dynamics procedure, Sum of Interactions Between Fragments Ab initio computed (SIBFA), showed good correlations with this ∆E(QC) ranking. These validations are an important step toward the use of polarizable molecular dynamics simulations on DTG or EVG derivatives in their complexes with the complete intasome, an application now motivated and enabled by the advent of currently developed and improved massively parallel software.
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Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Present address: Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Krystel El Hage
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
- Present address: Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U829, Université Evry-Val d’Essonne, Evry, France
| | - Jean-Philip Piquemal
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Institut Universitaire de France, Paris, France
| | - Serge Fermandjian
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
| | - Richard G. Maroun
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
| | - Zeina Hobaika
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
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2
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Zorrilla S, Mónico A, Duarte S, Rivas G, Pérez-Sala D, Pajares MA. Integrated approaches to unravel the impact of protein lipoxidation on macromolecular interactions. Free Radic Biol Med 2019; 144:203-217. [PMID: 30991143 DOI: 10.1016/j.freeradbiomed.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022]
Abstract
Protein modification by lipid derived reactive species, or lipoxidation, is increased during oxidative stress, a common feature observed in many pathological conditions. Biochemical and functional consequences of lipoxidation include changes in the conformation and assembly of the target proteins, altered recognition of ligands and/or cofactors, changes in the interactions with DNA or in protein-protein interactions, modifications in membrane partitioning and binding and/or subcellular localization. These changes may impact, directly or indirectly, signaling pathways involved in the activation of cell defense mechanisms, but when these are overwhelmed they may lead to pathological outcomes. Mass spectrometry provides state of the art approaches for the identification and characterization of lipoxidized proteins/residues and the modifying species. Nevertheless, understanding the complexity of the functional effects of protein lipoxidation requires the use of additional methodologies. Herein, biochemical and biophysical methods used to detect and measure functional effects of protein lipoxidation at different levels of complexity, from in vitro and reconstituted cell-like systems to cells, are reviewed, focusing especially on macromolecular interactions. Knowledge generated through innovative and complementary technologies will contribute to comprehend the role of lipoxidation in pathophysiology and, ultimately, its potential as target for therapeutic intervention.
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Affiliation(s)
- Silvia Zorrilla
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Andreia Mónico
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Sofia Duarte
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Germán Rivas
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Pérez-Sala
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María A Pajares
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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3
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Kamba PF, Dickson DA, White NA, Ekstrom JL, Koslowsky DJ, Hoogstraten CG. The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein. Sci Rep 2018; 8:16989. [PMID: 30451852 PMCID: PMC6242908 DOI: 10.1038/s41598-018-34377-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/15/2018] [Indexed: 01/30/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins, a helical repeat family of organellar RNA binding proteins, play essential roles in post-transcriptional RNA processing. In Trypanosoma brucei, an expanded family of PPR proteins localize to the parasite’s single mitochondrion, where they are believed to perform important roles in both RNA processing and translation. We studied the RNA binding specificity of the simplest T. brucei PPR protein (KRIPP11) using electrophoretic mobility shift assays, fluorescence anisotropy, circular dichroism spectroscopy, and in vitro selection. We found KRIPP11 to be an RNA binding protein with specificity for sequences of four or more consecutive guanosine residues (G-tracts). Such G-tracts are dramatically enriched in T. brucei mitochondrial transcripts that are destined for extensive uridine insertion/deletion editing but are not present in mRNAs following editing. We further found that the quadruplex oligoguanosine RNA conformation is preferentially recognized by KRIPP11 over other conformational forms, and is bound without disruption of the quadruplex structure. In combination with prior data demonstrating association of KRIPP11 with the small ribosomal subunit, these results suggest possible roles for KRIPP11 in bridging mRNA maturation and translation or in facilitating translation of unusual dual-coded open reading frames.
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Affiliation(s)
- Pakoyo F Kamba
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Makerere University, Kampala, Uganda
| | - David A Dickson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, Massachusetts, USA
| | - Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jennifer L Ekstrom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Donna J Koslowsky
- Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824-1319, USA
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.
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4
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Xu X, Wang L, Zhu D, Wang Y, Jiang W. Protein binding protection in combination with DNA masking for sensitive and reliable transcription factor detection. Talanta 2018; 186:293-298. [DOI: 10.1016/j.talanta.2018.04.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/04/2018] [Accepted: 04/15/2018] [Indexed: 10/17/2022]
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5
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Taylor EL, Kesavan PM, Wolfe AE, O'Brien PJ. Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase. Biochemistry 2018; 57:4440-4454. [PMID: 29940097 DOI: 10.1021/acs.biochem.8b00531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) recognizes many alkylated and deaminated purine lesions and excises them to initiate the base excision DNA repair pathway. AAG employs facilitated diffusion to rapidly scan nonspecific sites and locate rare sites of damage. Nonspecific DNA binding interactions are critical to the efficiency of this search for damage, but little is known about the binding footprint or the affinity of AAG for nonspecific sites. We used biochemical and biophysical approaches to characterize the binding of AAG to both undamaged and damaged DNA. Although fluorescence anisotropy is routinely used to study DNA binding, we found unexpected complexities in the data for binding of AAG to DNA. Systematic comparison of different fluorescent labels and different lengths of DNA allowed binding models to be distinguished and demonstrated that AAG can bind with high affinity and high density to nonspecific DNA. Fluorescein-labeled DNA gave the most complex behavior but also showed the greatest potential to distinguish specific and nonspecific binding modes. We suggest a unified model that is expected to apply to many DNA binding proteins that exhibit affinity for nonspecific DNA. Although AAG strongly prefers to excise lesions from duplex DNA, nonspecific binding is comparable for single- and double-stranded nonspecific sites. The electrostatically driven binding of AAG to small DNA sites (∼5 nucleotides of single-stranded and ∼6 base pairs of duplex) facilitates the search for DNA damage in chromosomal DNA, which is bound by nucleosomes and other proteins.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Preethi M Kesavan
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Abigail E Wolfe
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Patrick J O'Brien
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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6
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El Khoury L, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir. Biochem Biophys Res Commun 2017; 488:433-438. [PMID: 28478035 DOI: 10.1016/j.bbrc.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/01/2017] [Indexed: 01/03/2023]
Abstract
The Human Immunodeficiency Virus-1 integrase is responsible for the covalent insertion of a newly synthesized double-stranded viral DNA into the host cells, and is an emerging target for antivirus drug design. Raltegravir (RAL) and elvitegravir (EVG) are the first two integrase strand transfer inhibitors used in therapy. However, treated patients eventually develop detrimental resistance mutations. By contrast, a recently approved drug, dolutegravir (DTG), presents a high barrier to resistance. This study aims to understand the increased efficiency of DTG upon focusing on its interaction properties with viral DNA. The results showed DTG to be involved in more extended interactions with viral DNA than EVG. Such interactions involve the halobenzene and scaffold of DTG and EVG and bases 5'G-43', 3'A35'and 3'C45'.
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Affiliation(s)
- Léa El Khoury
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, B.P. 11-514 Riad El Solh, Beirut 1107 2050, Lebanon; Laboratoire de Chimie Théorique, UMR7616 CNRS, UPMC, Sorbonne Universités, Paris 75005, France.
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR7616 CNRS, UPMC, Sorbonne Universités, Paris 75005, France; Institut Universitaire de France, Paris Cedex 05, 75231, France; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, United States.
| | - Serge Fermandjian
- Chemistry and Biology Nucleo(S)Tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale, Paris, France.
| | - Richard G Maroun
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, B.P. 11-514 Riad El Solh, Beirut 1107 2050, Lebanon.
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616 CNRS, UPMC, Sorbonne Universités, Paris 75005, France.
| | - Zeina Hobaika
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, B.P. 11-514 Riad El Solh, Beirut 1107 2050, Lebanon.
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7
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Zhu D, Wang L, Xu X, Jiang W. Colocalization recognition-activated cascade signal amplification strategy for ultrasensitive detection of transcription factors. Biosens Bioelectron 2017; 89:978-983. [DOI: 10.1016/j.bios.2016.09.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 01/10/2023]
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8
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Aptamer based lysozyme assay using fluorescent CuInS2 quantum dots and graphene oxide, and its application to inhibitor screening. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1934-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Ammar FF, Hobaika Z, Abdel-Azeim S, Zargarian L, Maroun RG, Fermandjian S. A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity. FEBS Open Bio 2016; 6:234-50. [PMID: 27239438 PMCID: PMC4821353 DOI: 10.1002/2211-5463.12025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/25/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022] Open
Abstract
We recently reported that viral DNA could be the primary target of raltegravir (RAL), an efficient anti‐HIV‐1 drug, which acts by inhibiting integrase. To elucidate this mechanism, we conducted a comparative analysis of RAL and TB11, a diketoacid abandoned as an anti‐HIV‐1 drug for its weak efficiency and marked toxicity, and tested the effects of the catalytic cofactor Mg2+ (5 mm) on drug‐binding properties. We used circular dichroism and fluorescence to determine drug affinities for viral DNA long terminal repeats (LTRs) and peptides derived from the integrase active site and DNA retardation assays to assess drug intercalation into DNA base pairs. We found that RAL bound more tightly to LTR ends than did TB11 (a diketo acid bearing an azido group) and that Mg2+ significantly increased the affinity of both RAL and TB11. We also observed a good relationship between drug binding with processed LTR and strand transfer inhibition. This unusual type of inhibition was caused by Mg2+‐assisted binding of drugs to DNA substrate, rather than to enzyme. Notably, while RAL bound exclusively to the cleavable/cleaved site, TB11 further intercalated into DNA base pairs and interacted with the integrase‐derived peptides. These unwanted binding sites explain the weaker bioavailability and higher toxicity of TB11 compared with the more effective RAL.
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Affiliation(s)
- Farah F Ammar
- Centre d'Analyses et de Recherche UR EGFEM Faculté des Sciences Université Saint-Joseph Beirut Lebanon; LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France
| | - Zeina Hobaika
- Centre d'Analyses et de Recherche UR EGFEM Faculté des Sciences Université Saint-Joseph Beirut Lebanon
| | - Safwat Abdel-Azeim
- LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France
| | - Loussinée Zargarian
- LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France
| | - Richard G Maroun
- Centre d'Analyses et de Recherche UR EGFEM Faculté des Sciences Université Saint-Joseph Beirut Lebanon
| | - Serge Fermandjian
- LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France; Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy UMR8601 CNRS Paris Cedex 06 France
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10
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Liu Z, Tian C, Lu L, Su X. A novel aptamer-mediated CuInS2quantum dots@graphene oxide nanocomposites-based fluorescence “turn off–on” nanosensor for highly sensitive and selective detection of kanamycin. RSC Adv 2016. [DOI: 10.1039/c5ra22753d] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel aptamer-mediated fluorescence “turn off–on” nanosensor for highly sensitive and selective detection of kanamycin using CuInS2quantum dots@graphene oxide.
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Affiliation(s)
- Ziping Liu
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Chengshuo Tian
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Lehui Lu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Xingguang Su
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
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11
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Liu X, Na W, Qu Z, Su X. Turn-off–on fluorescence probe based on 3-mercaptopropionic acid-capped CdS quantum dots for selective and sensitive lysozyme detection. RSC Adv 2016. [DOI: 10.1039/c6ra14420a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The fluorescence of CdS QDs was first quenched by hemoglobin and then restored with the increasing concentration of the lysozyme in a certain range. Therefore, a fluorescence assay for the determination of lysozyme was established.
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Affiliation(s)
- Xiaotong Liu
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun
- China
| | - Weidan Na
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun
- China
| | - Zhengyi Qu
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun
- China
| | - Xingguang Su
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun
- China
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12
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Abstract
Steady-state measurements of fluorescence polarization have been widely adopted in the field of high-throughput screening for the study of biomolecular interactions. This chapter reviews the basic theory of fluorescence polarization, the underlying principle for using fluorescence polarization to study interactions between small-molecule fluorophores and macromolecular targets, and representative applications of fluorescence polarization in high-throughput screening.
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Affiliation(s)
- Xinyi Huang
- Immunology, Inflammation and Infectious Diseases Discovery and Translational Area Roche Pharma Research & Early Development, Roche Innovation Center Shanghai, Roche R&D Center (China) Ltd, 720 Cai Lun Road, Bldg 5, Pudong, Shanghai, 201203, China.
| | - Ann Aulabaugh
- Immunology, Inflammation and Infectious Diseases Discovery and Translational Area Roche Pharma Research & Early Development, Roche Innovation Center Shanghai, Roche R&D Center (China) Ltd, 720 Cai Lun Road, Bldg 5, Pudong, Shanghai, 201203, China
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13
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Zhu D, Wang L, Xu X, Jiang W. Label-free and enzyme-free detection of transcription factors with graphene oxide fluorescence switch-based multifunctional G-quadruplex-hairpin probe. Biosens Bioelectron 2015; 75:155-60. [PMID: 26318784 DOI: 10.1016/j.bios.2015.08.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/13/2015] [Accepted: 08/17/2015] [Indexed: 11/30/2022]
Abstract
Transcription factors (TFs) play pivotal roles in the regulation of a variety of essential cellular processes and some of them have been recognized as potential diagnostic markers and therapeutic targets of some diseases. Sensitive and accurate detection of TFs is of great importance to better understanding their roles in gene regulation and evaluation of disease state. Here, we developed a simple, label-free and enzyme-free new fluorescent strategy for the detection of TFs by graphene oxide (GO) fluorescence switch-based multifunctional G-quadruplex-hairpin probe (MGHP). The MGHP possessed of three functions simultaneously, adsorbing onto GO with the loop part, binding to target with the stem part and serving as signal carrier with the terminal G-quadruplex. First, the MGHP was adsorbed quickly to GO. Next, the TF bound to the stem part of MGHP to form a huge target-MGHP complex, which led to desorption of the complex from GO. Finally, NMM was inserted into G-quadruplex in the complex to yield an enhanced fluorescence response. The GO used here, as a fluorescence switch, could quickly and efficiently quench the fluorescence of NMM inserted into the MGHP absorbed on the GO, guaranteeing a high signal-to-noise ratio. Sensitive detection of purified NF-κB p50 and HeLa cell nuclear extracts were achieved with detection limits of 0.2nM and 7.8ng/µL, respectively. Moreover, this proposed strategy could be used to screen inhibitors of NF-κB p50 activity. The strategy proposed here might offer a new potential approach for reliable quantification of TFs in clinical diagnostics and treatment research of some diseases.
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Affiliation(s)
- Desong Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | - Lei Wang
- School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China.
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14
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Xu Y, Strickland EC, Fitzgerald MC. Thermodynamic Analysis of Protein Folding and Stability Using a Tryptophan Modification Protocol. Anal Chem 2014; 86:7041-8. [DOI: 10.1021/ac501278j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yingrong Xu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Erin C. Strickland
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael C. Fitzgerald
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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15
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Zhu D, Zhu J, Zhu Y, Wang L, Jiang W. Sensitive detection of transcription factors using an Ag+-stabilized self-assembly triplex DNA molecular switch. Chem Commun (Camb) 2014; 50:14987-90. [DOI: 10.1039/c4cc06205a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple, enzyme-free and sensitive new fluorescent strategy for detection of transcription factors was proposed based on a bifunctional Ag+-stabilized self-assembly triplex DNA molecular switch.
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Affiliation(s)
- Desong Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
| | - Jing Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
| | - Ye Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
| | - Lei Wang
- School of Pharmacy
- Shandong University
- Jinan 250012, P. R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
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16
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Geng S, Liu G, Li W, Cui F. Molecular interaction of ctDNA and HSA with sulfadiazine sodium by multispectroscopic methods and molecular modeling. LUMINESCENCE 2013; 28:785-92. [DOI: 10.1002/bio.2457] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/14/2012] [Accepted: 10/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Shaoguang Geng
- School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang; 453007; China
| | - Guosheng Liu
- College of Life Sciences; Henan Normal University; Xinxiang; 453007; China
| | - Wei Li
- School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang; 453007; China
| | - Fengling Cui
- School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang; 453007; China
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17
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Deng L, Kitova EN, Klassen JS. Dissociation kinetics of the streptavidin-biotin interaction measured using direct electrospray ionization mass spectrometry analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:49-56. [PMID: 23247970 DOI: 10.1007/s13361-012-0533-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Dissociation rate constants (k (off)) for the model high affinity interaction between biotin (B) and the homotetramer of natural core streptavidin (S(4)) were measured at pH 7 and temperatures ranging from 15 to 45 °C using electrospray ionization mass spectrometry (ESI-MS). Two different approaches to data analysis were employed, one based on the initial rate of dissociation of the (S(4) + 4B) complex, the other involving nonlinear fitting of the time-dependent relative abundances of the (S(4) + iB) species. The two methods were found to yield k (off) values that are in good agreement, within a factor of two. The Arrhenius parameters for the dissociation of the biotin-streptavidin interaction in solution were established from the k (off) values determined by ESI-MS and compared with values measured using a radiolabeled biotin assay. Importantly, the dissociation activation energies determined by ESI-MS agree, within 1 kcal mol(-1), with the reported value. In addition to providing a quantitative measure of k (off), the results of the ESI-MS measurements revealed that the apparent cooperative distribution of (S(4) + iB) species observed at short reaction times is of kinetic origin and that sequential binding of B to S(4) occurs in a noncooperative fashion with the four ligand binding sites being kinetically and thermodynamically equivalent and independent.
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Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Liyanage R, Devarapalli N, Pyland DB, Puckett LM, Phan NH, Starch JA, Okimoto MR, Gidden J, Stites WE, Lay JO. Theory of the Protein Equilibrium Population Snapshot by H/D Exchange Electrospray Ionization Mass Spectrometry (PEPS-HDX-ESI-MS) Method used to obtain Protein Folding Energies/Rates and Selected Supporting Experimental Evidence. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 330-332:63-70. [PMID: 23436981 PMCID: PMC3578662 DOI: 10.1016/j.ijms.2012.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein equilibrium snapshot by hydrogen/deuterium exchange electrospray ionization mass spectrometry (PEPS-HDX-ESI-MS or PEPS) is a method recently introduced for estimating protein folding energies and rates. Herein we describe the basis for this method using both theory and new experiments. Benchmark experiments were conducted using ubiquitin because of the availability of reference data for folding and unfolding rates from NMR studies. A second set of experiments was also conducted to illustrate the surprising resilience of the PEPS to changes in HDX time, using staphylococcal nuclease and time frames ranging from a few seconds to several minutes. Theory suggests that PEPS experiments should be conducted at relatively high denaturant concentrations, where the protein folding/unfolding rates are slow with respect to HDX and the life times of both the closed and open states are long enough to be sampled experimentally. Upon deliberate denaturation, changes in folding/unfolding are correlated with associated changes in the ESI-MS signal upon fast HDX. When experiments are done quickly, typically within a few seconds, ESI-MS signals, corresponding to the equilibrium population of the native (closed) and denatured (open) states can both be detected. The interior of folded proteins remains largely un-exchanged. Amongst MS methods, the simultaneous detection of both states in the spectrum is unique to PEPS and provides a "snapshot" of these populations. The associated ion intensities are used to estimate the protein folding equilibrium constant (or the free energy change, ΔG). Linear extrapolation method (LEM) plots of derived ΔG values for each denaturant concentration can then be used to calculate ΔG in the absence of denaturant, ΔG(H(2)O). In accordance with the requirement for detection of signals for both the folded and unfolded states, this theoretical framework predicts that PEPS experiments work best at the middle of the denaturation curve where natured and denatured protein molecules are equilibrated at easily detectable ratios, namely 1:1. It also requires that closed and open states have lifetimes measurable in the time frame of the HDX experiment. Because both conditions are met by PEPS, these measurements can provide an accurate assessment of closed/open state populations and thus protein folding energies/rates.
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Affiliation(s)
- Rohana Liyanage
- Department of Chemistry and Biochemistry University of Arkansas, Fayetteville, AR 72701
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19
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Ammar FF, Abdel-Azeim S, Zargarian L, Hobaika Z, Maroun RG, Fermandjian S. Unprocessed viral DNA could be the primary target of the HIV-1 integrase inhibitor raltegravir. PLoS One 2012; 7:e40223. [PMID: 22768342 PMCID: PMC3388078 DOI: 10.1371/journal.pone.0040223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/02/2012] [Indexed: 12/18/2022] Open
Abstract
Integration of HIV DNA into host chromosome requires a 3'-processing (3'-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3'-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5'C(4)pA(3)3' step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance.
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Affiliation(s)
- Farah F. Ammar
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Safwat Abdel-Azeim
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
| | - Loussinée Zargarian
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
| | - Zeina Hobaika
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Richard G. Maroun
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Serge Fermandjian
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
- * E-mail:
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20
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Liu JJ, Song XR, Wang YW, Chen GN, Yang HH. A graphene oxide (GO)-based molecular beacon for DNA-binding transcription factor detection. NANOSCALE 2012; 4:3655-3659. [PMID: 22581162 DOI: 10.1039/c2nr30499f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A GO-based molecular beacon assay was developed for rapid, sensitive and cost-efficient detection of transcription factor proteins. Furthermore, this assay can be employed for screening inhibitors of transcription factor proteins.
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Affiliation(s)
- Jing-Jing Liu
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry and Chemical Engineering, Fuzhou University, Fuzhou 350108, PR China
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21
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Leung CH, Chan DSH, He HZ, Cheng Z, Yang H, Ma DL. Luminescent detection of DNA-binding proteins. Nucleic Acids Res 2012; 40:941-55. [PMID: 21967849 PMCID: PMC3273792 DOI: 10.1093/nar/gkr763] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 01/07/2023] Open
Abstract
Transcription factors play a central role in cell development, differentiation and growth in biological systems due to their ability to regulate gene expression by binding to specific DNA sequences within the nucleus. The dysregulation of transcription factor signaling has been implicated in the pathogenesis of a number of cancers, developmental disorders, inflammation and autoimmunity. There is thus a high demand for convenient high-throughput methodologies able to detect sequence-specific DNA-binding proteins and monitor their DNA-binding activities. Traditional approaches for protein detection include gel mobility shift assays, DNA footprinting and enzyme-linked immunosorbent assays (ELISAs) which tend to be tedious, time-consuming, and may necessitate the use of radiographic labeling. By contrast, luminescence technologies offer the potential for rapid, sensitive and low-cost detection that are amenable to high-throughput and real-time analysis. The discoveries of molecular beacons and aptamers have spear-headed the development of new luminescent methodologies for the detection of proteins over the last decade. We survey here recent advances in the development of luminescent detection methods for DNA-binding proteins, including those based on molecular beacons, aptamer beacons, label-free techniques and exonuclease protection.
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Affiliation(s)
- Chung-Hang Leung
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Daniel Shiu-Hin Chan
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Hong-Zhang He
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Zhen Cheng
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Hui Yang
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Dik-Lung Ma
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
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22
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Wetzler DE, Comin MJ, Krajewski K, Gallo M. New human papilloma virus E2 transcription factor mimics: a tripyrrole-peptide conjugate with tight and specific DNA-recognition. PLoS One 2011; 6:e22409. [PMID: 21799846 PMCID: PMC3143144 DOI: 10.1371/journal.pone.0022409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/21/2011] [Indexed: 12/02/2022] Open
Abstract
Background Human papillomavirus (HPV) is the main causative agent of cervical cancer, particularly high risk strains such us HPV-16, -18 and -31. The viral encoded E2 protein acts as a transcriptional modulator and exerts a key role in viral DNA replication. Thus, E2 constitutes an attractive target for developing antiviral agents. E2 is a homodimeric protein that interacts with the DNA target through an α-helix of each monomer. However, a peptide corresponding to the DNA recognition helix of HPV-16 E2 binds DNA with lower affinity than its full-length DNA binding domain. Therefore, in an attempt to promote the DNA binding of the isolated peptide, we have designed a conjugate compound of the E2 α-helix peptide and a derivative of the antibiotic distamycin, which involves simultaneous minor- and major-groove interactions. Methodology/Principal Findings An E2 α-helix peptide-distamycin conjugate was designed and synthesized. It was characterized by NMR and CD spectroscopy, and its DNA binding properties were investigated by CD, DNA melting and gel shift experiments. The coupling of E2 peptide with distamycin does not affect its structural properties. The conjugate improves significantly the affinity of the peptide for specific DNA. In addition, stoichiometric amounts of specific DNA increase meaningfully the helical population of the peptide. The conjugate enhances the DNA binding constant 50-fold, maintaining its specificity. Conclusions/Significance These results demonstrate that peptide-distamycin conjugates are a promising tool to obtain compounds that bind the E2 target DNA-sequences with remarkable affinity and suggest that a bipartite major/minor groove binding scaffold can be a useful approach for therapeutic treatment of HPV infection.
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Affiliation(s)
- Diana E. Wetzler
- Department of Biological Chemistry, FCEN, University of Buenos Aires, Buenos Aires, Argentina
| | - Maria J. Comin
- Center for Research and Development in Chemistry, INTI, Buenos Aires, Argentina
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mariana Gallo
- Fundación Instituto Leloir, Buenos Aires, Argentina
- * E-mail:
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Geiss BJ, Stahla-Beek HJ, Hannah AM, Gari HH, Henderson BR, Saeedi BJ, Keenan SM. A high-throughput screening assay for the identification of flavivirus NS5 capping enzyme GTP-binding inhibitors: implications for antiviral drug development. ACTA ACUST UNITED AC 2011; 16:852-61. [PMID: 21788392 DOI: 10.1177/1087057111412183] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There are no effective antivirals currently available for the treatment of flavivirus infection in humans. As such, the identification and characterization of novel drug target sites are critical to developing new classes of antiviral drugs. The flavivirus NS5 N-terminal capping enzyme (CE) is vital for the formation of the viral RNA cap structure, which directs viral polyprotein translation and stabilizes the 5' end of the viral genome. The structure of the flavivirus CE has been solved, and a detailed understanding of the CE-guanosine triphosphate (GTP) and CE-RNA cap interactions is available. Because of the essential nature of the interaction for viral replication, disrupting CE-GTP binding is an attractive approach for drug development. The authors have previously developed a robust assay for monitoring CE-GTP binding in real time. They adapted this assay for high-throughput screening and performed a pilot screen of 46 323 commercially available compounds. A number of small-molecule inhibitors capable of displacing a fluorescently labeled GTP in vitro were identified, and a second functional assay was developed to identify false positives. The results presented indicate that the flavivirus CE cap-binding site is a valuable new target site for antiviral drug discovery and should be further exploited for broad-spectrum anti-flaviviral drug development.
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Affiliation(s)
- Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
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24
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Ma DL, Xu T, Chan DSH, Man BYW, Fong WF, Leung CH. A highly selective, label-free, homogenous luminescent switch-on probe for the detection of nanomolar transcription factor NF-kappaB. Nucleic Acids Res 2011; 39:e67. [PMID: 21398636 PMCID: PMC3105395 DOI: 10.1093/nar/gkr106] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transcription factors are involved in a number of important cellular processes. The transcription factor NF-κB has been linked with a number of cancers, autoimmune and inflammatory diseases. As a result, monitoring transcription factors potentially represents a means for the early detection and prevention of diseases. Most methods for transcription factor detection tend to be tedious and laborious and involve complicated sample preparation, and are not practical for routine detection. We describe herein the first label-free luminescence switch-on detection method for transcription factor activity using Exonuclease III and a luminescent ruthenium complex, [Ru(phen)2(dppz)]2+. As a proof of concept for this novel assay, we have designed a double-stranded DNA sequence bearing two NF-κB binding sites. The results show that the luminescence response was proportional to the concentration of the NF-κB subunit p50 present in the sample within a wide concentration range, with a nanomolar detection limit. In the presence of a known NF-κB inhibitor, oridonin, a reduction in the luminescence response of the ruthenium complex was observed. The reduced luminescence response of the ruthenium complex in the presence of small molecule inhibitors allows the assay to be applied to the high-throughput screening of chemical libraries to identify new antagonists of transcription factor DNA binding activity. This will allow the rapid and low cost identification and development of novel scaffolds for the treatment of diseases caused by the deregulation of transcription factor activity.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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25
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West GM, Thompson JW, Soderblom EJ, Dubois LG, DeArmond PD, Moseley MA, Fitzgerald MC. Mass Spectrometry-Based Thermal Shift Assay for Protein−Ligand Binding Analysis. Anal Chem 2010; 82:5573-81. [DOI: 10.1021/ac100465a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Graham M. West
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
| | - J. Will Thompson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
| | - Erik J. Soderblom
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
| | - Laura G. Dubois
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
| | - Patrick D. DeArmond
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
| | - M. Arthur Moseley
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, and Institute for Genome Science and Policy, Duke University Medical Center, Durham, North Carolina 27708
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26
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Liyanage R, Devarapalli N, Puckett LM, Phan NH, Gidden J, Stites WE, Lay JO. Comparison of Two ESI MS Based H/D Exchange Methods for Extracting Protein Folding Energies. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2009; 287:96-104. [PMID: 22427739 PMCID: PMC3306186 DOI: 10.1016/j.ijms.2008.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this report, the model proteins staphylococcal nuclease and ubiquitin were used to test the applicability of two new hydrogen/deuterium exchange (HX) electrospray ionization mass spectrometry (ESI-MS) methods for estimating protein folding energies. Both methods use the H/D exchange of globally protected amide protons (amide protons which are buried in the hydrophobic core) to elucidate protein folding energies. One method is a kinetic-based method and the other is equilibrium-based. The first method, the HX ESI-MS kinetic-based approach is conceptually identical to SUPREX (stability of unpurified proteins from rates of H/D exchange) method but is based on ESI-MS rather than MALDI-MS (matrix assisted laser desorption mass spectrometry). This method employs the time-dependence of H/D exchange using various denaturant concentrations to extract folding energies. Like SUPREX, this approach requires the assumption of EX2 exchange kinetics. The second method, which we call a protein equilibrium population snapshot (PEPS) by HX ESI-MS uses data collected only for a single time point (usually the shortest possible) to obtain a snapshot of the open and closed populations of the protein. The PEPS approach requires few assumptions in the derivation of the equations used for calculation of the folding energies. The extraction of folding energies from mass spectral data is simple and straightforward. The PEPS method is applicable for proteins that follow either EX1 or EX2 HX mechanisms. In our experiments the kinetic-based method produced less accurate ΔG(H(2)O) and m(GdHCl) values for wild-type staphylococcal nuclease and mutants undergoing H/D exchange by EX1, as would be expected. Better results were obtained for ubiquitin which undergoes HX by an EX2 mechanism. Using the PEPS method we obtained ΔG(H(2)O) and m(GdHCl) values that were in good agreement with literature values for both staphylococcal nuclease (EX1) and ubiquitin (EX2). We also show that the observation of straight lines in linear extrapolation method (LEM) plots is not a reliable indicator of the validity of the data obtained using the LEM approach.
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Affiliation(s)
- Rohana Liyanage
- Department of Chemistry and Biochemistry University of Arkansas, Fayetteville, AR 72701
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27
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Merad H, Porumb H, Zargarian L, René B, Hobaika Z, Maroun RG, Mauffret O, Fermandjian S. An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF. PLoS One 2009; 4:e4081. [PMID: 19119323 PMCID: PMC2607020 DOI: 10.1371/journal.pone.0004081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 12/04/2008] [Indexed: 01/29/2023] Open
Abstract
Background Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149–186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the α4 and α5 helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer. Principal Findings We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the α4 and α5 helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat) ends of virus DNA with a Kd (dissociation constant) in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD) but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor) lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (α4) which has the role of DNA recognition helix, while the C terminal helix (α5) would rather contribute to the motif stabilization by interactions with the α4 helix. Conclusion The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.
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Affiliation(s)
- Hayate Merad
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Horea Porumb
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Loussiné Zargarian
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Brigitte René
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Zeina Hobaika
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Richard G. Maroun
- Département des Sciences de la Vie et de la Terre, Faculté des Sciences, Université Saint Joseph, CST-Mar Roukos, B. P. 1514, Beyrouth, Liban
| | - Olivier Mauffret
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Serge Fermandjian
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
- * E-mail:
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28
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Abstract
Steady-state measurements of fluorescence polarization have been widely adopted in the field of high-throughput screening for the study of biomolecular interactions. This chapter reviews the basic theory of fluorescence polarization, the underlying principle for using fluorescence polarization to study interactions between small-molecule fluorophores and macromolecular targets, and representative applications of fluorescence polarization in high-throughput screening.
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Affiliation(s)
- Xinyi Huang
- Chemical and Screening Sciences, Wyeth Research, Collegeville, PA, USA
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29
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Liyanage MR, Zaidi A, Johnson CK. Fluorescence polarization assay for calmodulin binding to plasma membrane Ca2+-ATPase: dependence on enzyme and Ca2+ concentrations. Anal Biochem 2008; 385:1-6. [PMID: 19000896 DOI: 10.1016/j.ab.2008.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 10/17/2008] [Accepted: 10/18/2008] [Indexed: 10/21/2022]
Abstract
Calmodulin (CaM) is a Ca2+ signaling protein that binds to a wide variety of target proteins, and it is important to establish methods for rapid characterization of these interactions. Here we report the use of fluorescence polarization (FP) to measure the Kd for the interaction of CaM with the plasma membrane Ca2+-ATPase (PMCA), a Ca2+ pump regulated by binding of CaM. Previous assays of PMCA-CaM interactions were indirect, based on activity or kinetics measurements. We also investigated the Ca2+ dependence of CaM binding to PMCA. FP assays directly detect CaM-target interactions and are rapid, sensitive, and suitable for high-throughput screening assay formats. Values for the dissociation constant K(d) in the nanomolar range are readily measured. We measured the changes in anisotropy of CaM labeled with Oregon Green 488 on titration with PMCA, yielding a K(d) value of CaM with PMCA (5.8 +/- 0.5 nM) consistent with previous indirect measurements. We also report the binding affinity of CaM with oxidatively modified PMCA (K(d) = 9.8 +/- 2.0 nM), indicating that the previously reported loss in CaM-stimulated activity for oxidatively modified PMCA is not a result of reduced CaM binding. The Ca2+ dependence follows a simple Hill plot demonstrating cooperative binding of Ca2+ to the binding sites in CaM.
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30
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Xu X, Zhao Z, Qin L, Wei W, Levine JE, Mirkin CA. Fluorescence recovery assay for the detection of protein-DNA binding. Anal Chem 2008; 80:5616-21. [PMID: 18498181 PMCID: PMC8192077 DOI: 10.1021/ac8007016] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a novel and straightforward fluorescence recovery assay which enables the detection of protein-DNA interactions and simultaneously determines relative binding affinities of sequence-specific DNA-binding proteins for a variety of DNA sequences in a multiplexed format. The detection of protein-DNA binding is accomplished by monitoring fluorescence recovery during exonuclease digestion of DNA sequences that are modified with fluorophore-quencher pairs. Retardation of fluorescence recovery occurs with binding of the protein to the putative DNA binding element, which arrests exonuclease digestion. The assay detects protein-DNA binding in a homogeneous solution simply, quickly, and reliably without using radioisotopes. Multiplexing is possible by labeling different DNA sequences with spectrally distinct dyes, allowing simultaneous analysis of experimental and control binding reactions in the same mixture.
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Affiliation(s)
| | | | | | | | - Jon E. Levine
- To whom correspondence should be addressed. (C.A.M.), (J.E.L.). Fax: (+1) 847-467-5123 (C.A.M.), (+1) 847-491-7180 (J.E.L.)
| | - Chad A. Mirkin
- To whom correspondence should be addressed. (C.A.M.), (J.E.L.). Fax: (+1) 847-467-5123 (C.A.M.), (+1) 847-491-7180 (J.E.L.)
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31
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Li J, Ren C, Zhang Y, Liu X, Yao X, Hu Z. Human serum albumin interaction with honokiol studied using optical spectroscopy and molecular modeling methods. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.08.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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West GM, Tang L, Fitzgerald MC. Thermodynamic Analysis of Protein Stability and Ligand Binding Using a Chemical Modification- and Mass Spectrometry-Based Strategy. Anal Chem 2008; 80:4175-85. [DOI: 10.1021/ac702610a] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Graham M. West
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Liangjie Tang
- Department of Chemistry, Duke University, Durham, North Carolina 27708
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33
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Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. J Mol Biol 2008; 377:1460-73. [PMID: 18321528 PMCID: PMC2680229 DOI: 10.1016/j.jmb.2008.01.096] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 01/23/2008] [Accepted: 01/25/2008] [Indexed: 01/07/2023]
Abstract
Tex is a highly conserved bacterial protein that likely functions in a variety of transcriptional processes. Here, we describe two crystal structures of the 86-kDa Tex protein from Pseudomonas aeruginosa at 2.3 and 2.5 A resolution, respectively. These structures reveal a relatively flat and elongated protein, with several potential nucleic acid binding motifs clustered at one end, including an S1 domain near the C-terminus that displays considerable structural flexibility. Tex binds nucleic acids, with a preference for single-stranded RNA, and the Tex S1 domain is required for this binding activity. Point mutants further demonstrate that the primary nucleic acid binding site corresponds to a surface of the S1 domain. Sequence alignment and modeling indicate that the eukaryotic Spt6 transcription factor adopts a similar core structure. Structural analysis further suggests that the RNA polymerase and nucleosome interacting regions of Spt6 flank opposite sides of the Tex-like scaffold. Therefore, the Tex structure may represent a conserved scaffold that binds single-stranded RNA to regulate transcription in both eukaryotic and prokaryotic organisms.
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Affiliation(s)
- Sean J. Johnson
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300,Joint first authors
| | - Devin Close
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650,Joint first authors
| | - Howard Robinson
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973
| | - Isabelle Vallet-Gely
- Division of Infectious Diseases, Children’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Simon L. Dove
- Division of Infectious Diseases, Children’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Christopher P. Hill
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650,Corresponding author
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34
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Zeeh JC, Antonny B, Cherfils J, Zeghouf M. In vitro assays to characterize inhibitors of the activation of small G proteins by their guanine nucleotide exchange factors. Methods Enzymol 2008; 438:41-56. [PMID: 18413240 DOI: 10.1016/s0076-6879(07)38004-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Guanine nucleotide exchange factors (GEFs) are essential regulators of the spatiotemporal conditions of small GTP-binding protein (SMG) activation. Their cellular activities combine the biochemical stimulation of GDP/GTP exchange, which leads to the active conformation of the SMG, to the detection of upstream signals and, in some cases, interaction with downstream effectors. Inhibition of GEF activities by small molecules has become recently a very active field, both for understanding biology with the tools of chemistry and because GEFs are emerging as therapeutic targets. The natural compound brefeldin A (BFA) was the first inhibitor of a GEF to be characterized, and several inhibitors of SMG activation have since been discovered using a variety of screening methods. An essential step toward their use in basic research or as leads in therapeutics is the characterization of their mechanism of inhibition. GEFs function according to a multistep mechanism, involving transient ternary (nucleotide-bound) and binary (nucleotide-free) intermediates. This mechanism thereby offers many opportunities for blockage, but a thorough analysis is necessary to define the inhibition mechanism and the steps of the reaction that are affected by the inhibitor. Here, based on the case study of how BFA inhibits the activation of Arf activation by Sec7 domains, we describe a flowchart of assays to decipher the mechanism of inhibitors of the activation of SMGs by their GEFs.
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Affiliation(s)
- Jean-Christophe Zeeh
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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35
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LiCata VJ, Wowor AJ. Applications of Fluorescence Anisotropy to the Study of Protein–DNA Interactions. Methods Cell Biol 2008; 84:243-62. [DOI: 10.1016/s0091-679x(07)84009-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Kim YC, Cheng Kao C. Biochemical analyses of the interactions between viral polymerases and RNAs. Methods Mol Biol 2008; 451:185-200. [PMID: 18370256 DOI: 10.1007/978-1-59745-102-4_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The interaction between viral polymerases and their cognate RNAs is vital to regulate the timing and abundance of viral replication products. Despite this, only minimal detailed information is available for the interaction between viral polymerases and cognate RNAs. We study the biochemical interactions using two viral polymerases that could serve as models for other plus-strand RNA viruses: the replicase from the tripartite brome mosaic virus (BMV), and the recombinant RNA-dependent RNA polymerase (RdRp) from hepatitis C virus (HCV). Replicase binding sites in the BMV RNAs were mapped using a template competition assay. The minimal length of RNA required for RNA binding by the HCV RdRp was determined using fluorescence spectroscopy. Lastly, regions of the HCV RdRp that contact the RNA were determined by a method coupling reversible protein-RNA crosslinking, affinity purification, and mass spectrometry. These analyses of RdRp-RNA interaction will be presented as three topics in this chapter.
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Affiliation(s)
- Young-Chan Kim
- Department of Biochemistry & Biophysics, 103 Biochemistry/Biophysics Building, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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37
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Abstract
The elementary steps in complex biochemical reaction schemes (isomerization, dissociation, and association reactions) ultimately determine how fast any system can react in responding to incoming signals and in adapting to new conditions. Many of these steps have associated rate constants that result in subsecond responses to incoming signals or externally applied changes. This chapter is concerned with the techniques that have been developed to study such rapidly reacting systems in vitro and to determine the values of the rate constants for the individual steps. We focus principally on two classes of techniques: (1) flow techniques, in which two solutions are mixed within a few milliseconds and the ensuing reaction monitored over milliseconds to seconds, and (2) relaxation techniques, in which a small perturbation to an existing equilibrium is applied within a few microseconds and the response of the system is followed over microseconds to hundreds of milliseconds. These reactions are most conveniently monitored by recording the change in some optical signal, such as absorbance or fluorescence. We discuss the instrumentation that is (commercially) available to study fast reactions and describe a number of optical probes (chromophores) that can be used to monitor the changes. We discuss the experimental design appropriate for the different experimental techniques and reaction mechanisms, as well as the fundamental theoretical concepts behind the analysis of the data obtained.
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Affiliation(s)
- John F Eccleston
- Division of Physical Biochemistry, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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38
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pH Induces Thermal Unfolding of UTI: An Implication of Reversible and Irreversible Mechanism Based on the Analysis of Thermal Stability, Thermodynamic, Conformational Characterization. J Fluoresc 2007; 18:305-17. [DOI: 10.1007/s10895-007-0270-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 10/08/2007] [Indexed: 11/26/2022]
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39
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Linked equilibria in regulation of transcription initiation. Methods Cell Biol 2007. [PMID: 17964927 DOI: 10.1016/s0091-679x(07)84002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Assembly of transcriptional regulatory complexes often involves multiple binding processes and these binding processes are frequently coupled to one another. Small molecule binding can promote or inhibit DNA-binding or protein-protein interactions. DNA binding may be coupled to protein association. Finally, proteins may bind cooperatively to multiple sites in a transcriptional regulatory region. The level of transcription initiation at a promoter reflects the assembly of regulatory complexes in a transcription control region. Quantitative mechanistic understanding of regulatory complex assembly requires dissection of the assembly process into its constituent interactions followed by measurements of linkage between the individual binding processes. Methods and approaches to achieving this quantitative understanding of transcription regulation are outlined in this chapter.
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40
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Yeh HC, Puleo CM, Lim TC, Ho YP, Giza PE, Huang RCC, Wang TH. A microfluidic-FCS platform for investigation on the dissociation of Sp1-DNA complex by doxorubicin. Nucleic Acids Res 2006; 34:e144. [PMID: 17108358 PMCID: PMC1669725 DOI: 10.1093/nar/gkl787] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The transcription factor (TF) Sp1 is a well-known RNA polymerase II transcription activator that binds to GC-rich recognition sites in a number of essential cellular and viral promoters. In addition, direct interference of Sp1 binding to DNA cognate sites using DNA-interacting compounds may provide promising therapies for suppression of cancer progression and viral replication. In this study, we present a rapid, sensitive and cost-effective evaluation of a GC intercalative drug, doxorubicin (DOX), in dissociating the Sp1–DNA complex using fluorescence correlation spectroscopy (FCS) in a microfluidic system. FCS allows assay miniaturization without compromising sensitivity, making it an ideal analytical method for integration of binding assays into high-throughput, microfluidic platforms. A polydimethylsiloxane (PDMS)-based microfluidic chip with a mixing network is used to achieve specific drug concentrations for drug titration experiments. Using FCS measurements, the IC50 of DOX on the dissociation of Sp1–DNA complex is estimated to be 0.55 μM, which is comparable to that measured by the electrophoretic mobility shift assay (EMSA). However, completion of one drug titration experiment on the proposed microfluidic-FCS platform is accomplished using only picograms of protein and DNA samples and less than 1 h total assay time, demonstrating vast improvements over traditional ensemble techniques.
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Affiliation(s)
- Hsin-Chih Yeh
- Department of Mechanical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Christopher M. Puleo
- Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Teck Chuan Lim
- Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Yi-Ping Ho
- Department of Mechanical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Paul E. Giza
- Department of Biology, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Ru Chih C. Huang
- Department of Biology, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
- Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
- Whitaker Biomedical Engineering Institute, The Johns Hopkins UniversityBaltimore, MD 21218, USA
- To whom correspondence should be addressed. Tel: +1 410 516 7086; Fax: +1 410 516 7254;
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41
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Abstract
Sliding clamps and clamp loaders are processivity factors required for efficient DNA replication. Sliding clamps are ring-shaped complexes that tether DNA polymerases to DNA to increase the processivity of synthesis. Clamp loaders assemble these ring-shaped clamps onto DNA in an ATP-dependent reaction. The overall process of clamp loading is dynamic in that protein-protein and protein-DNA interactions must actively change in a coordinated fashion to complete the mechanical clamp-loading reaction cycle. The clamp loader must initially have a high affinity for both the clamp and DNA to bring these macromolecules together, but then must release the clamp on DNA for synthesis to begin. Evidence is presented for a mechanism in which the clamp-loading reaction comprises a series of binding reactions to ATP, the clamp, DNA, and ADP, each of which promotes some change in the conformation of the clamp loader that alters interactions with the next component of the pathway. These changes in interactions must be rapid enough to allow the clamp loader to keep pace with replication fork movement. This review focuses on the measurement of dynamic and transient interactions required to assemble the Escherichia coli sliding clamp on DNA.
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Affiliation(s)
- Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA.
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42
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Katilius E, Woodbury NW. Multiphoton excitation of fluorescent DNA base analogs. JOURNAL OF BIOMEDICAL OPTICS 2006; 11:044004. [PMID: 16965161 DOI: 10.1117/1.2337521] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Multiphoton excitation was used to investigate properties of the fluorescent DNA base analogs, 2-aminopurine (2AP) and 6-methylisoxanthopterin (6MI). 2-aminopurine, a fluorescent analog of adenine, was excited by three-photon absorption. Fluorescence correlation measurements were attempted to evaluate the feasibility of using three-photon excitation of 2AP for DNA-protein interaction studies. However, high excitation power and long integration times needed to acquire high signal-to-noise fluorescence correlation curves render three-photon excitation FCS of 2AP not very useful for studying DNA base dynamics. The fluorescence properties of 6-methylisoxanthopterin, a guanine analog, were investigated using two-photon excitation. The two-photon absorption cross-section of 6MI was estimated to be about 2.5 x 10(-50) cm(4)s (2.5 GM units) at 700 nm. The two-photon excitation spectrum was measured in the spectral region from 700 to 780 nm; in this region the shape of the two-photon excitation spectrum is very similar to the shape of single-photon excitation spectrum in the near-UV spectral region. Two-photon excitation of 6MI is suitable for fluorescence correlation measurements. Such measurements can be used to study DNA base dynamics and DNA-protein interactions over a broad range of time scales.
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Affiliation(s)
- Evaldas Katilius
- Arizona State University, Biodesign Institute, Department of Chemistry and Biochemistry and the Center for BioOptical Nanotechnology, Tempe, Arizona 85287-5201, USA.
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43
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Blakaj DM, Kattamuri C, Khrapunov S, Hegde RS, Brenowitz M. Indirect readout of DNA sequence by papillomavirus E2 proteins depends upon net cation uptake. J Mol Biol 2006; 358:224-40. [PMID: 16513133 DOI: 10.1016/j.jmb.2006.01.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Revised: 01/08/2006] [Accepted: 01/27/2006] [Indexed: 10/25/2022]
Abstract
The papillomavirus E2 proteins bind with high affinity to palindromic DNA sequences consisting of two highly conserved four base-pair sequences flanking a variable "spacer" of identical length (ACCG NNNN CGGT). While intimate contacts are observed between the bound proteins and conserved DNA in the available co-crystal structures, no contact is seen between the proteins and the spacer DNA. The ability of human papillomavirus strain 16 (HPV-16) E2 and bovine papillomavirus strain 1 (BPV-1) E2 to discriminate among binding sites with different spacer sequences is dependent on their sensitivity to the unique conformational and/or dynamic properties of the spacer DNA in a process termed "indirect readout". Differential sequence-specific K(+) uptake in low ionic strength solutions lacking Mg(2+) is observed upon E2 protein binding to sites containing the AATT, TTAA or ACGT spacer sequences. In contrast, the cation displacement typical of protein-DNA complex formation is observed at high K(+) concentrations or in the presence of Mg(2+). These results are interpreted to reflect the sequence-specific stabilization of bent DNA conformations by cations localized within the narrowed minor grooves of the protein-bound DNA and the intrinsic structure and flexibility of the DNA target. Mg(2+) differentially affects the binding of the HPV-16 E2 DNA binding domain (HPV16-E2/D) and the BPV-1 E2 DNA binding domain (BPV1-E2/D) to sites bearing different spacer sequences. This study suggests that monovalent and divalent cations contribute to the discrimination of DNA structure and flexibility that could in turn contribute to the specificity with which HPV16-E2/D and BPV1-E2/D mediate DNA replication and gene transcription.
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Affiliation(s)
- Dukagjin M Blakaj
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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44
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Mao C, Flavin KG, Wang S, Dodson R, Ross J, Shapiro DJ. Analysis of RNA-protein interactions by a microplate-based fluorescence anisotropy assay. Anal Biochem 2006; 350:222-32. [PMID: 16448619 DOI: 10.1016/j.ab.2005.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 11/29/2005] [Accepted: 12/05/2005] [Indexed: 11/29/2022]
Abstract
Quantitative studies of RNA-protein interactions are quite cumbersome using traditional methods. We developed a rapid microplate-based fluorescence anisotropy (FA)/fluorescence polarization assay that works well, even with RNA probes >90 nucleotides long. We analyzed binding of RNA targets by vigilin/DDP1/SCP160p and by c-myc coding region instability determinant (CRD) binding protein, CRD-BP. Vigilin is essential for cell viability and functions in heterochromatin formation and mRNA decay. The CRD-BP stabilizes c-myc mRNA. Vigilin bound to a vitellogenin mRNA 3'-UTR probe with a two to three-fold lower affinity than to a Drosophila dodecasatellite ssDNA binding site and bound to the c-myc CRD with a two- to three-fold lower affinity than to the vitellogenin mRNA 3'-UTR. Competition between vigilin and CRD-BP for binding to the CRD may therefore play a role in regulating c-myc mRNA degradation. We analyzed suitability of the microplate-based FA assay for high-throughput screening for small-molecule regulators of RNA-protein interactions. The assay exhibits high reproducibility and precision and works well in 384-well plates and in 5 microl to 20 microl samples. To demonstrate the potential of this assay for screening libraries of small molecules to identify novel regulators of RNA-protein interactions, we identified neomycin and H33342 as inhibitors of binding of vigilin to the vitellogenin mRNA 3'-UTR.
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Affiliation(s)
- Chengjian Mao
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801-3602, USA
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45
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McClelland SE, Dryden DTF, Szczelkun MD. Continuous assays for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleases. J Mol Biol 2005; 348:895-915. [PMID: 15843021 DOI: 10.1016/j.jmb.2005.03.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 02/14/2005] [Accepted: 03/04/2005] [Indexed: 11/25/2022]
Abstract
Fluorescent assays and accompanying kinetic models are described for the analysis of DNA translocation independent of duplex unwinding. A triplex binding site (TBS) was introduced into DNA substrates at precise loci downstream of recognition sequences for type IA, IB and IC restriction endonucleases (EcoKI, EcoAI and EcoR124I, respectively). Each endonuclease was incubated (without ATP) with substrates on which a hexachlorofluoroscein-labelled triplex-forming oligonucleotide (HEX-TFO) was pre-bound. Following addition of ATP, 1-D enzyme motion resulted in collision with, and displacement of, the HEX-TFO, producing a >twofold increase in fluorescent intensity. Alternatively, a decrease in anisotropy following displacement of a rhodamine-labelled TFO was monitored. Using rapid mixing in a stopped-flow fluorimeter, continuous kinetic profiles were produced in which displacement is preceded by a lag-phase, directly proportional to the distance moved. For each enzyme, we obtained not only the translocation rate but also information on slow isomerisation step(s) at initiation. Furthermore, we demonstrated that enzymes deficient in DNA cleavage but with maximal ATPase activity showed initiation and translocation rates identical to wild-type, confirming that DNA strand breaks are not a pre-requisite of motion.
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Affiliation(s)
- Sarah E McClelland
- DNA-Protein Interactions Group, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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46
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Raymond AC, Staker BL, Burgin AB. Substrate Specificity of Tyrosyl-DNA Phosphodiesterase I (Tdp1). J Biol Chem 2005; 280:22029-35. [PMID: 15811850 DOI: 10.1074/jbc.m502148200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase I (Tdp1) hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and tyrosine in vitro. Tdp1 is involved in the repair of DNA lesions created by topoisomerase I, although the in vivo substrate is not known. Here we study the kinetic and binding properties of human Tdp1 (hTdp1) to identify appropriate 3'-phosphotyrosyl DNA substrates. Genetic studies argue that Tdp1 is involved in double and single strand break repair pathways; however, x-ray crystal structures suggest that Tdp1 can only bind single strand DNA. Separate kinetic and binding experiments show that hTdp1 has a preference for single-stranded and blunt-ended duplex substrates over nicked and tailed duplex substrate conformations. Based on these results, we present a new model to explain Tdp1/DNA binding properties. These results suggest that Tdp1 only acts upon double strand breaks in vivo, and the roles of Tdp1 in yeast and mammalian cells are discussed.
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Affiliation(s)
- Amy C Raymond
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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47
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Unruh JR, Gokulrangan G, Lushington GH, Johnson CK, Wilson GS. Orientational dynamics and dye-DNA interactions in a dye-labeled DNA aptamer. Biophys J 2005; 88:3455-65. [PMID: 15731389 PMCID: PMC1305492 DOI: 10.1529/biophysj.104.054148] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the picosecond and nanosecond timescale rotational dynamics of a dye-labeled DNA oligonucleotide or "aptamer" designed to bind specifically to immunoglobulin E. Rotational dynamics in combination with fluorescence lifetime measurements provide information about dye-DNA interactions. Comparison of Texas Red (TR), fluorescein, and tetramethylrhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for biophysical studies employing such conjugates. Time-resolved anisotropy studies demonstrate that the TR- and TAMRA-aptamer anisotropy decays are dominated by the overall rotation of the aptamer, whereas the fluorescein-aptamer anisotropy decay displays a subnanosecond rotational correlation time much shorter than that expected for the overall rotation of the aptamer. Docking and molecular dynamics simulations suggest that the low mobility of TR is a result of binding in the groove of the DNA helix. Additionally, associated anisotropy analysis of the TAMRA-aptamer reveals both quenched and unquenched states that experience significant coupling to the DNA motion. Therefore, quenching of TAMRA by guanosine must depend on the configuration of the dye bound to the DNA. The strong coupling of TR to the rotational dynamics of the DNA aptamer, together with the absence of quenching of its fluorescence by DNA, makes it a good probe of DNA orientational dynamics. The understanding of the nature of dye-DNA interactions provides the basis for the development of bioconjugates optimized for specific biophysical measurements and is important for the sensitivity of anisotropy-based DNA-protein interaction studies employing such conjugates.
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Affiliation(s)
- Jay R Unruh
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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48
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Wang J, Li T, Guo X, Lu Z. Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins. Nucleic Acids Res 2005; 33:e23. [PMID: 15687381 PMCID: PMC548379 DOI: 10.1093/nar/gni021] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We describe a new method for the assay of sequence-specific DNA-binding proteins in this paper. In this method, the sensitive fluorescence resonance energy transfer (FRET) technology is combined with the common DNA footprinting assay in order to develop a simple, rapid and high-throughput approach for quantitatively detecting the sequence-specific DNA-binding proteins. We named this method as exonuclease III (ExoIII) protection assay with FRET probe. The FRET probe used in this assay was a duplex DNA which was designed to contain one FRET pair in the center and two flanking protein-binding sites. During protein detection, if a target protein exists, it will bind to the two protein-binding sites of the FRET probe and thus protect the FRET pair from ExoIII digestion, resulting in high FRET. However, if the target protein does not exist, the FRET pair on the naked FRET probe will be degraded by ExoIII, resulting in low FRET. Three kinds of recombinant transcription factors including NF-κB, SP1 and p50, and the target protein of NF-κB in HeLa cell nuclear extracts, were successfully detected by the assay. This assay can be extensively used in biomedical research targeted at DNA-binding proteins.
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Affiliation(s)
- Jinke Wang
- To whom correspondence should be addressed. Tel/Fax: +86 25 83619983;
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49
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Ma L, Fitzgerald MC. A new H/D exchange- and mass spectrometry-based method for thermodynamic analysis of protein-DNA interactions. ACTA ACUST UNITED AC 2004; 10:1205-13. [PMID: 14700628 DOI: 10.1016/j.chembiol.2003.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The application of SUPREX (stability of unpurified proteins from rates of H/D exchange) to the thermodynamic analysis of protein-DNA complexes is described. A series of five model protein-DNA complexes involving two known DNA binding proteins, Arc repressor and CopG, were analyzed in order to determine the accuracy, precision, and generality of the SUPREX technique for quantifying the strength of protein-DNA interactions. For protein-DNA complexes that reversibly unfold in a two-state manner, we demonstrate that reasonably precise Kd values in agreement with those determined by conventional techniques can be determined by SUPREX. In the case of protein-DNA complexes that are not well modeled by a two-state unfolding mechanism, we find that relative binding affinities can be determined in the SUPREX experiment.
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Affiliation(s)
- Liyuan Ma
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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50
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Khrapunov S, Brenowitz M. Comparison of the effect of water release on the interaction of the Saccharomyces cerevisiae TATA binding protein (TBP) with "TATA Box" sequences composed of adenosine or inosine. Biophys J 2004; 86:371-83. [PMID: 14695279 PMCID: PMC1303802 DOI: 10.1016/s0006-3495(04)74113-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The formation of sequence-specific complexes of TATA binding protein (TBP) with the minor groove of DNA results in the burial of large nonpolar surfaces and the exclusion of water from these interfaces. The release of water is thus expected to provide a significant entropic driving force for formation of the transcription-preinitiated complexes mediated by the binding of TBP to specific sequences. In this article are described equilibrium-binding studies of Saccharomyces cerevisiae TBP to 14 bp oligonucleotides bearing either the tightly bound and efficiently transcribed adenovirus major late promoter (TATAAAAG) or its inosine-substituted derivative (TITIIIIG) as a function of neutral osmolyte concentration. These two DNA sequences present the same pattern of minor groove hydrogen-bond donors and acceptors to the protein. TBP-DNA complex formation was monitored by steady-state fluorescence resonance energy transfer measurements of the oligonucleotides end-labeled with fluorescein (donor) and TAMRA (acceptor). Correct interpretation of the results obtained with the inosine-substituted sequence required careful consideration of the optical properties of the dyes as a function of osmolyte concentration to demonstrate that the relative change in the end-to-end distances for TATAAAAG- and TITIIIIG-bearing oligonucleotides is the same upon TBP binding. Although the affinity of TBP is slightly greater for the adenosine compared with the inosine-substituted TATA sequence in the absence of osmolyte, the end-to-end distances of the bound DNA in complex with TBP, the enthalpic and electrostatic components of binding, are identical within experimental precision. However, approximately 18 additional molecules of water are released upon TBP binding the TATAAAAG as compared with the TITIIIIG sequence resulting in an entropic advantage to the binding of the natural promoter sequence. These results are considered with regard to differences in the flexibility and hydration of the two DNA sequences.
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Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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