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Dunlap T, Cao Y. Physiological Considerations for Modeling in vivo Antibody-Target Interactions. Front Pharmacol 2022; 13:856961. [PMID: 35281913 PMCID: PMC8912916 DOI: 10.3389/fphar.2022.856961] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The number of therapeutic antibodies in development pipelines is increasing rapidly. Despite superior success rates relative to small molecules, therapeutic antibodies still face many unique development challenges. There is often a translational gap from their high target affinity and specificity to the therapeutic effects. Tissue microenvironment and physiology critically influence antibody-target interactions contributing to apparent affinity alterations and dynamic target engagement. The full potential of therapeutic antibodies will be further realized by contextualizing antibody-target interactions under physiological conditions. Here we review how local physiology such as physical stress, biological fluid, and membrane characteristics could influence antibody-target association, dissociation, and apparent affinity. These physiological factors in the early development of therapeutic antibodies are valuable toward rational antibody engineering, preclinical candidate selection, and lead optimization.
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Affiliation(s)
- Tyler Dunlap
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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2
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Dunbar CA, Callaway HM, Parrish CR, Jarrold MF. Probing Antibody Binding to Canine Parvovirus with Charge Detection Mass Spectrometry. J Am Chem Soc 2018; 140:15701-15711. [PMID: 30398860 DOI: 10.1021/jacs.8b08050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There are many techniques for monitoring and measuring the interactions between proteins and ligands. Most of these techniques are ensemble methods that can provide association constants and in some cases stoichiometry. Here we use charge detection mass spectrometry (CDMS), a single particle technique, to probe the interactions of antigen binding fragments (Fabs) from a series of antibodies with the canine parvovirus (CPV) capsid. In addition to providing the average number of bound Fabs as a function of Fab concentration (i.e., the binding curve), CDMS measurements provide information about the distribution of bound Fabs. We show that the distribution of bound ligands is much better at distinguishing between different binding models than the binding curve. The binding of Fab E to CPV is a textbook example. A maximum of 60 Fabs bind and the results are consistent with a model where all sites have the same binding affinity. However, for Fabs B, F, and 14, the distributions can only be fit by a model where there are distinct virus subpopulations with different binding affinities. This behavior can be distinguished from a situation where all CPV particles are identical, and each particle has the same distribution of sites with different binding affinities. The different responses to viral heterogeneity can be traced to the Fab binding sites. A comparison of Fab binding to new and aged CPV capsids reveals that a post-translational modification at the binding site for Fab E (M569) probably reduces the binding affinity.
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Affiliation(s)
- Carmen A Dunbar
- Department of Chemistry , Indiana University , 800 E. Kirkwood Ave. , Bloomington , Indiana 47405 , United States
| | - Heather M Callaway
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , New York 14850 , United States
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , New York 14850 , United States
| | - Martin F Jarrold
- Department of Chemistry , Indiana University , 800 E. Kirkwood Ave. , Bloomington , Indiana 47405 , United States
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3
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Bulseco DA, Wolf DE. Fluorescence correlation spectroscopy: molecular complexing in solution and in living cells. Methods Cell Biol 2014; 114:489-524. [PMID: 23931520 DOI: 10.1016/b978-0-12-407761-4.00021-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
This chapter describes how the microscope can be used to measure a fluorescence signal from a small, confined volume of the sample-the confocal volume-and how these measurements are used to quantitate the dynamics and complexing of molecules, the technique of fluorescence correlation spectroscopy (FCS). FCS represents a significant example of how the microscope can be used to extract information beyond the resolution limit of classical optics. FCS enables studying events at the level of single molecules. With FCS, one can measure the diffusion times and the interaction of macromolecules, the absolute concentration of fluorescently labeled particles, and the kinetics of chemical reactions. Practical applications of FCS include studies on ligand-receptor binding, protein-protein and protein-DNA interactions, and the aggregation of fluorescently labeled particles. The chapter focuses on the principles of FCS, demonstrates how FCS is used to study macromolecular interactions in solution and in living cells, and examines critical experimental parameters that must be considered. The chapter also discusses the minimum requirements for building a microscope-based FCS instrument and illustrates the key criteria for both instrument sensitivity and analysis of FCS data. It can be used to study single molecules both in solution and in living cells and can be used to monitor a variety of macromolecular interactions. When used as an in vitro technique, FCS measurements are easy to conduct and can be made on simplified instrumentation. When used in vivo on living cells, many additional factors must be considered when evaluating experimental data. Despite these concerns, FCS represents a new approach that has broad applicability for the determination of molecular stoichiometry both in vivo and in vitro for a variety of membrane and soluble receptor systems.
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4
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Safenkova IV, Zherdev AV, Dzantievf BB. Application of atomic force microscopy for characteristics of single intermolecular interactions. BIOCHEMISTRY (MOSCOW) 2013; 77:1536-52. [PMID: 23379527 DOI: 10.1134/s000629791213010x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.
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Affiliation(s)
- I V Safenkova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
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5
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Hong S, Tsou PH, Chou CK, Yamaguchi H, Su CB, Hung MC, Kameoka J. Microfluidic three-dimensional hydrodynamic flow focusing for the rapid protein concentration analysis. BIOMICROFLUIDICS 2012; 6:24132. [PMID: 23785388 PMCID: PMC3391308 DOI: 10.1063/1.4730332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/04/2012] [Indexed: 05/23/2023]
Abstract
A simple microfluidic 3D hydrodynamic flow focusing device has been developed and demonstrated quantitative determinations of quantum dot 525 with antibody (QD525-antibody) and hemagglutinin epitope tagged MAX (HA-MAX) protein concentrations. This device had a step depth cross junction structure at a hydrodynamic flow focusing point at which the analyte stream was flowed into a main detection channel and pinched not only horizontally but also vertically by two sheath streams. As a result, a triangular cross-sectional flow profile of the analyte stream was formed and the laser was focused on the top of the triangular shaped analyte stream. Since the detection volume was smaller than the radius of laser spot, a photon burst histogram showed Gaussian distribution, which was necessary for the quantitative analysis of protein concentration. By using this approach, a linear concentration curve of QD525-antibody down to 10 pM was demonstrated. In addition, the concentration of HA-MAX protein in HEK293 cell lysate was determined as 0.283 ± 0.015 nM. This approach requires for only 1 min determining protein concentration. As the best of our knowledge, this is the first time to determinate protein concentration by using single molecule detection techniques.
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Affiliation(s)
- Sungmin Hong
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
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Perevoshchikova IV, Kotova EA, Antonenko YN. Fluorescence correlation spectroscopy in biology, chemistry, and medicine. BIOCHEMISTRY (MOSCOW) 2011; 76:497-516. [PMID: 21639831 DOI: 10.1134/s0006297911050014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.
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Affiliation(s)
- I V Perevoshchikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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7
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Teles FSRR. Biosensors and rapid diagnostic tests on the frontier between analytical and clinical chemistry for biomolecular diagnosis of dengue disease: a review. Anal Chim Acta 2011; 687:28-42. [PMID: 21241843 PMCID: PMC7094386 DOI: 10.1016/j.aca.2010.12.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/09/2010] [Accepted: 12/07/2010] [Indexed: 11/26/2022]
Abstract
The past decades have witnessed enormous technological improvements towards the development of simple, cost-effective and accurate rapid diagnostic tests for detection and identification of infectious pathogens. Among them is dengue virus, the etiologic agent of the mosquito-borne dengue disease, one of the most important emerging infectious pathologies of nowadays. Dengue fever may cause potentially deadly hemorrhagic symptoms and is endemic in the tropical and sub-tropical world, being also a serious threat to temperate countries in the developed world. Effective diagnostics for dengue should be able to discriminate among the four antigenically related dengue serotypes and fulfill the requirements for successful decentralized (point-of-care) testing in the harsh environmental conditions found in most tropical regions. The accurate identification of circulating serotypes is crucial for the successful implementation of vector control programs based on reliable epidemiological predictions. This paper briefly summarizes the limitations of the main conventional techniques for biomolecular diagnosis of dengue disease and critically reviews some of the most relevant biosensors and rapid diagnostic tests developed, implemented and reported so far for point-of-care testing of dengue infections. The invaluable contributions of microfluidics and nanotechnology encompass the whole paper, while evaluation concerns of rapid diagnostic tests and foreseen technological improvements in this field are also overviewed for the diagnosis of dengue and other infectious and tropical diseases as well.
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Key Words
- cdc, centers for disease control
- denv1–4, dengue virus serotypes (1–4)
- ssrna, single-stranded ribonucleic acid
- orf, open-reading frame
- ns1, non-structural 1
- dhf, dengue hemorrhagic fever
- dss, dengue shock syndrome
- who, world health organization
- hi, hemagglutination-inhibition
- mac-eia, monoclonal antibody capture-enzyme linked immunosorbent assay
- rt-pcr, reverse transcription-polymerase chain reaction
- 3′-nr, 3′noncoding region
- rna, ribonucleic acid
- igg, immunoglobulin g
- igm, immunoglobulin m
- dna, deoxyribonucleic acid
- qcm, quartz-crystal microbalance
- mip, molecularly imprinted polymer
- gnp, gold nanoparticle
- sam, self-assembled monolayer
- bsa, bovine serum albumin
- spr, surface plasmon resonance
- nasba, nucleic acid sequence-based amplification
- s/n, signal-to-noise ratio
- cmos, complementary metal oxide semiconductor
- fia, flow-injection analysis
- fccs, fluorescence cross-correlation spectroscopy
- fcs, fluorescence correlation spectroscopy
- eis, electrochemical impedance spectroscopy
- bst, barium strontium titanate
- fet, field-effect transistor
- pna, peptide nucleic-acid
- lod, limit of detection
- cdna, complementary dna
- tdr, special programme for research and training in tropical diseases
- undp, united nations development programme
- pdvi, pediatric dengue vaccine initiative
- stard, standards for reporting of diagnostic accuracy
- fiocruz, fundação oswaldo cruz
- dpp®, dual-path platform
- blm, bilayer lipid membrane
- qd, quantum dot
- cnt, carbon nanotube
- ms, mass spectrometry
- sars, severe acute respiratory syndrome
- biosensor
- dengue
- diagnosis
- evaluation
- rapid test
- tropical disease
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Affiliation(s)
- Fernando Sérgio Rodrigues Ribeiro Teles
- Centre for Malaria and Tropical Diseases, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisboa, Portugal.
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8
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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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9
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Schlaman HRM, Schmidt K, Ottenhof D, van Es MH, Oosterkamp TH, Spaink HP. Analysis of interactions of signaling proteins with phage-displayed ligands by fluorescence correlation spectroscopy. ACTA ACUST UNITED AC 2008; 13:766-76. [PMID: 18753688 DOI: 10.1177/1087057108323124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fluorescent correlation spectroscopy (FCS) was used to measure binding affinities of ligands to ligates that are expressed by phage-display technology. Using this method we have quantified the binding of the 14-3-3 signaling protein to artificial peptide ligand. As a ligand we used the R18 artificial peptide expressed as a fusion in the cpIII coat protein that is present in 3 to 5 copies in an M13 phage. Comparisons of binding affinities were made with free R18 ligands using FCS. The result showed a relatively high binding affinity for the phage-displayed R18 peptide compared with binding to free fluorescently labeled R18. Quantification was supported by titration of the phage numbers using atomic force microscopy (AFM). AFM was shown to accurately determine phage numbers in solution as a good alternative for electron microscopy. It was shown to give reliable data that correlated perfectly with those of the viable phage numbers determined by classical bacterial infection studies. In conclusion, a very fast and sensitive method for the selection of new peptide ligands or ligates based on a quantitative assay in solution has been developed.
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Affiliation(s)
- Helmi R M Schlaman
- Institute of Biology Leiden, Leiden University, Clusius Laboratory, Leiden, The Netherlands
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10
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Bulseco DA, Wolf DE. Fluorescence correlation spectroscopy: molecular complexing in solution and in living cells. Methods Cell Biol 2007; 81:525-59. [PMID: 17519183 DOI: 10.1016/s0091-679x(06)81025-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Dylan A Bulseco
- Sensor Technologies, LLC, Shrewsbury, Massachusetts 01545, USA
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11
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Földes-Papp Z. 'True' single-molecule molecule observations by fluorescence correlation spectroscopy and two-color fluorescence cross-correlation spectroscopy. Exp Mol Pathol 2006; 82:147-55. [PMID: 17258199 DOI: 10.1016/j.yexmp.2006.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Accepted: 12/04/2006] [Indexed: 01/09/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) and two-color fluorescence cross-correlation spectroscopy (FCCS) are a measure of fluctuations of detected light as a fluorescence molecule diffuses through a femtoliter detection volume caused by a tightly focused laser and confocal optics. Fluorescence from a single molecule can easily be distinguished from the slight background associated with a femtoliter of solvent. At a solution concentration of about 1 nM, the probability that there is an analyte molecule in the probe volume is less than one. Although fluorescence from individual molecules is collected, the data are analyzed by autocorrelation or two-color cross-correlation functions that are the average of thousands of molecules. Properties of single molecules are not obtained. I have been working on problems and opportunities associated with very dilute solutions. The molecule in the confocal probe volume is most probably the molecule that just diffused out, turned around, and diffused back in, i.e., reentered. For the first time, some theoretical results of the novel theory of the meaningful time are presented that enable study of just one single molecule over extended periods of times without immobilization or hydrodynamic focusing. Reentries that may also be called reoccurrences or encounters of a single molecule are significant because during measurement times they give rise to fluctuation phenomena such as molecule number fluctuations. Likewise, four criteria have been developed that can be used to verify that there is only one "selfsame" molecule in the laser probe volume during the experiment: (Földes-Papp, Z., 2006. What it means to measure a single molecule in a solution by fluorescence fluctuation spectroscopy. Exp. Mol. Pathol. 80 (3) 209-218).
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Affiliation(s)
- Zeno Földes-Papp
- Medical University of Graz, Department of Internal Medicine, Riesstrasse 58a/5, A-8047 Graz, Austria.
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12
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Slootweg EJ, Keller HJHG, Hink MA, Borst JW, Bakker J, Schots A. Fluorescent T7 display phages obtained by translational frameshift. Nucleic Acids Res 2006; 34:e137. [PMID: 17040895 PMCID: PMC1635266 DOI: 10.1093/nar/gkl600] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lytic phages form a powerful platform for the display of large cDNA libraries and offer the possibility to screen for interactions with almost any substrate. To visualize these interactions directly by fluorescence microscopy, we constructed fluorescent T7 phages by exploiting the flexibility of phages to incorporate modified versions of its capsid protein. By applying translational frameshift sequences, helper plasmids were constructed that expressed a fixed ratio of both wild-type capsid protein (gp10) and capsid protein fused to enhanced yellow fluorescent protein (EYFP). The frameshift sequences were inserted between the 3′ end of the capsid gene and the sequence encoding EYFP. Fluorescent fusion proteins are only formed when the ribosome makes a −1 shift in reading frame during translation. Using standard fluorescence microscopy, we could sensitively monitor the enrichment of specific binders in a cDNA library displayed on fluorescent T7 phages. The perspectives of fluorescent display phages in the fast emerging field of single molecule detection and sorting technologies are discussed.
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Affiliation(s)
- Erik J Slootweg
- Laboratory of Molecular Recognition and Antibody Technology, Wageningen University Binnenhaven 5, 6709 PD, Wageningen, The Netherlands.
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Zhang Y, Bahns JT, Jin Q, Divan R, Chen L. Toward the detection of single virus particle in serum. Anal Biochem 2006; 356:161-70. [PMID: 16908003 DOI: 10.1016/j.ab.2006.06.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 03/17/2006] [Accepted: 06/28/2006] [Indexed: 11/22/2022]
Abstract
There is a grand challenge for the detection of target molecules at single molecule sensitivity in a bulk body fluid for the early diagnosis of diseases. We report our progress on tackling this challenge via the combination of fluorescence cross-correlation spectroscopy (FCCS) and micro fabricated devices toward highly sensitive detection of the dengue virus. We demonstrate that by using a dengue-specific antibody, we can probe the individual dengue virus in a nanomolar bulk solution by following the specific association of dengue antibody using FCCS. Consequently, we designed and fabricated a microfluidic chamber array structure and were able to compartmentalize the bulk aqueous dengue sample into femtoliter volumes using such a device. More importantly we demonstrate that we can differentiate between the compartments containing the dengue virus and the virus-free compartments. Our experiment suggests that by expanding the throughput using microfluidic devices integrated with FCCS, both of which can be achieved practically, we should be able to detect single virus particle in human body fluids in the near future.
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Affiliation(s)
- Yuexing Zhang
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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14
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Bahns JT, Liu CM, Chen L. Characterizing specific phage-protein interactions by fluorescence correlation spectroscopy. Protein Sci 2004; 13:2578-87. [PMID: 15388856 PMCID: PMC2286549 DOI: 10.1110/ps.04695704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 06/03/2004] [Accepted: 07/02/2004] [Indexed: 10/26/2022]
Abstract
The interactions of several affinity reagent displayed T7 and M13 phage particles with their corresponding target molecules were examined using Fluorescence Correlation Spectroscopy (FCS). Diffusion times, relative fractions of each component in the recognition reactions at the equilibrium state, and ultimately the dissociation constants were deduced from analyzing the fluorescence autocorrelation curves. Although the sample preparation and FCS characterization of icosahedral T7-related systems were relatively straight forward, procedures with filamentous M13-related systems were complicated by the physical size of M13 and its aggregate formation. Methods that accommodate the FCS measurement of the M13 phage via changing confocal optics, fitting procedures, and aggregate discrimination are presented and discussed.
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Affiliation(s)
- John T Bahns
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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15
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Bulseco DA, Wolf DE. Fluorescence correlation spectroscopy: molecular complexing in solution and in living cells. Methods Cell Biol 2004; 72:465-98. [PMID: 14719345 DOI: 10.1016/s0091-679x(03)72022-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
FCS is an important technique for biophysicists, biochemists, and cell biologists. FCS represents an example of how one can make use of the microscope and electronics to extract information beyond the resolution limit of classical optics. It can be used to study single-molecules both in solution and in living cells and can be used to monitor a wide variety of macromolecular interactions. When used as an in vitro technique, FCS measurements are easy to conduct and can be made on simplified instrumentation. When used in vivo on living cells, many additional factors must be considered when evaluating experimental data. Despite these concerns, FCS represents a new approach that has broad applicability for the determination of molecular stoichiometry both in vivo and in vitro for a variety of membrane and soluble receptor systems.
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Affiliation(s)
- Dylan A Bulseco
- Sensor Technologies, LLC, Shrewsbury, Massachusetts 01545, USA
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16
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Földes-Papp Z, Demel U, Tilz GP. A new concept for ultrasensitive fluorescence measurements of molecules in solution and membrane:. J Immunol Methods 2004; 286:1-11. [PMID: 15087217 DOI: 10.1016/j.jim.2004.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 12/14/2003] [Accepted: 01/08/2004] [Indexed: 11/17/2022]
Abstract
Just because there is an average of one molecule in the observation volume of a solution or membrane (single-phase), one cannot say that this is an individual molecule since many different single molecules measured one by one or the same single, individual molecule not leaving the detection volume on time average can cause a single-molecule event. The latter case is of interest and allows the continuous observation of one and the same single molecule without averaging over many 'different' single molecules. For the first time a universal theoretical and experimental framework is presented for the continuous observation of the same single, individual molecule without immobilization, hydrodynamic flow, or burst size histograms of fluorescence intensity traces. In this original article, the stochastic approach is derived and its main characteristics are demonstrated with the free fluorophore rhodamine-green in solution for simpler experimental realization. Single (solution)-phase single-molecule fluorescence auto- (or two-color cross-) correlation spectroscopy (SPSM-FCS) is used as a specific application in order to count the absolute number of molecules in the observation volume. The absolute number of molecules, the diffusion coefficient of the single fluorescent molecule, the lower limit of distance, and the molar concentration of the bulk phase (solution) were directly obtained from the measured auto- or (cross)-correlation curves of the SPSM-FCS experiments. For this purpose, the detection volume that was measured was less then 1 fl (10(-15) l). Then, a concentration of the bulk solution was chosen in such a way that the probability of detecting more than one molecule in the detection volume was very small. The Poisson probability was experimentally determined for the absolute number of molecules depending upon a specified bulk concentration. From the diffusion coefficient of the molecule, it was found that the probability of the molecule diffusing out of the probe volume during the measurements was negligibly small.
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Affiliation(s)
- Zeno Földes-Papp
- Clinical Immunology and Jean Dausset Laboratory, Graz University Medical School and Hospital, Auenbruggerplatz 8, A-8036 Graz, LKH, Austria.
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17
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Földes-Papp Z, Demel U, Domej W, Tilz GP. A new dimension for the development of fluorescence-based assays in solution: from physical principles of FCS detection to biological applications. Exp Biol Med (Maywood) 2002; 227:291-300. [PMID: 11976399 DOI: 10.1177/153537020222700501] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ultrasensitive detection methods such as laser-induced fluorescence represent the current state-of-the-art in analytics. Single-molecule detection in solution has received a remarkable amount of attention in the last few years because of its applicability to life sciences. Studies have been performed on the fundamentals of the detection processes themselves and on some biological systems. Fluorescence correlation spectroscopy (FCS) is the link for ultrasensitive multicomponent analysis, showing possibilities for experiments on molecular interactions. Based on the theoretical background of FCS, this article gives full explanation of FCS and an update of highlights in experimental biology and medicine studied by FCS. We focus on a repertoire of diverse immunoglobulin specificities, a ribosome display system, single-molecule DNA sequencing, and a mutant enzyme generated by random mutagenesis of amino acids. We describe the usefulness and the enormous potential of the methodology. Further, this contribution clearly indicates that FCS is a valuable tool for solution-phase single-molecule (SPSM) experiments in immunobiology and medicine. In experiments with the Goodpasture autoantibody, we worked out conditions for the design of experiments on a complex single molecule in solution. The possibility to use SPSM-FCS as a quantitation methodology opens up other important applications beyond the scope of this article. Original results extending the published studies are presented for the rational foundation of SPSM-FCS. In this original contribution, we deal with experimental systems for biology and medicine where the number of molecules in solution is very small. This article is mandatory for gaining confidence in the interpretation of experimental SPSM-FCS results on the selfsame, individual single molecule in solution.
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Affiliation(s)
- Zeno Földes-Papp
- Clinical Immunology and Jean Dausset Laboratory, Graz University Medical School and Hospital, Auenbruggerplatz 8, A-8036 Graz, LKH, Austria.
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