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Löffler T, Krüger A, Zirak P, Winterhalder MJ, Müller AL, Fischbach A, Mangerich A, Zumbusch A. Influence of chain length and branching on poly(ADP-ribose)-protein interactions. Nucleic Acids Res 2023; 51:536-552. [PMID: 36625274 PMCID: PMC9881148 DOI: 10.1093/nar/gkac1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/16/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Hundreds of proteins interact with poly(ADP-ribose) (PAR) via multiple PAR interaction motifs, thereby regulating their physico-chemical properties, sub-cellular localizations, enzymatic activities, or protein stability. Here, we present a targeted approach based on fluorescence correlation spectroscopy (FCS) to characterize potential structure-specific interactions of PAR molecules of defined chain length and branching with three prime PAR-binding proteins, the tumor suppressor protein p53, histone H1, and the histone chaperone APLF. Our study reveals complex and structure-specific PAR-protein interactions. Quantitative Kd values were determined and binding affinities for all three proteins were shown to be in the nanomolar range. We report PAR chain length dependent binding of p53 and H1, yet chain length independent binding of APLF. For all three PAR binders, we found a preference for linear over hyperbranched PAR. Importantly, protein- and PAR-structure-specific binding modes were revealed. Thus, while the H1-PAR interaction occurred largely on a bi-molecular 1:1 basis, p53-and potentially also APLF-can form complex multivalent PAR-protein structures. In conclusion, our study gives detailed and quantitative insight into PAR-protein interactions in a solution-based setting at near physiological buffer conditions. The results support the notion of protein and PAR-structure-specific binding modes that have evolved to fit the purpose of the respective biochemical functions and biological contexts.
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Affiliation(s)
| | | | - Peyman Zirak
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | | | - Anna-Lena Müller
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | - Arthur Fischbach
- Department of Biology, Universität Konstanz, Konstanz D-78457, Germany
| | - Aswin Mangerich
- To whom correspondence should be addressed. Tel: +49 33200 88 5301;
| | - Andreas Zumbusch
- Correspondence may also be addressed to Andreas Zumbusch. Tel: +49 7531 882027;
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Borges-Araújo L, Monteiro ME, Mil-Homens D, Bernardes N, Sarmento MJ, Coutinho A, Prieto M, Fernandes F. Impact of Ca 2+-Induced PI(4,5)P 2 Clusters on PH-YFP Organization and Protein-Protein Interactions. Biomolecules 2022; 12:912. [PMID: 35883468 PMCID: PMC9312469 DOI: 10.3390/biom12070912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its low abundance, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a key modulator of membrane-associated signaling events in eukaryotic cells. Temporal and spatial regulation of PI(4,5)P2 concentration can achieve localized increases in the levels of this lipid, which are crucial for the activation or recruitment of peripheral proteins to the plasma membrane. The recent observation of the dramatic impact of physiological divalent cation concentrations on PI(4,5)P2 clustering, suggests that protein anchoring to the plasma membrane through PI(4,5)P2 is likely not defined solely by a simple (monomeric PI(4,5)P2)/(protein bound PI(4,5)P2) equilibrium, but instead depends on complex protein interactions with PI(4,5)P2 clusters. The insertion of PI(4,5)P2-binding proteins within these clusters can putatively modulate protein-protein interactions in the membrane, but the relevance of such effects is largely unknown. In this work, we characterized the impact of Ca2+ on the organization and protein-protein interactions of PI(4,5)P2-binding proteins. We show that, in giant unilamellar vesicles presenting PI(4,5)P2, the membrane diffusion properties of pleckstrin homology (PH) domains tagged with a yellow fluorescent protein (YFP) are affected by the presence of Ca2+, suggesting direct interactions between the protein and PI(4,5)P2 clusters. Importantly, PH-YFP is found to dimerize in the membrane in the absence of Ca2+. This oligomerization is inhibited in the presence of physiological concentrations of the divalent cation. These results confirm that cation-dependent PI(4,5)P2 clustering promotes interactions between PI(4,5)P2-binding proteins and has the potential to dramatically influence the organization and downstream interactions of PI(4,5)P2-binding proteins in the plasma membrane.
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Affiliation(s)
- Luís Borges-Araújo
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Marina E. Monteiro
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (M.E.M.); (M.J.S.)
| | - Dalila Mil-Homens
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Nuno Bernardes
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Maria J. Sarmento
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (M.E.M.); (M.J.S.)
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Avenida Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana Coutinho
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Manuel Prieto
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Fábio Fernandes
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
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3
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Stoddart LA, Goulding J, Briddon SJ. Advances in the application of fluorescence correlation spectroscopy to study detergent purified and encapsulated membrane proteins. Int J Biochem Cell Biol 2022; 146:106210. [PMID: 35390493 DOI: 10.1016/j.biocel.2022.106210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a quantitative spectroscopy technique which could potentially increase throughput and sensitivity of screening for ligand, substrate and inhibitor binding to membrane proteins in solution. However, the purification of membrane proteins in their active forms is complex, as the lipid bilayer provides stability and its removal often causes the protein to become conformationally unstable. This has limited the application of biophysical techniques such as FCS to study the function of membrane proteins. The recent application of native extraction techniques such as styrene maleic acid lipid particles (SMALPs) has resolved this issue and FCS has emerged as a powerful option for studying proteins extracted in this way. This review will discuss the application of FCS to study purified membrane proteins in detergent micelles, nanodiscs and SMALPs and its potential to be used routinely in membrane protein drug discovery.
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Affiliation(s)
- Leigh A Stoddart
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK
| | - Joëlle Goulding
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK
| | - Stephen J Briddon
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK.
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4
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Zhou C, Ji C, Nie Y, Yang J, Zhao J. Poly(ethylene oxide) Is Positively Charged in Aqueous Solutions. Gels 2022; 8:gels8040213. [PMID: 35448114 PMCID: PMC9029200 DOI: 10.3390/gels8040213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
There have been controversies about the binding of cations to poly(ethylene oxide) (PEO) chains in aqueous solutions. In the current study, single molecular evidence of charging PEO chains by cation binding in aqueous solutions is provided. From the adoption of the photon-counting histogram method, it is discovered that the local pH value at the vicinity of the PEO chain is higher than the bulk solution, showing that the PEO chain is positively charged. Such a situation exists with and without the presence of salt (NaCl) in the solution, presumably due to the binding of cations, such as hydronium and sodium ions. Single molecular electrophoresis experiments using fluorescence correlation spectroscopy demonstrate that the PEO chains are weakly charged with a charging extent of ~5%. In comparison to the salt-free condition, the addition of external salt (NaCl) at moderate concentrations further charges the chain. The charging causes the PEO chains to expand and a further increase in the salt concentration causes the chain to shrink, exhibiting a polyelectrolyte-like behavior, demonstrated by the hydrodynamic radii of a single PEO chain. The effect of ion identity is discovered with alkali cations, with the order of the charging capacity of Li+ < Na+ < Cs+ < K+.
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Affiliation(s)
- Chao Zhou
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (C.Z.); (C.J.); (Y.N.); (J.Y.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunda Ji
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (C.Z.); (C.J.); (Y.N.); (J.Y.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuchen Nie
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (C.Z.); (C.J.); (Y.N.); (J.Y.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Yang
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (C.Z.); (C.J.); (Y.N.); (J.Y.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Zhao
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (C.Z.); (C.J.); (Y.N.); (J.Y.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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Lucey M, Ashik T, Marzook A, Wang Y, Goulding J, Oishi A, Broichhagen J, Hodson DJ, Minnion J, Elani Y, Jockers R, Briddon SJ, Bloom SR, Tomas A, Jones B. Acylation of the Incretin Peptide Exendin-4 Directly Impacts Glucagon-Like Peptide-1 Receptor Signaling and Trafficking. Mol Pharmacol 2021; 100:319-334. [PMID: 34315812 PMCID: PMC8626645 DOI: 10.1124/molpharm.121.000270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/14/2021] [Indexed: 11/22/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is a class B G protein-coupled receptor and mainstay therapeutic target for the treatment of type 2 diabetes and obesity. Recent reports have highlighted how biased agonism at the GLP-1R affects sustained glucose-stimulated insulin secretion through avoidance of desensitization and downregulation. A number of GLP-1R agonists (GLP-1RAs) feature a fatty acid moiety to prolong their pharmacokinetics via increased albumin binding, but the potential for these chemical changes to influence GLP-1R function has rarely been investigated beyond potency assessments for cAMP. Here, we directly compare the prototypical GLP-1RA exendin-4 with its C-terminally acylated analog, exendin-4-C16. We examine relative propensities of each ligand to recruit and activate G proteins and β-arrestins, endocytic and postendocytic trafficking profiles, and interactions with model and cellular membranes in HEK293 and HEK293T cells. Both ligands had similar cAMP potency, but exendin-4-C16 showed ∼2.5-fold bias toward G protein recruitment and a ∼60% reduction in β-arrestin-2 recruitment efficacy compared with exendin-4, as well as reduced GLP-1R endocytosis and preferential targeting toward recycling pathways. These effects were associated with reduced movement of the GLP-1R extracellular domain measured using a conformational biosensor approach and a ∼70% increase in insulin secretion in INS-1 832/3 cells. Interactions with plasma membrane lipids were enhanced by the acyl chain. Exendin-4-C16 showed extensive albumin binding and was highly effective for lowering of blood glucose in mice over at least 72 hours. Our study highlights the importance of a broad approach to the evaluation of GLP-1RA pharmacology. SIGNIFICANCE STATEMENT: Acylation is a common strategy to enhance the pharmacokinetics of peptide-based drugs. This work shows how acylation can also affect various other pharmacological parameters, including biased agonism, receptor trafficking, and interactions with the plasma membrane, which may be therapeutically important.
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Affiliation(s)
- Maria Lucey
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Tanyel Ashik
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Amaara Marzook
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Yifan Wang
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Joëlle Goulding
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Atsuro Oishi
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Johannes Broichhagen
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - David J Hodson
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - James Minnion
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Yuval Elani
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Ralf Jockers
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Stephen J Briddon
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Stephen R Bloom
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Alejandra Tomas
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine (M.L., T.A., A.M., J.M., S.R.B., B.J.) and Section of Cell Biology and Functional Genomics (Y.W., A.T.), Department of Metabolism, Digestion and Reproduction, and Department of Chemical Engineering (Y.E.), Imperial College London, London, United Kingdom; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (J.G., S.J.B.); Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, United Kingdom (J.G., D.J.H., S.J.B.); Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France (A.O., R.J.); Department of Anatomy, Kyorin University Faculty of Medicine, Tokyo, Japan (A.O.); Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany (J.B.); Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom (D.J.H.); and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom (D.J.H.)
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6
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Goulding J, Kondrashov A, Mistry SJ, Melarangi T, Vo NTN, Hoang DM, White CW, Denning C, Briddon SJ, Hill SJ. The use of fluorescence correlation spectroscopy to monitor cell surface β2-adrenoceptors at low expression levels in human embryonic stem cell-derived cardiomyocytes and fibroblasts. FASEB J 2021; 35:e21398. [PMID: 33710675 DOI: 10.1096/fj.202002268r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 12/31/2022]
Abstract
The importance of cell phenotype in determining the molecular mechanisms underlying β2 -adrenoceptor (β2AR) function has been noted previously when comparing responses in primary cells and recombinant model cell lines. Here, we have generated haplotype-specific SNAP-tagged β2AR human embryonic stem (ES) cell lines and applied fluorescence correlation spectroscopy (FCS) to study cell surface receptors in progenitor cells and in differentiated fibroblasts and cardiomyocytes. FCS was able to quantify SNAP-tagged β2AR number and diffusion in both ES-derived cardiomyocytes and CRISPR/Cas9 genome-edited HEK293T cells, where the expression level was too low to detect using standard confocal microscopy. These studies demonstrate the power of FCS in investigating cell surface β2ARs at the very low expression levels often seen in endogenously expressing cells. Furthermore, the use of ES cell technology in combination with FCS allowed us to demonstrate that cell surface β2ARs internalize in response to formoterol-stimulation in ES progenitor cells but not following their differentiation into ES-derived fibroblasts. This indicates that the process of agonist-induced receptor internalization is strongly influenced by cell phenotype and this may have important implications for drug treatment with long-acting β2AR agonists.
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Affiliation(s)
- Joëlle Goulding
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Alexander Kondrashov
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Sarah J Mistry
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Tony Melarangi
- Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Nguyen T N Vo
- Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Duc M Hoang
- Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK.,Department of Cellular Manufacturing, Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Carl W White
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Harry Perkins Institute of Medical Research and Centre for Medical Research, QEII Medical Centre, The University of Western Australia, Nedlands, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics Technologies, Melbourne, VIC, Australia
| | - Chris Denning
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Stephen J Hill
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
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7
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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8
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Perego E, Köster S. Exploring early time points of vimentin assembly in flow by fluorescence fluctuation spectroscopy. LAB ON A CHIP 2021; 21:735-745. [PMID: 33491697 DOI: 10.1039/d0lc00985g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite the importance for cellular processes, the dynamics of molecular assembly, especially on fast time scales, is not yet fully understood. To this end, we present a multi-layer microfluidic device and combine it with fluorescence fluctuation spectroscopy. We apply this innovative combination of methods to investigate the early steps in assembly of vimentin intermediate filaments (IFs). These filaments, together with actin filaments and microtubules, constitute the cytoskeleton of cells of mesenchymal origin and greatly influence their mechanical properties. We are able to directly follow the two-step assembly process of vimentin IFs and quantify the time scale of the first lateral step to tens of ms with a lag time of below 3 ms. Although demonstrated for a specific biomolecular system here, our method may potentially be employed for a wide range of fast molecular reactions in biological or, more generally, soft matter systems, as it allows for a precise quantification of the kinetics underlying the aggregation and assembly.
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Affiliation(s)
- Eleonora Perego
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany.
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany. and Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
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9
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Zhao J. Studying the physics of charged macromolecules by single molecule fluorescence spectroscopy. J Chem Phys 2020; 153:170903. [PMID: 33167636 DOI: 10.1063/5.0024324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
It is well documented that conventional methods such as dynamic light scattering have encountered difficulties in characterizing charged macromolecules and, therefore, it is desirable that new methods and techniques are introduced. With the ultra-high sensitivity, single molecule fluorescence spectroscopy has successfully lowered the detection limit considerably and enabled measurement under extreme dilution conditions-around the concentration of 10-9M-at which the effect of inter-chain electrostatic repulsion is suppressed. Furthermore, the excellent spatial and temporal resolution as well as the capacity of molecular recognition of these methods help in obtaining rich information of charged macromolecules. This paper summarizes the applications of single molecule fluorescence spectroscopy, especially fluorescence correlation spectroscopy and photon counting histogram, in the studies on charged macromolecules in aqueous solutions and plenty of new information has been revealed on the molecular conformation, counterion distribution, and a few important governing factors. The powerfulness and effectiveness of single molecule fluorescence spectroscopy make it promising in the investigations of charged macromolecules.
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Affiliation(s)
- Jiang Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and The University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Scales N, Swain PS. Resolving fluorescent species by their brightness and diffusion using correlated photon-counting histograms. PLoS One 2019; 14:e0226063. [PMID: 31887113 PMCID: PMC6936799 DOI: 10.1371/journal.pone.0226063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/19/2019] [Indexed: 12/27/2022] Open
Abstract
Fluorescence fluctuation spectroscopy (FFS) refers to techniques that analyze fluctuations in the fluorescence emitted by fluorophores diffusing in a small volume and can be used to distinguish between populations of molecules that exhibit differences in brightness or diffusion. For example, fluorescence correlation spectroscopy (FCS) resolves species through their diffusion by analyzing correlations in the fluorescence over time; photon counting histograms (PCH) and related methods based on moment analysis resolve species through their brightness by analyzing fluctuations in the photon counts. Here we introduce correlated photon counting histograms (cPCH), which uses both types of information to simultaneously resolve fluorescent species by their brightness and diffusion. We define the cPCH distribution by the probability to detect both a particular number of photons at the current time and another number at a later time. FCS and moment analysis are special cases of the moments of the cPCH distribution, and PCH is obtained by summing over the photon counts in either channel. cPCH is inherently a dual channel technique, and the expressions we develop apply to the dual colour case. Using simulations, we demonstrate that two species differing in both their diffusion and brightness can be better resolved with cPCH than with either FCS or PCH. Further, we show that cPCH can be extended both to longer dwell times to improve the signal-to-noise and to the analysis of images. By better exploiting the information available in fluorescence fluctuation spectroscopy, cPCH will be an enabling methodology for quantitative biology.
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Affiliation(s)
- Nathan Scales
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Peter S. Swain
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, United Kingdom
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11
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Zheng K, Chen K, Ren W, Yang J, Zhao J. Counterion Cloud Expansion of a Polyelectrolyte by Dilution. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kaikai Zheng
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Kuo Chen
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Weibin Ren
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Jingfa Yang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Jiang Zhao
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of
Sciences, Beijing 100049, China
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12
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Ren W, Zheng K, Liao C, Yang J, Zhao J. Charge evolution during the unfolding of a single DNA i-motif. Phys Chem Chem Phys 2018; 20:916-924. [PMID: 29230450 DOI: 10.1039/c7cp06235d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effective charge and evolution of single chains of a DNA i-motif during its unfolding process are investigated at the single molecule level. Using fluorescence correlation spectroscopy and photon counting histograms, the single chain dimensions and electrical potential of cytosine-rich human telomeric oligonucleotides are monitored, during their unfolding from the i-motif to the random coil state. It is discovered that the effective charge density of the DNA chain is very sensitive to conformation changes and the results remarkably expose the existence of an intermediate state of the unfolding process. A huge difference in pH value exists in the vicinity of the DNA chain and the bulk solution, depending on the salt concentration, as reflected by a down-shift in the pH value of unfolding. The presence of an external salt in the solution helps to stabilize the i-motif structure at low pH values due to the reduction of the effective charge density. It can also destabilize the folded structure in the pH range of the conformation transition due to the elevation of the local pH value, encouraging the deprotonation of the cytosine groups. These results provide new information for understanding the structure and stability of i-motif DNA, and its biological function, as well as the building blocks for smart nanomaterials.
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Affiliation(s)
- Weibin Ren
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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13
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Xu G, Luo S, Yang Q, Yang J, Zhao J. Single chains of strong polyelectrolytes in aqueous solutions at extreme dilution: Conformation and counterion distribution. J Chem Phys 2016; 145:144903. [DOI: 10.1063/1.4964649] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Guofeng Xu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuangjiang Luo
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingbo Yang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jingfa Yang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiang Zhao
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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14
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Nurse NP, Yuan C. Cis and trans internucleosomal interactions of H3 and H4 tails in tetranucleosomes. Biopolymers 2016; 103:33-40. [PMID: 25196374 DOI: 10.1002/bip.22560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 08/22/2014] [Indexed: 11/09/2022]
Abstract
Chromatin structure and the transcriptional state of a gene can be modulated by modifications made on H3 and H4 tails of histones. Elucidating the internucleosomal interactions of these tails is vital to understanding epigenetic regulation. Differentiation between cis (intra-nucleosomal) and trans (inter-nucleosomal) interactions is often difficult with conventional techniques since H3 and H4 tails are flexible. The distinction, however, is important because these interactions model short- and long-range chromatin interactions respectively and have different bearings in biological processes. Combining FCS and PCH analysis, we can decouple the contribution of histone tails to cis and trans effects. A Mg(2+) gradient was employed to facilitate compaction and oligomerization of tetranucleosomes with H3 and/or H4 tail truncations. H3 tails were found to play a multifunctional role and exhibit the ability to partake in both attractive cis and trans interactions simultaneously. H4 tails partake in attractive cis and repulsive trans interactions at low [Mg(2+)]. These interactions are diminished at higher [Mg(2+)]. Simultaneous H3 and H4 tail truncation inhibited array oligomerization but maintained local array compaction at relatively high [Mg(2+)]. The established experimental approach can be extended to study the detailed molecular interactions mediated by epigenetic modification of flexible histone tails.
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Affiliation(s)
- Nathan P Nurse
- School of Chemical Engineering, Purdue University, West Lafayette, IN, 47906
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15
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Wong K, Briddon SJ, Holliday ND, Kerr ID. Plasma membrane dynamics and tetrameric organisation of ABCG2 transporters in mammalian cells revealed by single particle imaging techniques. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:19-29. [DOI: 10.1016/j.bbamcr.2015.10.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/17/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
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16
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Skakun VV, Novikov EG, Apanasovich TV, Apanasovich VV. Fluorescence cumulants analysis with non-ideal observation profiles. Methods Appl Fluoresc 2015; 3:045003. [PMID: 29148513 DOI: 10.1088/2050-6120/3/4/045003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
One of the challenges of fluorescence fluctuation fpectroscopy (FFS) is an adequate approximation of a brightness profile. The key feature of fluorescence intensity distribution analysis (FIDA) is a polynomial approximation of a brightness profile. A broad range of brightness profile shapes can be well described by this approximation. A different approach consisting of the introduction of additional fitting parameters, defined as a relative difference between integrals of the actual brightness profile and its Gaussian approximation, is used in photon counting histogram (PCH) analysis. It is sufficient to introduce only one additional fitting parameter (first-order correction) to get an adequate fit to the experimental data in many practical applications. In the current study, we apply these approaches to the theory of time integrated fluorescence cumulants analysis. We demonstrate that developed corrections improve results of FFS analysis applied to simulated and experimental data. The use of different brightness profile approximations and normalizations in PCH and FIDA leads to different estimates of brightness and the number of molecules, even though they represent the same physical quantities. Based on the developed theory, we derive equations that relate brightness and the number of molecules in PCH and FIDA.
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Affiliation(s)
- Victor V Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, Minsk, Belarus
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17
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Inoue N, Hagihara Y, Wright D, Suzuki T, Wada I. Oocyte-triggered dimerization of sperm IZUMO1 promotes sperm-egg fusion in mice. Nat Commun 2015; 6:8858. [PMID: 26568141 PMCID: PMC4660202 DOI: 10.1038/ncomms9858] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 10/10/2015] [Indexed: 01/17/2023] Open
Abstract
Sperm-egg fusion is indispensable for completing mammalian fertilization. Although the underlying molecular mechanisms are poorly understood, requirement of two spermatozoon factors, IZUMO1 and SPACA6, and two oocyte factors, CD9 and the IZUMO1 counter-receptor JUNO, has been proven by gene disruption, and the binding of cells to an oocyte can be reconstituted by ectopic expression of IZUMO1. Here we demonstrate that robust IZUMO1-dependent adhesion of sperm with an oocyte accompanies the dimerization of IZUMO1. Despite the intrinsic dimeric property of its N-terminal region, IZUMO1 is monomeric in spermatozoa. Interestingly, JUNO associates with monomeric IZUMO1, which is then quickly removed as tight adhesion of the two cells is subsequently established. We therefore propose that global structural rearrangement of IZUMO1 occurs on JUNO recognition and that this rearrangement may then initiate force generation to overcome repulsion between the juxtaposing membranes, through an unidentified receptor on the egg.
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Affiliation(s)
- Naokazu Inoue
- Department of Cell Science, Institutes for Biomedical Sciences, School of Medicine, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima 960-1295, Japan
| | - Yoshihisa Hagihara
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Danelle Wright
- Department of Cell Science, Institutes for Biomedical Sciences, School of Medicine, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima 960-1295, Japan
| | - Takahisa Suzuki
- Department of Cell Science, Institutes for Biomedical Sciences, School of Medicine, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima 960-1295, Japan
| | - Ikuo Wada
- Department of Cell Science, Institutes for Biomedical Sciences, School of Medicine, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima 960-1295, Japan
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18
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Backer AS, Moerner WE. Determining the rotational mobility of a single molecule from a single image: a numerical study. OPTICS EXPRESS 2015; 23:4255-76. [PMID: 25836463 PMCID: PMC4394761 DOI: 10.1364/oe.23.004255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/18/2015] [Accepted: 02/04/2015] [Indexed: 05/23/2023]
Abstract
Measurements of the orientational freedom with which a single molecule may rotate or 'wobble' about a fixed axis have provided researchers invaluable clues about the underlying behavior of a variety of biological systems. In this paper, we propose a measurement and data analysis procedure based on a widefield fluorescence microscope image for quantitatively distinguishing individual molecules that exhibit varying degrees of rotational mobility. Our proposed technique is especially applicable to cases in which the molecule undergoes rotational motions on a timescale much faster than the framerate of the camera used to record fluorescence images. Unlike currently available methods, sophisticated hardware for modulating the polarization of light illuminating the sample is not required. Additional polarization optics may be inserted in the microscope's imaging pathway to achieve superior measurement precision, but are not essential. We present a theoretical analysis, and benchmark our technique with numerical simulations using typical experimental parameters for single-molecule imaging.
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Affiliation(s)
- Adam S. Backer
- Institute for Computational and Mathematical Engineering, Stanford University, 475 Via Ortega, Stanford, CA 94305,
USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305,
USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305,
USA
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19
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Monillas ES, Caplan JL, Thévenin AF, Bahnson BJ. Oligomeric state regulated trafficking of human platelet-activating factor acetylhydrolase type-II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:469-75. [PMID: 25707358 DOI: 10.1016/j.bbapap.2015.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/06/2015] [Accepted: 02/12/2015] [Indexed: 01/19/2023]
Abstract
The intracellular enzyme platelet-activating factor acetylhydrolase type-II (PAFAH-II) hydrolyzes platelet-activating factor and oxidatively fragmented phospholipids. PAFAH-II in its resting state is mainly cytoplasmic, and it responds to oxidative stress by becoming increasingly bound to endoplasmic reticulum and Golgi membranes. Numerous studies have indicated that this enzyme is essential for protecting cells from oxidative stress induced apoptosis. However, the regulatory mechanism of the oxidative stress response by PAFAH-II has not been fully resolved. Here, changes to the oligomeric state of human PAFAH-II were investigated as a potential regulatory mechanism toward enzyme trafficking. Native PAGE analysis in vitro and photon counting histogram within live cells showed that PAFAH-II is both monomeric and dimeric. A Gly-2-Ala site-directed mutation of PAFAH-II demonstrated that the N-terminal myristoyl group is required for homodimerization. Additionally, the distribution of oligomeric PAFAH-II is distinct within the cell; homodimers of PAFAH-II were localized to the cytoplasm while monomers were associated to the membranes of the endoplasmic reticulum and Golgi. We propose that the oligomeric state of PAFAH-II drives functional protein trafficking. PAFAH-II localization to the membrane is critical for substrate acquisition and effective oxidative stress protection. It is hypothesized that the balance between monomer and dimer serves as a regulatory mechanism of a PAFAH-II oxidative stress response.
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Affiliation(s)
- Elizabeth S Monillas
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Jeffrey L Caplan
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Anastasia F Thévenin
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Brian J Bahnson
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716, USA.
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20
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Beyler AP, Bischof TS, Cui J, Coropceanu I, Harris DK, Bawendi MG. Sample-averaged biexciton quantum yield measured by solution-phase photon correlation. NANO LETTERS 2014; 14:6792-8. [PMID: 25409496 PMCID: PMC4346255 DOI: 10.1021/nl5027953] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The brightness of nanoscale optical materials such as semiconductor nanocrystals is currently limited in high excitation flux applications by inefficient multiexciton fluorescence. We have devised a solution-phase photon correlation measurement that can conveniently and reliably measure the average biexciton-to-exciton quantum yield ratio of an entire sample without user selection bias. This technique can be used to investigate the multiexciton recombination dynamics of a broad scope of synthetically underdeveloped materials, including those with low exciton quantum yields and poor fluorescence stability. Here, we have applied this method to measure weak biexciton fluorescence in samples of visible-emitting InP/ZnS and InAs/ZnS core/shell nanocrystals, and to demonstrate that a rapid CdS shell growth procedure can markedly increase the biexciton fluorescence of CdSe nanocrystals.
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21
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Skakun VV, Digris AV, Apanasovich VV. Global analysis of autocorrelation functions and photon counting distributions in fluorescence fluctuation spectroscopy. Methods Mol Biol 2014; 1076:719-741. [PMID: 24108652 DOI: 10.1007/978-1-62703-649-8_33] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis, the same experimental fluorescence intensity fluctuations are used, but each analytical method focuses on a different property of the signal. The time-dependent decay of the correlation of fluorescence fluctuations is measured in FCS yielding molecular diffusion coefficients and triplet-state parameters such as fraction and decay time. The amplitude distribution of these fluctuations is calculated by PCH analysis yielding the molecular brightness. Both FCS and PCH give information about the molecular concentration. Here we describe a global analysis protocol that simultaneously recovers relevant and common parameters in model functions of FCS and PCH from a single fluorescence fluctuation trace. Application of a global analysis approach allows increasing the information content available from a single measurement that results in more accurate values of molecular diffusion coefficients and triplet-state parameters and also in robust, time-independent estimates of molecular brightness and number of molecules.
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Affiliation(s)
- Victor V Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, Minsk, Belarus
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22
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Shingaryov IP, Skakun VV, Apanasovich VV. Simulation of autocorrelation function and photon counting distribution in fluorescence fluctuation spectroscopy. Methods Mol Biol 2014; 1076:743-755. [PMID: 24108653 DOI: 10.1007/978-1-62703-649-8_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In modern fluorescence fluctuation spectroscopy, the autocorrelation function and photon counting distribution are two widely used statistical characteristics of the measured fluctuating fluorescence intensity signal. Applying special analysis methods such as fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) to these properties, it is possible to recover values of different parameters of fluorescent molecules such as the concentration, diffusion coefficient, molecular brightness, and kinetic rate constants. The development of new analysis methods is senseless without testing their validity, accuracy, and robustness. The most appropriate check of a method is its application to experimental data. However, sometimes it is more convenient and easier to verify a method on simulated data. Simulation is also useful for better understanding the processes that were modeled during the development of analysis methods. Here, we present two simulation models providing an autocorrelation function and photon counting distribution of a sequence of photon arrival times detected in fluorescence fluctuation spectroscopy.
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Affiliation(s)
- Igor P Shingaryov
- Department of Systems Analysis and Computer Simulation, Belarusian State University, Minsk, Belarus
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23
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Schlau-Cohen GS, Bockenhauer S, Wang Q, Moerner WE. Single-molecule spectroscopy of photosynthetic proteins in solution: exploration of structure–function relationships. Chem Sci 2014. [DOI: 10.1039/c4sc00582a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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24
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Wu B, Singer RH, Mueller JD. Time-integrated fluorescence cumulant analysis and its application in living cells. Methods Enzymol 2013; 518:99-119. [PMID: 23276537 DOI: 10.1016/b978-0-12-388422-0.00005-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Time-integrated fluorescence cumulant analysis (TIFCA) is a data analysis technique for fluorescence fluctuation spectroscopy (FFS) that extracts information from the cumulants of the integrated fluorescence intensity. It is the first exact theory that describes the effect of sampling time on FFS experiment. Rebinning of data to longer sampling times helps to increase the signal/noise ratio of the experimental cumulants of the photon counts. The sampling time dependence of the cumulants encodes both brightness and diffusion information of the sample. TIFCA analysis extracts this information by fitting the cumulants to model functions. Generalization of TIFCA to multicolor FFS experiment is straightforward. Here, we present an overview of the theory, its implementation, as well as the benefits and requirements of TIFCA. The questions of why, when, and how to use TIFCA will be discussed. We give several examples of practical applications of TIFCA, particularly focused on measuring molecular interaction in living cells.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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25
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Hussain N, Siegel A, Ge Y, Jordan R, Naumann C. Bilayer asymmetry influences integrin sequestering in raft-mimicking lipid mixtures. Biophys J 2013; 104:2212-21. [PMID: 23708361 PMCID: PMC3660629 DOI: 10.1016/j.bpj.2013.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/15/2013] [Accepted: 04/09/2013] [Indexed: 12/25/2022] Open
Abstract
There is growing recognition that lipid heterogeneities in cellular membranes play an important role in the distribution and functionality of membrane proteins. However, the detection and characterization of such heterogeneities at the cellular level remains challenging. Here we report on the poorly understood relationship between lipid bilayer asymmetry and membrane protein sequestering in raft-mimicking model membrane mixtures using a powerful experimental platform comprised of confocal spectroscopy XY-scan and photon-counting histogram analyses. This experimental approach is utilized to probe the domain-specific sequestering and oligomerization state of αvβ3 and α5β1 integrins in bilayers, which contain coexisting liquid-disordered/liquid-ordered (ld/lo) phase regions exclusively in the top leaflet of the bilayer (bottom leaflet contains ld phase). Comparison with previously reported integrin sequestering data in bilayer-spanning lo-ld phase separations demonstrates that bilayer asymmetry has a profound influence on αvβ3 and α5β1 sequestering behavior. For example, both integrins sequester preferentially to the lo phase in asymmetric bilayers, but to the ld phase in their symmetric counterparts. Furthermore, our data show that bilayer asymmetry significantly influences the role of native ligands in integrin sequestering.
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Affiliation(s)
- Noor F. Hussain
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indiana
| | - Amanda P. Siegel
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indiana
| | - Yifan Ge
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indiana
| | - Rainer Jordan
- Makromolekulare Chemie, Dresden University of Technology, Dresden, Germany
| | - Christoph A. Naumann
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indiana
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26
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Luo S, Jiang X, Zou L, Wang F, Yang J, Chen Y, Zhao J. Resolving the Difference in Electric Potential within a Charged Macromolecule. Macromolecules 2013. [DOI: 10.1021/ma302276b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shuangjiang Luo
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiubo Jiang
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zou
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Yang
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yongming Chen
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiang Zhao
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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27
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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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28
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Skakun VV, Engel R, Borst JW, Apanasovich VV, Visser AJWG. Simultaneous diffusion and brightness measurements and brightness profile visualization from single fluorescence fluctuation traces of GFP in living cells. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:1055-64. [PMID: 23064964 DOI: 10.1007/s00249-012-0864-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/12/2012] [Accepted: 09/21/2012] [Indexed: 10/27/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) and photon-counting histogram (PCH) analysis use the same experimental fluorescence intensity fluctuations, but each analytical method focuses on a different property of the signal. The time-dependent decay of the correlation of fluorescence fluctuations is measured in FCS yielding, for instance, molecular diffusion coefficients. The amplitude distribution of these fluctuations is calculated by PCH analysis yielding information about the molecular brightness of fluorescent species. Analysis of both FCS and PCH results in the molecular concentration of the sample. Using a previously described global analysis procedure we report here precise, simultaneous measurements of diffusion constants and brightness values from single fluorescence fluctuation traces of green-fluorescent protein (GFP, S65T) in the cytoplasm of Dictyostelium cells. The use of a polynomial profile in PCH analysis, describing the detected three-dimensional shape of the confocal volume, enabled us to obtain well fitting results for GFP in cells. We could visualize the polynomial profile and show its deviation from a Gaussian profile.
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Affiliation(s)
- Victor V Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, 220030 Minsk, Belarus.
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29
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Development of cysteine-free fluorescent proteins for the oxidative environment. PLoS One 2012; 7:e37551. [PMID: 22649538 PMCID: PMC3359384 DOI: 10.1371/journal.pone.0037551] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 04/25/2012] [Indexed: 11/19/2022] Open
Abstract
Molecular imaging employing fluorescent proteins has been widely used to highlight specific reactions or processes in various fields of the life sciences. Despite extensive improvements of the fluorescent tag, this technology is still limited in the study of molecular events in the extracellular milieu. This is partly due to the presence of cysteine in the fluorescent proteins. These proteins almost cotranslationally form disulfide bonded oligomers when expressed in the endoplasmic reticulum (ER). Although single molecule photobleaching analysis showed that these oligomers were not fluorescent, the fluorescent monomer form often showed aberrant behavior in folding and motion, particularly when fused to cysteine-containing cargo. Therefore we investigated whether it was possible to eliminate the cysteine without losing the brightness. By site-saturated mutagenesis, we found that the cysteine residues in fluorescent proteins could be replaced with specific alternatives while still retaining their brightness. cf(cysteine-free)SGFP2 showed significantly reduced restriction of free diffusion in the ER and marked improvement of maturation when fused to the prion protein. We further applied this approach to TagRFP family proteins and found a set of mutations that obtains the same level of brightness as the cysteine-containing proteins. The approach used in this study to generate new cysteine-free fluorescent tags should expand the application of molecular imaging to the extracellular milieu and facilitate its usage in medicine and biotechnology.
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30
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Shcherbakova DM, Hink MA, Joosen L, Gadella TWJ, Verkhusha VV. An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imaging. J Am Chem Soc 2012; 134:7913-23. [PMID: 22486524 PMCID: PMC3348967 DOI: 10.1021/ja3018972] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Multicolor imaging based on genetically encoded fluorescent proteins (FPs) is a powerful approach to study several dynamic processes in a live cell. We report a monomeric orange FP with a large Stokes shift (LSS), called LSSmOrange (excitation/emission at 437/572 nm), which fills up an existing spectral gap between the green-yellow and red LSSFPs. Brightness of LSSmOrange is five-fold larger than that of the brightest red LSSFP and similar to the green-yellow LSSFPs. LSSmOrange allows numerous multicolor applications using a single-excitation wavelength that was not possible before. Using LSSmOrange we developed four-color single-laser fluorescence cross-correlation spectroscopy, solely based on FPs. The quadruple cross-correlation combined with photon counting histogram techniques allowed quantitative single-molecule analysis of particles labeled with four FPs. LSSmOrange was further applied to simultaneously image two Förster resonance energy transfer pairs, one of which is the commonly used CFP-YFP pair, with a single-excitation laser line. The combination of LSSmOrange-mKate2 and CFP-YFP biosensors enabled imaging of apoptotic activity and calcium fluctuations in real time. The LSSmOrange mutagenesis, low-temperature, and isotope effect studies revealed a proton relay for the excited-state proton transfer responsible for the LSS phenotype.
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Affiliation(s)
- Daria M. Shcherbakova
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Mark A. Hink
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, NL-1098 XH, Amsterdam, The Netherlands
| | - Linda Joosen
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, NL-1098 XH, Amsterdam, The Netherlands
| | - Theodorus W. J. Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, NL-1098 XH, Amsterdam, The Netherlands
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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31
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Theory of the energy transfer efficiency and fluorescence lifetime distribution in single-molecule FRET. Proc Natl Acad Sci U S A 2012; 109:7747-52. [PMID: 22550169 DOI: 10.1073/pnas.1205120109] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In single-molecule FRET experiments with pulsed lasers, not only the colors of the photons but also the fluorescence lifetimes can be monitored. Although these quantities appear to be random, they are modulated by conformational dynamics. In order to extract information about such dynamics, we develop the theory of the joint distribution of FRET efficiencies and fluorescence lifetimes determined from bins (or bursts) of photons. Our starting point is a rigorous formal expression for the distribution of the numbers of donor and acceptor photons and donor lifetimes in a bin that treats the influence of conformational dynamics on all timescales. This formula leads to an analytic result for a two-state system interconverting on a timescale slower than the interphoton time and to an efficient simulation algorithm for multistate dynamics. The shape of the joint distribution contains more information about conformational dynamics than the FRET efficiency histogram alone. In favorable cases, the connectivity of the underlying conformational states can be determined directly by simple inspection of the projection of the joint distribution on the efficiency-lifetime plane.
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32
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Kilpatrick LE, Briddon SJ, Holliday ND. Fluorescence correlation spectroscopy, combined with bimolecular fluorescence complementation, reveals the effects of β-arrestin complexes and endocytic targeting on the membrane mobility of neuropeptide Y receptors. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1068-81. [PMID: 22487268 PMCID: PMC3793875 DOI: 10.1016/j.bbamcr.2012.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 01/22/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis are powerful ways to study mobility and stoichiometry of G protein coupled receptor complexes, within microdomains of single living cells. However, relating these properties to molecular mechanisms can be challenging. We investigated the influence of β-arrestin adaptors and endocytosis mechanisms on plasma membrane diffusion and particle brightness of GFP-tagged neuropeptide Y (NPY) receptors. A novel GFP-based bimolecular fluorescence complementation (BiFC) system also identified Y1 receptor-β-arrestin complexes. Diffusion co-efficients (D) for Y1 and Y2-GFP receptors in HEK293 cell plasma membranes were 2.22 and 2.15 × 10− 9 cm2 s− 1 respectively. At a concentration which promoted only Y1 receptor endocytosis, NPY treatment reduced Y1-GFP motility (D 1.48 × 10− 9 cm2 s− 1), but did not alter diffusion characteristics of the Y2-GFP receptor. Agonist induced changes in Y1 receptor motility were inhibited by mutations (6A) which prevented β-arrestin recruitment and internalisation; conversely they became apparent in a Y2 receptor mutant with increased β-arrestin affinity. NPY treatment also increased Y1 receptor-GFP particle brightness, changes which indicated receptor clustering, and which were abolished by the 6A mutation. The importance of β-arrestin recruitment for these effects was illustrated by reduced lateral mobility (D 1.20–1.33 × 10− 9 cm2 s− 1) of Y1 receptor-β-arrestin BiFC complexes. Thus NPY-induced changes in Y receptor motility and brightness reflect early events surrounding arrestin dependent endocytosis at the plasma membrane, results supported by a novel combined BiFC/FCS approach to detect the underlying receptor-β-arrestin signalling complex.
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Affiliation(s)
- Laura E Kilpatrick
- Cell Signaling Research Group, School of Biomedical Sciences, University of Nottingham, the Medical School, Queen's Medical Centre, Nottingham, UK
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33
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Leroux CE, Wang I, Derouard J, Delon A. Adaptive optics for fluorescence correlation spectroscopy. OPTICS EXPRESS 2011; 19:26839-49. [PMID: 22274266 DOI: 10.1364/oe.19.026839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fluorescence Correlation Spectroscopy (FCS) yields measurement parameters (number of molecules, diffusion time) that characterize the concentration and kinetics of fluorescent molecules within a supposedly known observation volume. Absolute derivation of concentrations and diffusion constants therefore requires preliminary calibrations of the confocal Point Spread Function with phantom solutions under perfectly controlled environmental conditions. In this paper, we quantify the influence of optical aberrations on single photon FCS and demonstrate a simple Adaptive Optics system for aberration correction. Optical aberrations are gradually introduced by focussing the excitation laser beam at increasing depths in fluorescent solutions with various refractive indices, which leads to drastic depth-dependent bias in the estimated FCS parameters. Aberration correction with a Deformable Mirror stabilizes these parameters within a range of several tens of μm into the solution. We also demonstrate, both theoretically and experimentally, that the molecular brightness scales as the Strehl ratio squared.
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34
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35
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Siegel A, Kimble-Hill A, Garg S, Jordan R, Naumann C. Native ligands change integrin sequestering but not oligomerization in raft-mimicking lipid mixtures. Biophys J 2011; 101:1642-50. [PMID: 21961590 PMCID: PMC3183796 DOI: 10.1016/j.bpj.2011.08.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/17/2011] [Accepted: 08/30/2011] [Indexed: 11/16/2022] Open
Abstract
Distinct lipid environments, including lipid rafts, are increasingly recognized as a crucial factor affecting membrane protein function in plasma membranes. Unfortunately, an understanding of their role in membrane protein activation and oligomerization has remained elusive due to the challenge of characterizing these often small and transient plasma membrane heterogeneities in live cells. To address this difficulty, we present an experimental model membrane platform based on polymer-supported lipid bilayers containing stable raft-mimicking domains (type I) and homogeneous cholesterol-lipid mixtures (type II) into which transmembrane proteins are incorporated (α(v)β(3) and α(5)β(1) integrins). These flexible lipid platforms enable the use of confocal fluorescence spectroscopy, including the photon counting histogram method, in tandem with epifluorescence microscopy to quantitatively probe the effect of the binding of native ligands from the extracellular matrix ligands (vitronectin and fibronectin for α(v)β(3) and α(5)β(1), respectively) on domain-specific protein sequestration and on protein oligomerization state. We found that both α(v)β(3) and α(5)β(1) sequester preferentially to nonraft domains in the absence of extracellular matrix ligands, but upon ligand addition, α(v)β(3) sequesters strongly into raft-like domains and α(5)β(1) loses preference for either raft-like or nonraft-like domains. A corresponding photon counting histogram analysis showed that integrins exist predominantly in a monomeric state. No change was detected in oligomerization state upon ligand binding in either type I or type II bilayers, but a moderate increase in oligomerization state was observed for increasing concentrations of cholesterol. The combined findings suggest a mechanism in which changes in integrin sequestering are caused by ligand-induced changes in integrin conformation and/or dynamics that affect integrin-lipid interactions without altering the integrin oligomerization state.
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Affiliation(s)
- Amanda P. Siegel
- Department of Chemistry and Chemical Biology, Indiana University Purdue University, Indianapolis, Indiana
| | - Ann Kimble-Hill
- Department of Chemistry and Chemical Biology, Indiana University Purdue University, Indianapolis, Indiana
| | - Sumit Garg
- Department of Chemistry and Chemical Biology, Indiana University Purdue University, Indianapolis, Indiana
| | - Rainer Jordan
- Department Chemie, Technische Universität Dresden, Dresden, Germany
| | - Christoph A. Naumann
- Department of Chemistry and Chemical Biology, Indiana University Purdue University, Indianapolis, Indiana
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36
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Anikovsky M, Wiltshire ZD, Weisshart K, Petersen NO. Photon counting histogram analysis for two-dimensional systems. Chemphyschem 2011; 12:2439-48. [PMID: 21805555 DOI: 10.1002/cphc.201100414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Indexed: 11/10/2022]
Abstract
Photon counting statistics in 3D photon counting histogram analysis for one-photon excitation is a function of the number of molecules of particular brightness in the excitation-detection volume of a confocal microscope. In mathematical form that volume is approximated by a three-dimensional Gaussian function which is embedded in the PCH theoretical equations. PCH theory assumes that a molecule can be found anywhere inside the excitation-detection volume with equal probability. However, one can easily imagine systems in which this assumption is violated because molecules are constrained by the geometry of the sample. For example, molecules on a surface or in a membrane would be constrained to two dimensions. To enable the analysis of such systems by PCH, the theoretical framework requires modification. Herein, we present an extension of the PCH analysis to systems where molecules exist in thin structures that are effectively two-dimensional. The method, aptly called two-dimensional photon counting histogram (2D PCH), recovers the number of fluorescent particles per unit area and their molecular brightness. Both theoretical background and experimental results are presented. The theory was tested using computer-simulated and experimental 2D PCHs obtained from confocal experiments. We demonstrate that this modification of the theoretical framework provides a tool to extract data that reveal states of aggregation, surface photophysics, and reactivity.
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Affiliation(s)
- Max Anikovsky
- National Institute for Nanotechnology, National Research Council and the University of Alberta, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2 M9, Canada
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37
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Delon A, Wang I, Lambert E, Mache S, Mache R, Derouard J, Motto-Ros V, Galland R. Measuring, in solution, multiple-fluorophore labeling by combining fluorescence correlation spectroscopy and photobleaching. J Phys Chem B 2010; 114:2988-96. [PMID: 20143802 DOI: 10.1021/jp910082h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the number of fluorescent entities that are coupled to a given molecule (DNA, protein, etc.) is a key point of numerous biological studies, especially those based on a single molecule approach. Reliable methods are important, in this context, not only to characterize the labeling process but also to quantify interactions, for instance within molecular complexes. We combined fluorescence correlation spectroscopy (FCS) and photobleaching experiments to measure the effective number of molecules and the molecular brightness as a function of the total fluorescence count rate on solutions of cDNA (containing a few percent of C bases labeled with Alexa Fluor 647). Here, photobleaching is used as a control parameter to vary the experimental outputs (brightness and number of molecules). Assuming a Poissonian distribution of the number of fluorescent labels per cDNA, the FCS-photobleaching data could be easily fit to yield the mean number of fluorescent labels per cDNA strand (approximately = 2). This number could not be determined solely on the basis of the cDNA brightness, because of both the statistical distribution of the number of fluorescent labels and their unknown brightness when incorporated in cDNA. The statistical distribution of the number of fluorophores labeling cDNA was confirmed by analyzing the photon count distribution (with the cumulant method), which showed clearly that the brightness of cDNA strands varies from one molecule to the other. We also performed complementary continuous photobleaching experiments and found that the photobleaching decay rate of Alexa Fluor 647 in the excited state decreases by about 30% when incorporated into cDNA, while its nonradiative decay rate is increased such that the brightness of individual Alexa labels is decreased by 25% compared to free Alexa dyes.
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Affiliation(s)
- Antoine Delon
- Laboratoire de Spectrométrie Physique UMR 5588, Université de Grenoble I/CNRS, BP 87, 38402 Saint Martin d'Hères, France.
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38
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Melnykov AV, Hall KB. Revival of high-order fluorescence correlation analysis: generalized theory and biochemical applications. J Phys Chem B 2010; 113:15629-38. [PMID: 19877707 DOI: 10.1021/jp906539k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of high-order correlations in fluorescence fluctuation spectroscopy was developed in the late 1980s but since then has been replaced by alternative brightness analysis methods. However, high-order correlation has important advantages in many experiments. We present a new cumulant-based formalism of high-order correlation that greatly simplifies data analysis. The new formalism is used to derive general expressions for variance of high-order correlations that show good agreement with experiment in a model system of fluorescently labeled DNA oligomers. A simulation of binary systems in which both diffusion time and brightness are varied illustrates clearly that high-order analysis has better sensitivity to brightness than fluorescence correlation spectroscopy (FCS). These results have implications for analysis of isomerization reactions and dual-beam FCS with flow. We also demonstrate that high-order correlations can detect photobleaching in the observation volume. The application of this formalism to many FCS-based experiments allows more accurate analysis in addition to describing more molecular parameters.
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Affiliation(s)
- Artem V Melnykov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Box 8231, St. Louis, Missouri 63110, USA
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39
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Blom H, Björk G. Lorentzian spatial intensity distribution in one-photon fluorescence correlation spectroscopy. APPLIED OPTICS 2009; 48:6050-6058. [PMID: 19881673 DOI: 10.1364/ao.48.006050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The theory of autocorrelation-function evaluation in fluorescence correlation spectroscopy is applied to a Lorentzian intensity distribution. An analytical solution to the autocorrelation function for diffusion is deduced for this spatial distribution. Experimental investigation of the distribution is performed using an enlarged detector aperture in a standard confocal setup. The data from the experiment are fitted to the derived autocorrelation function, and a reasonable estimate of the spatial distribution is provided. Estimates are also compared to values computed by molecular detection efficiency simulation. The use of Lorentzian intensity distributions complements conditions where a Gaussian intensity distribution applies, expanding the applicability range of analytical correlation functions.
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Affiliation(s)
- Hans Blom
- Department of Applied Physics, Royal Institute of Technology, AlbaNova/KTH,Roslagstullsbacken 21, 10691 Stockholm, Sweden.
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40
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Han JJ, Boo DW. Reversible immobilization of diffusive membrane-associated proteins using a liquid-gel bilayer phase transition: a case study of Annexin V monomers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3083-3088. [PMID: 19437714 DOI: 10.1021/la803903j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report a novel strategy for reversible immobilization of diffusive membrane-associated proteins in a native orientation using a liquid-gel bilayer phase transition, and its application to the single molecule study of Cy3-labeled Annexin V (A5) monomers on supported lipid bilayers containing phosphatidylserine (PS) in a Ca(2+)-rich environment. Total internal reflection fluorescence single molecule trajectory analysis revealed that, at low membrane occupancy, A5 monomers diffuse randomly on liquid phase bilayers and occasionally collide with other A5 monomers to form short-lived pseudodimers. During the liquid-to-gel bilayer phase transition, diffusive A5 monomers become immobilized mostly as isolated monomers, with some percentage of dimers and trimers. The EDTA-induced unbinding of immobilized Cy3-A5 spots indicates that Ca(2+)-bridges between A5 and PS lipids are preserved in the immobilized A5 monomers, confirming their native orientation on gel phase bilayers. Furthermore, the persistence of Ca(2+)-bridges during the liquid-to-gel phase transition, despite negligible A5 binding affinity to gel phase bilayers, strongly suggests the formation of tightly bound A5(Ca2+)m(PS)n complexes that diffuse and become immobilized as single units during the bilayer phase transition.
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Affiliation(s)
- Jason J Han
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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41
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Anikovsky MY, Petersen NO. Photon Counting Histogram Analysis as a Tool for Studying the Nature of Intermolecular Interactions. J Phys Chem B 2009; 113:3404-12. [DOI: 10.1021/jp809100a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Max Y. Anikovsky
- National Institute for Nanotechnology, National Research Council and the Department of Chemistry, the University of Alberta, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Nils O. Petersen
- National Institute for Nanotechnology, National Research Council and the Department of Chemistry, the University of Alberta, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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42
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Gielen E, vandeVen M, Margineanu A, Dedecker P, Auweraer MVD, Engelborghs Y, Hofkens J, Ameloot M. On the use of Z-scan fluorescence correlation experiments on giant unilamellar vesicles. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.12.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Perevoshchikova I, Zorov D, Antonenko Y. Peak intensity analysis as a method for estimation of fluorescent probe binding to artificial and natural nanoparticles: Tetramethylrhodamine uptake by isolated mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2182-90. [DOI: 10.1016/j.bbamem.2008.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 04/22/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
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44
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Mapping dynamic protein interactions in MAP kinase signaling using live-cell fluorescence fluctuation spectroscopy and imaging. Proc Natl Acad Sci U S A 2007; 104:20320-5. [PMID: 18077328 DOI: 10.1073/pnas.0710336105] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS), fluorescence cross-correlation spectroscopy (FCCS), and photon counting histograms (PCH) are fluctuation methods that emerged recently as potentially useful tools for obtaining parameters of molecular dynamics, interactions, and oligomerization in vivo. Here, we report the successful implementation of FCS, FCCS, and PCH in live yeast cells using fluorescent protein-tagged proteins expressed from their native chromosomal loci, examining cytosolic dynamics and interactions among components of the mitogen activated protein kinase (MAPK) cascade, a widely occurring signaling motif, in response to mating pheromone. FCS analysis detailed the diffusion characteristics and mobile concentrations of MAPK proteins. FCCS analysis using EGFP and mCherry-tagged protein pairs observed the interactions of Ste7 (MAPK kinase) with the MAPKs, Fus3 or Kss1, and of the scaffold protein, Ste5, with Ste7 and Ste11 (MAPK kinase kinase) in the cytosol, providing in vivo constants of their binding equilibrium. The interaction of Ste5 with Fus3 in the cytosol was below the limit of detection, suggesting a weak interaction, if it exists, with K(d) >400-500 nM. Using PCH, we show that cytosolic Ste5 were mostly monomers. Artificial dimerization of Ste5, as confirmed by PCH, using a dimerizing tag, stimulated the interaction between Ste5 and Fus3. Native Ste5 was found to bind Fus3 preferentially at the cortex in pheromone-treated cells, as detected by fluorescence resonance energy transfer (FRET). These results provide a quantitative spatial map of MAPK complexes in vivo and directly support the model that membrane association and regulation of the Ste5 scaffold are critical steps in MAPK activation.
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45
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Margineanu A, De Feyter S, Melnikov S, Marchand D, van Aerschot A, Herdewijn P, Habuchi S, De Schryver FC, Hofkens J. Complexation of lipofectamine and cholesterol-modified DNA sequences studied by single-molecule fluorescence techniques. Biomacromolecules 2007; 8:3382-92. [PMID: 17958438 DOI: 10.1021/bm700486q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipoplex formation for normal and cholesterol-modified oligonucleotides is investigated by fluorescence correlation spectroscopy (FCS). To overcome the problems related to the fitting of autocorrelation curves when fluorescence bursts are present, the baseline fluorescence levels and the fluorescence bursts in the same trace were separately analyzed. This approach was not previously used in FCS studies of lipoplexes and allowed a more detailed characterization of this heterogeneous system. From the baseline levels, the number of free/bound DNA molecules and the presence of tens to hundreds of nanometer-sized lipoplexes were estimated using various mathematical models. Analysis of the fluorescent bursts provided an indication about the sizes of the lipoplexes, the number of DNA molecules in these aggregates, and the relative amount of lipids in each aggregate. An explanation for the higher transfection efficiency previously reported for one of the cholesterol-modified oligonucleotide compounds was found in relation to the formation of large size lipoplexes.
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Affiliation(s)
- Anca Margineanu
- Laboratory of Photochemistry and Spectroscopy, Catholic University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
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46
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Abstract
The theory of photon counting histograms for fluorescent molecules diffusing through a laser spot is presented. Analytic expressions for the factorial cumulants of photon counts are obtained. For an arbitrary counting time window, it is shown how the exact histograms can be obtained by solving an appropriate reaction-diffusion equation. Our formalism reduces correctly when the molecules are immobile. The approximation used in fluorescence intensity multiple distribution analysis (FIMDA) is tested against the exact numerical solution of the problem. FIMDA works very well for a wide range of parameters except for small concentrations and long time windows.
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Affiliation(s)
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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47
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Whorton MR, Bokoch MP, Rasmussen SGF, Huang B, Zare RN, Kobilka B, Sunahara RK. A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein. Proc Natl Acad Sci U S A 2007; 104:7682-7. [PMID: 17452637 PMCID: PMC1863461 DOI: 10.1073/pnas.0611448104] [Citation(s) in RCA: 521] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G protein-coupled receptors (GPCRs) respond to a diverse array of ligands, mediating cellular responses to hormones and neurotransmitters, as well as the senses of smell and taste. The structures of the GPCR rhodopsin and several G proteins have been determined by x-ray crystallography, yet the organization of the signaling complex between GPCRs and G proteins is poorly understood. The observations that some GPCRs are obligate heterodimers, and that many GPCRs form both homo- and heterodimers, has led to speculation that GPCR dimers may be required for efficient activation of G proteins. However, technical limitations have precluded a definitive analysis of G protein coupling to monomeric GPCRs in a biochemically defined and membrane-bound system. Here we demonstrate that a prototypical GPCR, the beta2-adrenergic receptor (beta2AR), can be incorporated into a reconstituted high-density lipoprotein (rHDL) phospholipid bilayer particle together with the stimulatory heterotrimeric G protein, Gs. Single-molecule fluorescence imaging and FRET analysis demonstrate that a single beta2AR is incorporated per rHDL particle. The monomeric beta2AR efficiently activates Gs and displays GTP-sensitive allosteric ligand-binding properties. These data suggest that a monomeric receptor in a lipid bilayer is the minimal functional unit necessary for signaling, and that the cooperativity of agonist binding is due to G protein association with a receptor monomer and not receptor oligomerization.
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MESH Headings
- Animals
- Cattle
- Fluorescence Resonance Energy Transfer
- GTP-Binding Proteins/metabolism
- Humans
- Lipoproteins, HDL/chemistry
- Lipoproteins, HDL/metabolism
- Lipoproteins, HDL/ultrastructure
- Microscopy, Electron, Transmission
- Models, Molecular
- Protein Binding
- Protein Structure, Quaternary
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-2/isolation & purification
- Receptors, Adrenergic, beta-2/metabolism
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Affiliation(s)
- Matthew R. Whorton
- *Department of Pharmacology, University of Michigan Medical School, 1301 Medical Sciences Research Building III, Ann Arbor, MI 48109
| | - Michael P. Bokoch
- Department of Molecular and Cellular Physiology, Stanford University Medical School, Stanford, CA 94305
| | - Søren G. F. Rasmussen
- Department of Molecular and Cellular Physiology, Stanford University Medical School, Stanford, CA 94305
| | - Bo Huang
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Brian Kobilka
- Department of Molecular and Cellular Physiology, Stanford University Medical School, Stanford, CA 94305
| | - Roger K. Sunahara
- *Department of Pharmacology, University of Michigan Medical School, 1301 Medical Sciences Research Building III, Ann Arbor, MI 48109
- To whom correspondence should be addressed. E-mail:
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48
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Meng F, Ma H. A Comparison between Photon Counting Histogram and Fluorescence Intensity Distribution Analysis. J Phys Chem B 2006; 110:25716-20. [PMID: 17181211 DOI: 10.1021/jp063845r] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photon counting histogram (PCH) and fluorescence intensity distribution analysis (FIDA) are two methods that were developed independently but reported almost simultaneously. Both of them have been successfully applied to fluorescence fluctuation spectroscopy (FFS). Though publications have indicated that they are theoretically equivalent, they are still commonly considered as different methods, especially in their ways to treat the point spread functions (PSFs). In this paper, the two methods are examined in detail for a direct comparison. After a direct proof of the theoretical equivalence, the authors further point out that PCH and FIDA are completely equivalent in the way of modeling PSFs; that is, any modeling approach developed from one of them can always be applied to the other. It is also demonstrated that simplified FIDA and PCH formulas in the form of power series can be applied for fast and precise numerical calculations. The two methods are also compared for their merits in the calculation efficiency.
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Affiliation(s)
- Fanbo Meng
- Department of Physics and The Key Lab of Atomic and Molecular Nano Sciences, Ministry of Education, Tsinghua University, Beijing 100084, China
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49
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Terada N, Shimozawa T, Ishiwata S, Funatsu T. Size distribution of linear and helical polymers in actin solution analyzed by photon counting histogram. Biophys J 2006; 92:2162-71. [PMID: 17172301 PMCID: PMC1861771 DOI: 10.1529/biophysj.106.098871] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actin is a ubiquitous protein that is a major component of the cytoskeleton, playing an important role in muscle contraction and cell motility. At steady state, actin monomers and filaments (F-actin) coexist, and actin subunits continuously attach and detach at the filament ends. However, the size distribution of actin oligomers in F-actin solution has never been clarified. In this study, we investigated the size distribution of actin oligomers using photon-counting histograms. For this purpose, actin was labeled with a fluorescent dye, and the emitted photons were detected by confocal optics (the detection volume was of femtoliter (fL) order). Photon-counting histograms were analyzed to obtain the number distribution of actin oligomers in the detection area from their brightness, assuming that the brightness of an oligomer was proportional to the number of protomers. We found that the major populations at physiological ionic strength were 1-5mers. For data analysis, we successfully applied the theory of linear and helical aggregations of macromolecules. The model postulates three states of actin, i.e., monomers, linear polymers, and helical polymers. Here we obtained three parameters: the equilibrium constants for polymerization of linear polymers, K(l)=(5.2 +/- 1.1) x 10(6) M(-1), and helical polymers, K(h)=(1.6 +/- 0.5) x 10(7) M(-1); and the ratio of helical to linear trimers, gamma = (3.6 +/- 2.3) x 10(-2). The excess free energy of transforming a linear trimer to a helical trimer, which is assumed to be a nucleus for helical polymers, was calculated to be 2.0 kcal/mol. These analyses demonstrate that the oligomeric phase at steady state is predominantly composed of linear 1-5mers, and the transition from linear to helical polymers occurs on the level of 5-7mers.
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Affiliation(s)
- Naofumi Terada
- Integrated Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
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50
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Unruh JR, Price ES, Molla RG, Hui R, Johnson CK. Evaluation of a femtosecond fiber laser for two-photon fluorescence correlation spectroscopy. Microsc Res Tech 2006; 69:891-3. [PMID: 16886226 DOI: 10.1002/jemt.20358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This work evaluates a femtosecond fiber laser for use in two-photon fluorescence fluctuation spectroscopy. Fiber lasers present an attractive alternative to Ti:Sapphire systems because of their compact size and portability. Autocorrelation of the second harmonic generation signal from the laser demonstrates that its stability is sufficient for two-photon fluorescence correlation spectroscopy. Fluorescence correlation spectroscopy autocorrelation traces were well fit by a Gaussian-Lorentzian squared model with a beam waist near the diffraction limit for the 810 nm wavelength. A photon counting histogram collected with this system also fit nicely to a single-species model, further demonstrating the quality of the focal shape. The authors conclude that the output from the femtosecond fiber laser is sufficiently stable and has a high enough quality beam shape for fluctuation fluorescence methods, and thus represents an effective, compact, readily portable two-photon excitation source.
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Affiliation(s)
- Jay R Unruh
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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