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Schedler B, Yukhnovets O, Lindner L, Meyer A, Fitter J. The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection. Int J Mol Sci 2023; 24:16379. [PMID: 38003569 PMCID: PMC10671529 DOI: 10.3390/ijms242216379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions.
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Affiliation(s)
- Benno Schedler
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Lennart Lindner
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Alida Meyer
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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2
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Nguyen TT, Cramb DT. Elucidation of the mechanism and energy barrier for anesthetic triggered membrane fusion in model membranes. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane fusion is vital for cellular function and is generally mediated via fusogenic proteins and peptides. The mechanistic details and subsequently the transition state dynamics of membrane fusion will be dependent on the type of the fusogenic agent. We have previously established the potential of general anesthetics as a new class of fusion triggering agents in model membranes. We employed two-photon excitation fluorescence cross-correlation spectroscopy (TPE-FCCS) to report on vesicle association kinetics and steady-state fluorescence dequenching assays to monitor lipid mixing kinetics. Using halothane to trigger fusion in 110 nm diameter dioleoylphosphatidylcholine (DOPC) liposomes, we found that lipid rearrangement towards the formation of the fusion stalk was rate limiting. The activation barrier for halothane induced membrane fusion in 110 nm vesicles was found to be ∼40 kJ mol−1. We calculated the enthalpy and entropy of the transition state to be ∼40 kJ mol−1and ∼180 J mol−1K−1, respectively. We have found that the addition of halothane effectively lowers the energy barrier for membrane fusion in less curved vesicles largely due to entropic advantages.
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Affiliation(s)
- Trinh T. Nguyen
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - David T. Cramb
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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3
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Mikuni S, Kodama K, Sasaki A, Kohira N, Maki H, Munetomo M, Maenaka K, Kinjo M. Screening for FtsZ Dimerization Inhibitors Using Fluorescence Cross-Correlation Spectroscopy and Surface Resonance Plasmon Analysis. PLoS One 2015; 10:e0130933. [PMID: 26154290 PMCID: PMC4496089 DOI: 10.1371/journal.pone.0130933] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/01/2015] [Indexed: 01/16/2023] Open
Abstract
FtsZ is an attractive target for antibiotic research because it is an essential bacterial cell division protein that polymerizes in a GTP-dependent manner. To find the seed chemical structure, we established a high-throughput, quantitative screening method combining fluorescence cross-correlation spectroscopy (FCCS) and surface plasmon resonance (SPR). As a new concept for the application of FCCS to polymerization-prone protein, Staphylococcus aureus FtsZ was fragmented into the N-terminal and C-terminal, which were fused with GFP and mCherry (red fluorescent protein), respectively. By this fragmentation, the GTP-dependent head-to-tail dimerization of each fluorescent labeled fragment of FtsZ could be observed, and the inhibitory processes of chemicals could be monitored by FCCS. In the first round of screening by FCCS, 28 candidates were quantitatively and statistically selected from 495 chemicals determined by in silico screening. Subsequently, in the second round of screening by FCCS, 71 candidates were also chosen from 888 chemicals selected via an in silico structural similarity search of the chemicals screened in the first round of screening. Moreover, the dissociation constants between the highest inhibitory chemicals and Staphylococcus aureus FtsZ were determined by SPR. Finally, by measuring the minimum inhibitory concentration, it was confirmed that the screened chemical had antibacterial activity against Staphylococcus aureus, including methicillin-resistant Staphylococcus aureus (MRSA).
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Affiliation(s)
- Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kota Kodama
- Creative Research Institution, Hokkaido University, Sapporo, Japan
| | - Akira Sasaki
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Naoki Kohira
- Discovery Research Laboratory for Core Therapeutic Areas, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Hideki Maki
- Discovery Research Laboratory for Core Therapeutic Areas, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Masaharu Munetomo
- Information Initiative Center and Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
- * E-mail:
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4
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Huang Y, Kannan P, Zhang L, Chen T, Kim DH. Concave gold nanoparticle-based highly sensitive electrochemical IgG immunobiosensor for the detection of antibody–antigen interactions. RSC Adv 2015. [DOI: 10.1039/c5ra10990f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A concave gold nanocuboid-based electrochemical sensor was developed for the highly sensitive detection of antibody–antigen interactions.
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Affiliation(s)
- Youju Huang
- Division of Polymer and Composite Materials
- Ningbo Institute of Material Technology and Engineering
- Chinese Academy of Science
- Ningbo 315201
- China
| | - Palanisamy Kannan
- Singapore Centre on Environmental Life Science Engineering (SCELSE)
- Nanyang Technological University
- Singapore
| | - Lei Zhang
- Division of Polymer and Composite Materials
- Ningbo Institute of Material Technology and Engineering
- Chinese Academy of Science
- Ningbo 315201
- China
| | - Tao Chen
- Division of Polymer and Composite Materials
- Ningbo Institute of Material Technology and Engineering
- Chinese Academy of Science
- Ningbo 315201
- China
| | - Dong-Hwan Kim
- School of Chemical and Biomedical Engineering (SCBE)
- Nanyang Technological University
- Singapore
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5
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Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a single-molecule sensitive technique to quantitatively study interactions among fluorescently tagged biomolecules. Besides the initial implementation as dual-color FCCS (DC-FCCS), FCCS has several powerful derivatives, including single-wavelength FCCS (SW-FCCS), two-photon FCCS (TP-FCCS), and pulsed interleaved excitation FCCS (PIE-FCCS). However, to apply FCCS successfully, one needs to be familiar with procedures ranging from fluorescent labeling, instrumentation setup and alignment, sample preparation, and data analysis. Here, we describe the procedures to apply FCCS in various biological samples ranging from live cells to in vivo measurements, with the focus on DC-FCCS and SW-FCCS.
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6
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Li B, Ju H. Label-free optical biosensors based on a planar optical waveguide. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7401-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Supporting immunoassay design with biophysical tools. Anal Biochem 2013; 437:95-102. [DOI: 10.1016/j.ab.2013.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 11/15/2022]
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8
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Weidemann T, Schwille P. Dual-color fluorescence cross-correlation spectroscopy with continuous laser excitation in a confocal setup. Methods Enzymol 2013; 518:43-70. [PMID: 23276535 DOI: 10.1016/b978-0-12-388422-0.00003-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fluorescence correlation spectroscopy evaluates local signal fluctuations arising from stochastic movements of fluorescent particles in solution. The measured fluctuating signal is correlated in time and analyzed with appropriate model functions containing the parameters that describe the underlying molecular behavior. The dual-color extension, fluorescence cross-correlation spectroscopy (FCCS) allows for a comparison between spectrally well-separated channels to extract codiffusion events that reflect interactions between differently labeled molecules. In addition to solution measurements, FCCS can be applied with subcellular resolution and is therefore a very promising approach for a quantitative biochemical assessment of molecular networks in living cells. To derive thermodynamic and kinetic reaction parameters, the influence of a number of other factors like background noise, illumination intensity profiles, photophysical processes, and cross talk between the channels have to be treated. Here, we provide a roadmap to derive binding reaction data with dual-color FCCS using continuous wave laser excitation, as it is now accessible with many state-of-the-art confocal microscopes.
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Affiliation(s)
- Thomas Weidemann
- Biophysics/BIOTEC, Technische Universität Dresden, Dresden, Germany.
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9
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Studying Antibody–Antigen Interactions with Fluorescence Fluctuation Spectroscopy. Methods Enzymol 2013. [DOI: 10.1016/b978-0-12-405539-1.00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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10
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Sapsford KE, Tyner KM, Dair BJ, Deschamps JR, Medintz IL. Analyzing nanomaterial bioconjugates: a review of current and emerging purification and characterization techniques. Anal Chem 2011; 83:4453-88. [PMID: 21545140 DOI: 10.1021/ac200853a] [Citation(s) in RCA: 278] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kim E Sapsford
- Division of Biology, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA.
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11
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Skinner JP, Wu B, Mueller JD, Tetin SY. Determining antibody stoichiometry using time-integrated fluorescence cumulant analysis. J Phys Chem B 2011; 115:1131-8. [PMID: 21192730 PMCID: PMC3038621 DOI: 10.1021/jp106279r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We applied fluorescence fluctuation spectroscopy to resolve the binding heterogeneity of fluorescently labeled ligand derived from brain natriuretic peptide (BNP), a widely used diagnostic marker of heart failure, to a corresponding monoclonal antibody. This system includes three species: (1) free ligand molecules, (2) antibody with a single site occupied, and (3) antibody with both sites occupied. The method we used, time-integrated fluorescence cumulant analysis (TIFCA), utilizes cumulants of fluorescence fluctuations to resolve subpopulations of multiple fluorescent species freely diffusing in a solution. The values of the cumulants depend on the concentration, molecular brightness and diffusion time of the fluorescent molecules. The number of molecules in each species reflects the antibody affinity. We apply TIFCA to successfully establish the stoichiometry of the system, estimate affinity, and identify the presence of an inactive fraction of antigen in a single titration experiment.
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12
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Fluorescence Correlation and Cross-Correlation Spectroscopy Using Fluorescent Proteins for Measurements of Biomolecular Processes in Living Organisms. FLUORESCENT PROTEINS II 2011. [DOI: 10.1007/4243_2011_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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13
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Olejniczak ET, Ruan Q, Ziemann RN, Birkenmeyer LG, Saldana SC, Tetin SY. Rapid determination of antigenic epitopes in human NGAL using NMR. Biopolymers 2010; 93:657-67. [DOI: 10.1002/bip.21417] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Miller AE, Hollars CW, Lane SM, Laurence TA. Fluorescence cross-correlation spectroscopy as a universal method for protein detection with low false positives. Anal Chem 2009; 81:5614-22. [PMID: 19522509 DOI: 10.1021/ac9001645] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specific, quantitative, and sensitive protein detection with minimal sample preparation is an enduring need in biology and medicine. Protein detection assays ideally provide quick, definitive measurements that use only small amounts of material. Fluorescence cross-correlation spectroscopy (FCCS) has been proposed and developed as a protein detection assay for several years. Here, we combine several recent advances in FCCS apparatus and analysis to demonstrate it as an important method for sensitive, quantitative, information-rich protein detection with low false positives. The addition of alternating laser excitation (ALEX) to FCCS along with a method to exclude signals from occasional aggregates leads to a very low rate of false positives, allowing the detection and quantification of the concentrations of a wide variety of proteins. We detect human chorionic gonadotropin (hCG) using an antibody-based sandwich assay and quantitatively compare our results with calculations based on binding equilibrium equations. Furthermore, using our aggregate exclusion method, we detect smaller oligomers of the prion protein PrP by excluding bright signals from large aggregates.
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Affiliation(s)
- Abigail E Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
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15
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Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies. Anal Biochem 2009; 393:196-204. [DOI: 10.1016/j.ab.2009.06.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 06/10/2009] [Accepted: 06/24/2009] [Indexed: 11/18/2022]
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16
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Iki N, Takahashi M, Takahashi T, Hoshino H. Ligand-Substitution Mode Capillary Electrophoretic Reactor: Extending Capillary Electrophoretic Reactor toward Measurement of Slow Dissociation Kinetics with a Half-Life of Hours. Anal Chem 2009; 81:7849-54. [DOI: 10.1021/ac901296j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nobuhiko Iki
- Laboratory of Environmental Analytical Chemistry, Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Mariko Takahashi
- Laboratory of Environmental Analytical Chemistry, Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Toru Takahashi
- Laboratory of Environmental Analytical Chemistry, Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Hitoshi Hoshino
- Laboratory of Environmental Analytical Chemistry, Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba-ku, Sendai 980-8579, Japan
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17
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Jameson DM, Ross JA, Albanesi JP. Fluorescence fluctuation spectroscopy: ushering in a new age of enlightenment for cellular dynamics. Biophys Rev 2009; 1:105-118. [PMID: 21547245 DOI: 10.1007/s12551-009-0013-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Originally developed for applications in physics and physical chemistry, fluorescence fluctuation spectroscopy is becoming widely used in cell biology. This review traces the development of the method and describes some of the more important applications. Specifically, the methods discussed include fluorescence correlation spectroscopy (FCS), scanning FCS, dual color cross-correlation FCS, the photon counting histogram and fluorescence intensity distribution analysis approaches, the raster scanning image correlation spectroscopy method, and the Number and Brightness technique. The physical principles underlying these approaches will be delineated, and each of the methods will be illustrated using examples from the literature.
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Affiliation(s)
- David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB 222, Honolulu, HI 96813, USA
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18
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Burrows SM, Pappas D. Comparison of methods to classify and quantify free and bound states of complexes using single molecule fluorescence anisotropy. Analyst 2009; 134:1911-21. [DOI: 10.1039/b905847h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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19
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Schroeder U, Graff A, Buchmeier S, Rigler P, Silvan U, Tropel D, Jockusch BM, Aebi U, Burkhard P, Schoenenberger CA. Peptide nanoparticles serve as a powerful platform for the immunogenic display of poorly antigenic actin determinants. J Mol Biol 2008; 386:1368-81. [PMID: 19063898 DOI: 10.1016/j.jmb.2008.11.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 11/14/2008] [Accepted: 11/15/2008] [Indexed: 11/19/2022]
Abstract
The role of actin in transcription and RNA processing is now widely accepted but the form of nuclear actin remains enigmatic. Monomeric, oligomeric or polymeric forms of actin seem to be involved in nuclear functions. Moreover, uncommon forms of actin such as the "lower dimer" have been observed in vitro. Antibodies have been pivotal in revealing the presence and distribution of different forms of actin in different cellular locations. Because of its high degree of conservation, actin is a poor immunogen and only few specific actin antibodies are available. To unravel the mystery of less common forms of actin, in particular those in the nucleus, we chose to tailor monoclonal antibodies to recognize distinct forms of actin. To increase the immune response, we used a new approach based on peptide nanoparticles, which are designed to mimic an icosahedral virus capsid and allow the repetitive, ordered display of a specific epitope on their surface. Actin sequences representing the highly conserved "hydrophobic loop," which is buried in the filamentous actin filament, were grafted onto the surface of nanoparticles by genetic engineering. After immunization with "loop nanoparticles," a number of monoclonal antibodies were established that bind to the hydrophobic loop both in vitro and in situ. Immunofluorescence studies on cells revealed that filamentous actin filaments were only labeled once the epitope had been exposed. Our studies indicate that self-assembling peptide nanoparticles represent a versatile platform that can easily be customized to present antigenic determinants in repetitive, ordered arrays and elicit an immune response against poor antigens.
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Affiliation(s)
- Ulrich Schroeder
- M. E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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