151
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Dodecyl and octyl esters of fluorescein as protonophores and uncouplers of oxidative phosphorylation in mitochondria at submicromolar concentrations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:149-58. [DOI: 10.1016/j.bbabio.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/12/2013] [Accepted: 09/18/2013] [Indexed: 11/18/2022]
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152
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Klymchenko AS, Kreder R. Fluorescent probes for lipid rafts: from model membranes to living cells. ACTA ACUST UNITED AC 2013; 21:97-113. [PMID: 24361047 DOI: 10.1016/j.chembiol.2013.11.009] [Citation(s) in RCA: 335] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/22/2013] [Accepted: 11/04/2013] [Indexed: 01/10/2023]
Abstract
Membrane microdomains (rafts) remain one of the controversial issues in biophysics. Fluorescent molecular probes, which make these lipid nanostructures visible through optical techniques, are one of the tools currently used to study lipid rafts. The most common are lipophilic fluorescent probes that partition specifically into liquid ordered or liquid disordered phase. Their partition depends on the lipid composition of a given phase, which complicates their use in cellular membranes. A second class of probes is based on environment-sensitive dyes, which partition into both phases, but stain them by different fluorescence color, intensity, or lifetime. These probes can directly address the properties of each separate phase, but their cellular applications are still limited. The present review focuses on summarizing the current state in the field of developing and applying fluorescent molecular probes to study lipid rafts. We highlight an urgent need to develop new probes, specifically adapted for cell plasma membranes and compatible with modern fluorescence microscopy techniques to push the understanding of membrane microdomains forward.
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Affiliation(s)
- Andrey S Klymchenko
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 ILLKIRCH, France.
| | - Rémy Kreder
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 ILLKIRCH, France
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153
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Bag N, Wohland T. Imaging fluorescence fluctuation spectroscopy: new tools for quantitative bioimaging. Annu Rev Phys Chem 2013; 65:225-48. [PMID: 24328446 DOI: 10.1146/annurev-physchem-040513-103641] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence fluctuation spectroscopy (FFS) techniques provide information at the single-molecule level with excellent time resolution. Usually applied at a single spot in a sample, they have been recently extended into imaging formats, referred to as imaging FFS. They provide spatial information at the optical diffraction limit and temporal information in the microsecond to millisecond range. This review provides an overview of the different modalities in which imaging FFS techniques have been implemented and discusses present imaging FFS capabilities and limitations. A combination of imaging FFS and nanoscopy would allow one to record information with the detailed spatial information of nanoscopy, which is ∼20 nm and limited only by fluorophore size and labeling density, and the time resolution of imaging FFS, limited by the fluorescence lifetime. This combination would provide new insights into biological events by providing spatiotemporal resolution at unprecedented levels.
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Affiliation(s)
- Nirmalya Bag
- Departments of Biological Sciences and Chemistry, and NUS Center for Bio-Imaging Sciences (CBIS), National University of Singapore, 117557 Singapore; ,
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154
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Morelli E, Salvadori E, Bizzarri R, Cioni P, Gabellieri E. Interaction of CdSe/ZnS quantum dots with the marine diatom Phaeodactylum tricornutum and the green alga Dunaliella tertiolecta: A biophysical approach. Biophys Chem 2013; 182:4-10. [DOI: 10.1016/j.bpc.2013.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/11/2022]
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155
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Abstract
The structural flexibility found in human immunodeficiency virus (HIV) envelope glycoproteins creates a complex relationship between antigenicity and sensitivity to antiviral antibodies. The study of this issue in the context of viral particles is particularly problematic as conventional virus capture approaches can perturb antigenicity profiles. Here, we employed a unique analytical system based on fluorescence correlation spectroscopy (FCS), which measures antibody-virion binding with all reactants continuously in solution. Panels of nine anti-envelope monoclonal antibodies (MAbs) and five virus types were used to connect antibody binding profiles with neutralizing activities. Anti-gp120 MAbs against the 2G12 or b12 epitope, which marks functional envelope structures, neutralized viruses expressing CCR5-tropic envelopes and exhibited efficient virion binding in solution. MAbs against CD4-induced (CD4i) epitopes considered hidden on functional envelope structures poorly bound these viruses and were not neutralizing. Anti-gp41 MAb 2F5 was neutralizing despite limited virion binding. Similar antigenicity patterns occurred on CXCR4-tropic viruses, except that anti-CD4i MAbs 17b and 19e were neutralizing despite little or no virion binding. Notably, anti-gp120 MAb PG9 and anti-gp41 MAb F240 bound to both CCR5-tropic and CXCR4-tropic viruses without exerting neutralizing activity. Differences in the virus production system altered the binding efficiencies of some antibodies but did not enhance antigenicity of aberrant gp120 structures. Of all viruses tested, only JRFL pseudoviruses showed a direct relationship between MAb binding efficiency and neutralizing potency. Collectively, these data indicate that the antigenic profiles of free HIV particles generally favor the exposure of functional over aberrant gp120 structures. However, the efficiency of virion-antibody interactions in solution inconsistently predicts neutralizing activity in vitro.
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156
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Wang S, Jing B, Zhu Y. Molecule motion at polymer brush interfaces from single-molecule experimental perspectives. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/polb.23414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shengqin Wang
- Institute of Materials Research and Engineering; A*STAR (Agency for Science, Technology and Research); 3 Research Link Singapore 117602 Singapore
| | - Benxin Jing
- Department of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame Indiana 46556
| | - Yingxi Zhu
- Department of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame Indiana 46556
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157
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Peptide-induced membrane leakage by lysine derivatives of gramicidin A in liposomes, planar bilayers, and erythrocytes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2428-35. [DOI: 10.1016/j.bbamem.2013.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/10/2013] [Accepted: 06/13/2013] [Indexed: 11/21/2022]
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158
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Du C, Liu L, Zhang L, Guo J, Guo J, Ma H, He Y. Multi-channel hyperspectral fluorescence detection excited by coupled plasmon-waveguide resonance. SENSORS (BASEL, SWITZERLAND) 2013; 13:13892-13902. [PMID: 24129023 PMCID: PMC3859097 DOI: 10.3390/s131013892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/06/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
We propose in this paper a biosensor scheme based on coupled plasmon-waveguide resonance (CPWR) excited fluorescence spectroscopy. A symmetrical structure that offers higher surface electric field strengths, longer surface propagation lengths and depths is developed to support guided waveguide modes for the efficient excitation of fluorescence. The optimal parameters for the sensor films are theoretically and experimentally investigated, leading to a detection limit of 0.1 nM (for a Cy5 solution). Multiplex analysis possible with the fluorescence detection is further advanced by employing the hyperspectral fluorescence technique to record the full spectra for every pixel on the sample plane. We demonstrate experimentally that highly overlapping fluorescence (Cy5 and Dylight680) can be distinguished and ratios of different emission sources can be determined accurately. This biosensor shows great potential for multiplex detections of fluorescence analytes.
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Affiliation(s)
- Chan Du
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; E-Mails: (C.D.); (J.G.); (J.G.); (H.M.)
- Department of Physics, Tsinghua University, Beijing 100084, China
| | - Le Liu
- Laboratory of Advanced Power Source, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; E-Mail:
| | - Lin Zhang
- Graduate School at Shenzhen, Harbin Institute of Technology, Shenzhen 518055, China; E-Mail:
| | - Jun Guo
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; E-Mails: (C.D.); (J.G.); (J.G.); (H.M.)
| | - Jihua Guo
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; E-Mails: (C.D.); (J.G.); (J.G.); (H.M.)
| | - Hui Ma
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; E-Mails: (C.D.); (J.G.); (J.G.); (H.M.)
- Department of Physics, Tsinghua University, Beijing 100084, China
| | - Yonghong He
- Shenzhen Key Laboratory for Minimal Invasive Medical Technologies, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; E-Mails: (C.D.); (J.G.); (J.G.); (H.M.)
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159
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Balbo J, Mereghetti P, Herten DP, Wade RC. The shape of protein crowders is a major determinant of protein diffusion. Biophys J 2013; 104:1576-84. [PMID: 23561534 DOI: 10.1016/j.bpj.2013.02.041] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/29/2013] [Accepted: 02/19/2013] [Indexed: 11/15/2022] Open
Abstract
As a model for understanding how molecular crowding influences diffusion and transport of proteins in cellular environments, we combined experimental and theoretical approaches to study the diffusion of proteins in highly concentrated protein solutions. Bovine serum albumin and γ-Globulin were chosen as molecular crowders and as tracers. These two proteins are representatives of the main types of plasma protein and have different shapes and sizes. Solutions consisting of one or both proteins were studied. The self-diffusion coefficients of the fluorescently labeled tracer proteins were measured by means of fluorescence correlation spectroscopy at a total protein concentration of up to 400 g/L. γ-Globulin is found to have a stronger influence as a crowder on the tracer self-diffusion coefficient than Bovine serum albumin. Brownian dynamics simulations show that the excluded volume and the shape of the crowding protein have a significantly stronger influence on translational and rotational diffusion coefficients, as well as transient oligomerization, than hydrodynamic or direct interactions. Anomalous subdiffusion, which is not observed at the experimental fluorescence correlation spectroscopy timescales (>100 μs), appears only at very short timescales (<1 μs) in the simulations due to steric effects of the proteins. We envision that the combined experimental and computational approach employed here can be developed to unravel the different biophysical contributions to protein motion and interaction in cellular environments by systematically varying protein properties such as molecular weight, size, shape, and electrostatic interactions.
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Affiliation(s)
- Jessica Balbo
- CellNetworks Cluster and Physikalisch-Chemisches Institut, Heidelberg University, Heidelberg, Germany
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160
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FRAP in Pharmaceutical Research: Practical Guidelines and Applications in Drug Delivery. Pharm Res 2013; 31:255-70. [DOI: 10.1007/s11095-013-1146-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/09/2013] [Indexed: 01/02/2023]
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161
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Concentration measurement of particles by number fluctuation in dynamic light backscattering. POWDER TECHNOL 2013. [DOI: 10.1016/j.powtec.2013.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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162
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Nadappuram BP, McKelvey K, Al Botros R, Colburn AW, Unwin PR. Fabrication and characterization of dual function nanoscale pH-scanning ion conductance microscopy (SICM) probes for high resolution pH mapping. Anal Chem 2013; 85:8070-4. [PMID: 23919610 DOI: 10.1021/ac401883n] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The easy fabrication and use of nanoscale dual function pH-scanning ion conductance microscopy (SICM) probes is reported. These probes incorporate an iridium oxide coated carbon electrode for pH measurement and an SICM barrel for distance control, enabling simultaneous pH and topography mapping. These pH-SICM probes were fabricated rapidly from laser pulled theta quartz pipets, with the pH electrode prepared by in situ carbon filling of one of the barrels by the pyrolytic decomposition of butane, followed by electrodeposition of a thin layer of hydrous iridium oxide. The other barrel was filled with an electrolyte solution and Ag/AgCl electrode as part of a conductance cell for SICM. The fabricated probes, with pH and SICM sensing elements typically on the 100 nm scale, were characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and various electrochemical measurements. They showed a linear super-Nernstian pH response over a range of pH (pH 2-10). The capability of the pH-SICM probe was demonstrated by detecting both pH and topographical changes during the dissolution of a calcite microcrystal in aqueous solution. This system illustrates the quantitative nature of pH-SICM imaging, because the dissolution process changes the crystal height and interfacial pH (compared to bulk), and each is sensitive to the rate. Both measurements reveal similar dissolution rates, which are in agreement with previously reported literature values measured by classical bulk methods.
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163
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Hu Y, Cheng X, Daniel Ou-Yang H. Enumerating virus-like particles in an optically concentrated suspension by fluorescence correlation spectroscopy. BIOMEDICAL OPTICS EXPRESS 2013; 4:1646-53. [PMID: 24049685 PMCID: PMC3771835 DOI: 10.1364/boe.4.001646] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/14/2013] [Accepted: 07/23/2013] [Indexed: 06/02/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is one of the most sensitive methods for enumerating low concentration nanoparticles in a suspension. However, biological nanoparticles such as viruses often exist at a concentration much lower than the FCS detection limit. While optically generated trapping potentials are shown to effectively enhance the concentration of nanoparticles, feasibility of FCS for enumerating field-enriched nanoparticles requires understanding of the nanoparticle behavior in the external field. This paper reports an experimental study that combines optical trapping and FCS to examine existing theoretical predictions of particle concentration. Colloidal suspensions of polystyrene (PS) nanospheres and HIV-1 virus-like particles are used as model systems. Optical trapping energies and statistical analysis are used to discuss the applicability of FCS for enumerating nanoparticles in a potential well produced by a force field.
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Affiliation(s)
- Yi Hu
- Department of Physics, Lehigh University, Bethlehem, PA 18015
USA
- Current address: Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, MD 21201
USA
| | - Xuanhong Cheng
- Department of Material Science and Engineering, Lehigh University, Bethlehem, PA 18015
USA
- Emulsion Polymers Institute, Lehigh University, Bethlehem, PA 18015
USA
| | - H. Daniel Ou-Yang
- Department of Physics, Lehigh University, Bethlehem, PA 18015
USA
- Emulsion Polymers Institute, Lehigh University, Bethlehem, PA 18015
USA
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164
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Heikal AA. Time-resolved fluorescence anisotropy and fluctuation correlation analysis of major histocompatibility complex class I proteins in fibroblast cells. Methods 2013; 66:283-91. [PMID: 23811298 DOI: 10.1016/j.ymeth.2013.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/12/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022] Open
Abstract
Major histocompatibility complex class I proteins, MHC(I), are expressed in almost all nucleated cells and synthesized in the endoplasmic reticulum (ER). The orientation and mobility of these complexes are crucial in their biological function in the immune system, i.e., the cytosolic pathogen peptides loading and their presentation to T-cell receptors at the plasma membrane, where cell destruction is triggered. Here, we investigate the structural flexibility and associations of GFP-encoded MHC(I) alleles (H2L(d)), namely H2L(d)GFPin and H2L(d)GFPout, in cultured mouse fibroblast cells. Time-resolved fluorescence anisotropy of H2L(d)GFPin in the ER indicates a dominant overall tumbling motion of 56±7 ns (ER), with a fast conformational flexibility, as compared with a restricted rotation of H2L(d)GFPout. At the single-molecule level, the diffusion coefficient of H2L(d)GFPin and H2L(d)GFPout in the ER is (1.8±0.5)×10(-9) and (2.1±0.6)×10(-9) cm(2)/s, respectively, as revealed by fluorescence correlation spectroscopy. A complementary immunoblotting of H2L(d)GFP constructs, isolated from mouse fibroblast cells, reveals band at 75 kDa as compared with 29 kDa of the free EGFP. These real-time dynamics provide new insights into the structural flexibility and intracellular associations of GFP-labeled MHC(I) alleles (H2L(d)) in living cells.
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Affiliation(s)
- Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota-Duluth, Duluth, MN 55812, USA; Department of Pharmacy Practice and Pharmaceutical Sciences, College of Pharmacy, University of Minnesota-Duluth, Duluth, MN 55812, USA.
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165
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Sterling SM, Allgeyer ES, Fick J, Prudovsky I, Mason MD, Neivandt DJ. Phospholipid diffusion coefficients of cushioned model membranes determined via z-scan fluorescence correlation spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7966-74. [PMID: 23705855 PMCID: PMC3758428 DOI: 10.1021/la400768s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Model cellular membranes enable the study of biological processes in a controlled environment and reduce the traditional challenges associated with live or fixed cell studies. However, model membrane systems based on the air/water or oil/solution interface do not allow for incorporation of transmembrane proteins or for the study of protein transport mechanisms. Conversely, a phospholipid bilayer deposited via the Langmuir-Blodgett/Langmuir-Schaefer method on a hydrogel layer is potentially an effective mimic of the cross section of a biological membrane and facilitates both protein incorporation and transport studies. Prior to application, however, such membranes must be fully characterized, particularly with respect to the phospholipid bilayer phase transition temperature. Here we present a detailed characterization of the phase transition temperature of the inner and outer leaflets of a chitosan supported model membrane system. Specifically, the lateral diffusion coefficient of each individual leaflet has been determined as a function of temperature. Measurements were performed utilizing z-scan fluorescence correlation spectroscopy (FCS), a technique that yields calibration-free diffusion information. Analysis via the method of Wawrezinieck and co-workers revealed that phospholipid diffusion changes from raftlike to free diffusion as the temperature is increased-an insight into the dynamic behavior of hydrogel supported membranes not previously reported.
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Affiliation(s)
- Sarah M. Sterling
- Department of Chemical and Biological Engineering, University of Maine, Orono, Maine 04469
- Graduate School of Biomedical Sciences, University of Maine, Orono, Maine 04469
| | - Edward S. Allgeyer
- Department of Physics and Astronomy, University of Maine, Orono, Maine 04469
| | - Jörg Fick
- Department of Chemical and Biological Engineering, University of Maine, Orono, Maine 04469
| | - Igor Prudovsky
- Graduate School of Biomedical Sciences, University of Maine, Orono, Maine 04469
- Maine Medical Center Research Institute, Scarborough, ME 04074
- Institute for Molecular Biophysics, Orono, Maine 04469
| | - Michael D. Mason
- Department of Chemical and Biological Engineering, University of Maine, Orono, Maine 04469
- Institute for Molecular Biophysics, Orono, Maine 04469
| | - David J. Neivandt
- Department of Chemical and Biological Engineering, University of Maine, Orono, Maine 04469
- Graduate School of Biomedical Sciences, University of Maine, Orono, Maine 04469
- Institute for Molecular Biophysics, Orono, Maine 04469
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166
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Varriale A, Marabotti A, Mei G, Staiano M, D’Auria S. Correlation spectroscopy and molecular dynamics simulations to study the structural features of proteins. PLoS One 2013; 8:e64840. [PMID: 23750215 PMCID: PMC3672191 DOI: 10.1371/journal.pone.0064840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/19/2013] [Indexed: 11/24/2022] Open
Abstract
In this work, we used a combination of fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulation methodologies to acquire structural information on pH-induced unfolding of the maltotriose-binding protein from Thermus thermophilus (MalE2). FCS has emerged as a powerful technique for characterizing the dynamics of molecules and it is, in fact, used to study molecular diffusion on timescale of microsecond and longer. Our results showed that keeping temperature constant, the protein diffusion coefficient decreased from 84±4 µm2/s to 44±3 µm2/s when pH was changed from 7.0 to 4.0. An even more marked decrease of the MalE2 diffusion coefficient (31±3 µm2/s) was registered when pH was raised from 7.0 to 10.0. According to the size of MalE2 (a monomeric protein with a molecular weight of 43 kDa) as well as of its globular native shape, the values of 44 µm2/s and 31 µm2/s could be ascribed to deformations of the protein structure, which enhances its propensity to form aggregates at extreme pH values. The obtained fluorescence correlation data, corroborated by circular dichroism, fluorescence emission and light-scattering experiments, are discussed together with the MD simulations results.
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Affiliation(s)
- Antonio Varriale
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
- * E-mail: (AV); (SD)
| | - Anna Marabotti
- Department of Chemistry and Biology, University of Salerno, Fisciano (SA), Italy
- Laboratory for Bioinformatics, ISA-CNR, Avellino, Italy
| | - Giampiero Mei
- Department of Experimental Medicine and Biochemical Sciences, University of Roma “Tor Vergata”, Rome, Italy
| | - Maria Staiano
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
| | - Sabato D’Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
- * E-mail: (AV); (SD)
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167
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Wang J, Huang X, Ruan L, Lan T, Ren J. Size exclusion chromatography as a universal method for the purification of quantum dots bioconjugates. Electrophoresis 2013; 34:1764-71. [DOI: 10.1002/elps.201200649] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Jinjie Wang
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites; Shanghai Jiaotong University; Shanghai; P. R. China
| | - Xiangyi Huang
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites; Shanghai Jiaotong University; Shanghai; P. R. China
| | - Lingao Ruan
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites; Shanghai Jiaotong University; Shanghai; P. R. China
| | - Tao Lan
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites; Shanghai Jiaotong University; Shanghai; P. R. China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites; Shanghai Jiaotong University; Shanghai; P. R. China
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168
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Abstract
We present an overview on the applicability of fluorescence correlation
spectroscopy (FCS) for the accurate determination of translational diffusion
coefficients and thus, via the Stokes–Einstein relation, of molecular size. We
consider several of the most common sources of optical aberrations and their
impact on the outcome of conventional FCS measurements. We describe also a new
variant of FCS, dual-focus FCS, which is robust against most of the considered
aberrations, and we report reference values of diffusion coefficients for
several fluorescent dyes across the visible spectrum.
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Affiliation(s)
- Jörg Enderlein
- 1Third Institute of Physics–Biophysics, Georg-August-University, Göttingen, Germany
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169
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Höfling F, Franosch T. Anomalous transport in the crowded world of biological cells. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:046602. [PMID: 23481518 DOI: 10.1088/0034-4885/76/4/046602] [Citation(s) in RCA: 589] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.
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Affiliation(s)
- Felix Höfling
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, and Institut für Theoretische Physik IV, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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170
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Prudovsky I, Kumar TKS, Sterling S, Neivandt D. Protein-phospholipid interactions in nonclassical protein secretion: problem and methods of study. Int J Mol Sci 2013; 14:3734-72. [PMID: 23396106 PMCID: PMC3588068 DOI: 10.3390/ijms14023734] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 12/30/2022] Open
Abstract
Extracellular proteins devoid of signal peptides use nonclassical secretion mechanisms for their export. These mechanisms are independent of the endoplasmic reticulum and Golgi. Some nonclassically released proteins, particularly fibroblast growth factors (FGF) 1 and 2, are exported as a result of their direct translocation through the cell membrane. This process requires specific interactions of released proteins with membrane phospholipids. In this review written by a cell biologist, a structural biologist and two membrane engineers, we discuss the following subjects: (i) Phenomenon of nonclassical protein release and its biological significance; (ii) Composition of the FGF1 multiprotein release complex (MRC); (iii) The relationship between FGF1 export and acidic phospholipid externalization; (iv) Interactions of FGF1 MRC components with acidic phospholipids; (v) Methods to study the transmembrane translocation of proteins; (vi) Membrane models to study nonclassical protein release.
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Affiliation(s)
- Igor Prudovsky
- Maine Medical Center Research Institute, 81 Research Drive, Scarborough, ME 04074, USA
| | | | - Sarah Sterling
- Department of Chemical and Biological Engineering, University of Maine, Orono, ME 04469, USA; E-Mails: (S.S.); (D.N.)
| | - David Neivandt
- Department of Chemical and Biological Engineering, University of Maine, Orono, ME 04469, USA; E-Mails: (S.S.); (D.N.)
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171
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Regestein L, Maskow T, Tack A, Knabben I, Wunderlich M, Lerchner J, Büchs J. Non-invasive online detection of microbial lysine formation in stirred tank bioreactors by using calorespirometry. Biotechnol Bioeng 2013; 110:1386-95. [DOI: 10.1002/bit.24815] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/26/2012] [Accepted: 12/11/2012] [Indexed: 11/10/2022]
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172
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Ciubotaru M, Trexler AJ, Spiridon LN, Surleac MD, Rhoades E, Petrescu AJ, Schatz DG. RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes. Nucleic Acids Res 2013; 41:2437-54. [PMID: 23293004 PMCID: PMC3575807 DOI: 10.1093/nar/gks1294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
During V(D)J recombination, recombination activating gene proteins RAG1 and RAG2 generate DNA double strand breaks within a paired complex (PC) containing two complementary recombination signal sequences (RSSs), the 12RSS and 23RSS, which differ in the length of the spacer separating heptamer and nonamer elements. Despite the central role of the PC in V(D)J recombination, little is understood about its structure. Here, we use fluorescence resonance energy transfer to investigate the architecture of the 23RSS in the PC. Energy transfer was detected in 23RSS substrates in which the donor and acceptor fluorophores flanked the entire RSS, and was optimal under conditions that yield a cleavage-competent PC. The data are most easily explained by a dramatic bend in the 23RSS that reduces the distance between these flanking regions from >160 Å in the linear substrate to <80 Å in the PC. Analysis of multiple fluorescent substrates together with molecular dynamics modeling yielded a model in which the 23RSS adopts a U shape in the PC, with the spacer located centrally within the bend. We propose that this large bend facilitates simultaneous recognition of the heptamer and nonamer, is critical for proper positioning of the active site and contributes to the 12/23 rule.
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Affiliation(s)
- Mihai Ciubotaru
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar St., New Haven, CT 06511, USA
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173
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Selmke M, Schachoff R, Braun M, Cichos F. Twin-focus photothermal correlation spectroscopy. RSC Adv 2013. [DOI: 10.1039/c2ra22061j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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174
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Sanguigno L, Cosenza C, Causa F, Netti PA. Accounting for misalignments and thermal fluctuations in fluorescence correlation spectroscopy experiments on membranes. Analyst 2013; 138:1674-81. [DOI: 10.1039/c2an36681a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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175
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Unsay JD, García-Sáez AJ. Scanning fluorescence correlation spectroscopy in model membrane systems. Methods Mol Biol 2013; 1033:185-205. [PMID: 23996179 DOI: 10.1007/978-1-62703-487-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is an emerging technique employed in biophysical studies that exploits the temporal autocorrelation of fluorescence intensity fluctuations measured in a tiny volume (in the order of fL). The autocorrelation curve derived from the fluctuations can then be fitted with diffusion models to obtain parameters such as diffusion time and number of particles in the diffusion volume/area. Application of FCS to membranes allows studying membrane component dynamics, which includes mobility and interactions between the components. However, FCS encounters several difficulties like accurate positioning and stability of the setup when applied to membranes. Here, we describe the theoretical basis of point FCS as well as the scanning FCS (SFCS) approach, which is a practical way to address the challenges of FCS with membranes. We also list materials necessary for FCS experiments on two model membrane systems: (1) supported lipid bilayers and (2) giant unilamellar vesicles. Finally, we present simple protocols for the preparation of these model membrane systems, calibration of the microscope setup for FCS, and acquisition and analysis of point FCS and SFCS data so that diffusion coefficients and concentrations of fluorescent probes within lipid membranes can be calculated.
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176
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Steger K, Bollmann S, Noé F, Doose S. Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Phys Chem Chem Phys 2013; 15:10435-45. [DOI: 10.1039/c3cp50644d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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177
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Loumaigne M, Vasanthakumar P, Lombardi A, Richard A, Débarre A. One-photon excited luminescence of single gold particles diffusing in solution under pulsed illumination. Phys Chem Chem Phys 2013; 15:4154-62. [DOI: 10.1039/c2cp43294c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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178
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Koynov K, Butt HJ. Fluorescence correlation spectroscopy in colloid and interface science. Curr Opin Colloid Interface Sci 2012. [DOI: 10.1016/j.cocis.2012.09.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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179
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Wang Q, Goldsmith RH, Jiang Y, Bockenhauer SD, Moerner W. Probing single biomolecules in solution using the anti-Brownian electrokinetic (ABEL) trap. Acc Chem Res 2012; 45:1955-64. [PMID: 22616716 DOI: 10.1021/ar200304t] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single-molecule fluorescence measurements allow researchers to study asynchronous dynamics and expose molecule-to-molecule structural and behavioral diversity, which contributes to the understanding of biological macromolecules. To provide measurements that are most consistent with the native environment of biomolecules, researchers would like to conduct these measurements in the solution phase if possible. However, diffusion typically limits the observation time to approximately 1 ms in many solution-phase single-molecule assays. Although surface immobilization is widely used to address this problem, this process can perturb the system being studied and contribute to the observed heterogeneity. Combining the technical capabilities of high-sensitivity single-molecule fluorescence microscopy, real-time feedback control and electrokinetic flow in a microfluidic chamber, we have developed a device called the anti-Brownian electrokinetic (ABEL) trap to significantly prolong the observation time of single biomolecules in solution. We have applied the ABEL trap method to explore the photodynamics and enzymatic properties of a variety of biomolecules in aqueous solution and present four examples: the photosynthetic antenna allophycocyanin, the chaperonin enzyme TRiC, a G protein-coupled receptor protein, and the blue nitrite reductase redox enzyme. These examples illustrate the breadth and depth of information which we can extract in studies of single biomolecules with the ABEL trap. When confined in the ABEL trap, the photosynthetic antenna protein allophycocyanin exhibits rich dynamics both in its emission brightness and its excited state lifetime. As each molecule discontinuously converts from one emission/lifetime level to another in a primarily correlated way, it undergoes a series of state changes. We studied the ATP binding stoichiometry of the multi-subunit chaperonin enzyme TRiC in the ABEL trap by counting the number of hydrolyzed Cy3-ATP using stepwise photobleaching. Unlike ensemble measurements, the observed ATP number distributions depart from the standard cooperativity models. Single copies of detergent-stabilized G protein-coupled receptor proteins labeled with a reporter fluorophore also show discontinuous changes in emission brightness and lifetime, but the various states visited by the single molecules are broadly distributed. As an agonist binds, the distributions shift slightly toward a more rigid conformation of the protein. By recording the emission of a reporter fluorophore which is quenched by reduction of a nearby type I Cu center, we probed the enzymatic cycle of the redox enzyme nitrate reductase. We determined the rate constants of a model of the underlying kinetics through an analysis of the dwell times of the high/low intensity levels of the fluorophore versus nitrite concentration.
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Affiliation(s)
- Quan Wang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Randall H. Goldsmith
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Yan Jiang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Samuel D. Bockenhauer
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - W.E. Moerner
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
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180
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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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181
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Choudhury SD, Ray K, Lakowicz JR. Silver Nanostructures for Fluorescence Correlation Spectroscopy: Reduced Volumes and Increased Signal Intensities. J Phys Chem Lett 2012; 3:2915-2919. [PMID: 26855696 PMCID: PMC4743895 DOI: 10.1021/jz301229m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a widely used technique to investigate the interactions and dynamics of molecules, below micromolar concentrations. Silver nanostructure (AgNS) substrates can extend the applicability of FCS to higher concentrations, which is useful for many biologically relevant reactions. Additionally, these substrates can improve detection efficiency by increasing fluorescence signal intensities. The ease of preparation of the AgNS substrates in comparison to previously investigated materials prepared by top-down nanofabrication is expected to make them readily available and suitable for various FCS applications.
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182
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Kinkhabwala AA, Yu Z, Fan S, Moerner W. Fluorescence correlation spectroscopy at high concentrations using gold bowtie nanoantennas. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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183
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Blakeley BD, DePorter SM, Mohan U, Burai R, Tolbert BS, McNaughton BR. Methods for identifying and characterizing interactions involving RNA. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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184
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Prashanthi S, Lanke SR, Kumar PH, Siva D, Bangal PR. Determination of hydrodynamic properties of bare gold and silver nanoparticles as a fluorescent probe using its surface-plasmon-induced photoluminescence by fluorescence correlation spectroscopy. APPLIED SPECTROSCOPY 2012; 66:835-841. [PMID: 22710248 DOI: 10.1366/11-06511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Noble-metal nanoparticles labeled with fluorescent molecules are used in a variety of applications requiring the measurement of size and diffusion properties of single nanoprobes. We have successfully used intrinsic surface-plasmon-induced photoluminescence (SPPL) signatures of monodispersed bare gold and silver nanoparticles in water to detect and measure their precise diffusion coefficient, concentration and hydrodynamic radius by fluorescence correlation spectroscopy (FCS). Measurement of the effective hydrodynamic radius confirms particle size to be 80 ± 8 and 64 ± 14 nm for gold and silver, respectively, which is in excellent agreement with scanning electron microscopic measurements made on the same particles. Detection of bare gold and silver nanoparticles at the single-molecule level with moderately high value of "per particle brightness" (PPB) confirms those particles to be used as fluorescent probes in biological research and in different medical and biotechnology applications where fluorescence detection plays a vital role. Additionally, these results demonstrate an alternative method for measuring hydrodynamic properties, particularly the size-distribution of bare noble-metal nanoparticles in solution using data-fitting algorithm for FCS based on the maximum entropy method (MEMFCS).
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Affiliation(s)
- Suthari Prashanthi
- Inorganic and Physical Chemistry Division, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India
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185
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Tachikawa T, Majima T. Single-molecule, single-particle approaches for exploring the structure and kinetics of nanocatalysts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8933-8943. [PMID: 22324887 DOI: 10.1021/la300177h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this Article, we focus on the in situ observation of photochemical reactions on individual nanoobjects of solid catalysts using single-molecule, single-particle fluorescence spectroscopy. The use of high-resolution imaging techniques with suitable fluorogenic probes enables us to determine the location of the catalytically active sites that are related to the structural heterogeneities on the surface of the solid catalyst and the temporal fluctuation of photochemical reactivity. Furthermore, we present the real-time observation of metastable gold nanoclusters in polymer matrices at the single-cluster level. This Article encourages readers to explore the nanoworld in terms of practical applications in many fields such as fundamental physics and chemistry.
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Affiliation(s)
- Takashi Tachikawa
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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186
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Sergeev M, Godin AG, Kao L, Abuladze N, Wiseman PW, Kurtz I. Determination of membrane protein transporter oligomerization in native tissue using spatial fluorescence intensity fluctuation analysis. PLoS One 2012; 7:e36215. [PMID: 22558387 PMCID: PMC3338697 DOI: 10.1371/journal.pone.0036215] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Membrane transporter proteins exist in a complex dynamic equilibrium between various oligomeric states that include monomers, dimers, dimer of dimers and higher order oligomers. Given their sub-optical microscopic resolution size, the oligomerization state of membrane transporters is difficult to quantify without requiring tissue disruption and indirect biochemical methods. Here we present the application of a fluorescence measurement technique which combines fluorescence image moment analysis and spatial intensity distribution analysis (SpIDA) to determine the oligomerization state of membrane proteins in situ. As a model system we analyzed the oligomeric state(s) of the electrogenic sodium bicarbonate cotransporter NBCe1-A in cultured cells and in rat kidney. The approaches that we describe offer for the first time the ability to investigate the oligomeric state of membrane transporter proteins in their native state.
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Affiliation(s)
- Mikhail Sergeev
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Antoine G. Godin
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Liyo Kao
- David Geffen School Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Natalia Abuladze
- David Geffen School Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Paul W. Wiseman
- Department of Physics, McGill University, Montréal, Québec, Canada
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Ira Kurtz
- David Geffen School Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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187
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Abstract
High-throughput screening (HTS) is a key process used in drug discovery to identify hits from compound libraries that may become leads for medicinal chemistry optimization. This updated overview discusses the utilization of compound libraries, compounds derived from combinatorial and parallel synthesis campaigns and natural product sources; creation of mother and daughter plates; and compound storage, handling, and bar coding in HTS. The unit also presents an overview of established and emerging assay technologies (i.e., time-resolved fluorescence, fluorescence polarization, fluorescence-correlation spectroscopy, functional whole cell assays, and high-content assays) and their integration in automation hardware and IT systems. This revised unit provides updated descriptions of state-of-the-art instrumentation and technologies in this rapidly changing environment. The section on assay methodologies now also covers enzyme complementation assays and methods for high-throughput screening of ion channel activities. Finally, a section on criteria for assay robustness is included discussing the Z'-factor, which is now a widely accepted criterion for evaluation and validation of high throughput screening assays.
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Affiliation(s)
- Michael Entzeroth
- Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), Singapore
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188
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Liu H, Dong C, Huang X, Ren J. Spatially Resolved Scattering Correlation Spectroscopy Using a Total Internal Reflection Configuration. Anal Chem 2012; 84:3561-7. [DOI: 10.1021/ac2031833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Heng Liu
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Chaoqing Dong
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Xiangyi Huang
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
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189
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Chatterjee S, Lee JB, Valappil NV, Luo D, Menon VM. Probing Y-shaped DNA structure with time-resolved FRET. NANOSCALE 2012; 4:1568-1571. [PMID: 22297682 DOI: 10.1039/c2nr12039a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Self-assembly based on nucleic acid systems has become highly attractive for bottom-up fabrication of programmable matter due to the highly selective molecular recognition property of biomolecules. In this context, Y-shaped DNA (Y-DNA) provides an effective building block for forming unique self-assembled large-scale architectures. The dimension and growth of the nano- and microstructures depend significantly on the configurational stability of Y-DNA as a building block. Here we present structural studies of Y-DNA systems using a time-resolved FRET (Förster resonance energy transfer) technique. A fluorophore (Alexa 488) and an acceptor (DABCYL) were placed at two different ends of Y-DNA, and the lifetime of the fluorophore was measured to probe the relative distance between the donor and acceptor. Our results confirmed different distances between the arms of the Y-DNA and highlighted the overall structural integrity of the Y-DNA system as a leading building block for molecular self-assembly. Temperature dependent lifetime measurements indicated configurational changes in the overall Y-DNA nanoarchitecture above 40 °C.
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Affiliation(s)
- Subhasish Chatterjee
- Department of Physics, Queens College, and the Graduate Center of CUNY, 65-30 Kissena Blvd., Flushing, NY 13367, USA
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190
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Haldar S, Chattopadhyay K. Interconnection of salt-induced hydrophobic compaction and secondary structure formation depends on solution conditions: revisiting early events of protein folding at single molecule resolution. J Biol Chem 2012; 287:11546-55. [PMID: 22303014 DOI: 10.1074/jbc.m111.315648] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea.
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Affiliation(s)
- Shubhasis Haldar
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council for Scientific and Industrial Research, 4 Raja S.C. Mullick Rd., Kolkata 700032, India
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191
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Fluorescence Correlation Spectroscopy and Fluorescence Recovery After Photobleaching to study receptor kinase mobility in planta. Methods Mol Biol 2011; 779:225-42. [PMID: 21837570 DOI: 10.1007/978-1-61779-264-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Plasma-membrane-localized receptor kinases are essential for cell-cell communication and as sensors for the extracellular environment. Receptor function is dependent on their distribution in the membrane and interaction with other proteins that are either membrane-localized, present in the cytoplasm, or in the extracellular space. The organized distribution and mobility of receptor kinases is, therefore, thought to regulate the efficiency of downstream signaling. This chapter describes two methods to study receptor mobility in the plasma membrane. Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Recovery After Photobleaching (FRAP). Especially, the combination of FRAP and FCS provides a better insight into plasma membrane receptor mobility.
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192
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Xing B, Jiang T, Wu X, Liew R, Zhou J, Zhang D, Yeow EKL. Molecular Interactions between Glycopeptide Vancomycin and Bacterial Cell Wall Peptide Analogues. Chemistry 2011; 17:14170-7. [DOI: 10.1002/chem.201102195] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Indexed: 11/11/2022]
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193
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Intrinsic Motions in the N-Terminal Domain of an Ionotropic Glutamate Receptor Detected by Fluorescence Correlation Spectroscopy. J Mol Biol 2011; 414:96-105. [DOI: 10.1016/j.jmb.2011.09.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 09/01/2011] [Accepted: 09/22/2011] [Indexed: 01/20/2023]
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194
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Zustiak SP, Nossal R, Sackett DL. Hindered diffusion in polymeric solutions studied by fluorescence correlation spectroscopy. Biophys J 2011; 101:255-64. [PMID: 21723836 DOI: 10.1016/j.bpj.2011.05.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 05/09/2011] [Accepted: 05/13/2011] [Indexed: 11/15/2022] Open
Abstract
Diffusion of molecules in the crowded and charged interior of the cell has long been of interest for understanding cellular processes. Here, we introduce a model system of hindered diffusion that includes both crowding and binding. In particular, we obtained the diffusivity of the positively charged protein, ribonuclease A (RNase), in solutions of dextrans of various charges (binding) and concentrations (crowding), as well as combinations of both, in a buffer of physiological ionic strength. Using fluorescence correlation spectroscopy, we observed that the diffusivity of RNase was unaffected by the presence of positively charged or neutral dextrans in the dilute regime but was affected by crowding at higher polymer concentrations. Conversely, protein diffusivity was significantly reduced by negatively charged dextrans, even at 0.4 μM (0.02% w/v) dextran. The diffusivity of RNase decreased with increasing concentrations of negative dextran, and the amount of bound RNase increased until it reached a plateau of ∼80% bound RNase. High salt concentrations were used to establish the electrostatic nature of the binding. Binding of RNase to the negatively charged dextrans was further confirmed by ultrafiltration.
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Affiliation(s)
- Silviya P Zustiak
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Development, National Institutes of Health, Bethesda, Maryland, USA.
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195
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Abstract
Prions are infectious, self-propagating protein conformations. [PSI+], [RNQ+] and [URE3] are well characterized prions in Saccharomyces cerevisiae and represent the aggregated states of the translation termination factor Sup35, a functionally unknown protein Rnq1, and a regulator of nitrogen metabolism Ure2, respectively. Overproduction of Sup35 induces the de novo appearance of the [PSI+] prion in [RNQ+] or [URE3] strain, but not in non-prion strain. However, [RNQ+] and [URE3] prions themselves, as well as overexpression of a mutant Rnq1 protein, Rnq1Δ100, and Lsm4, hamper the maintenance of [PSI+]. These findings point to a bipolar activity of [RNQ+], [URE3], Rnq1Δ100, and Lsm4, and probably other yeast prion proteins as well, for the fate of [PSI+] prion. Possible mechanisms underlying the apparent bipolar activity of yeast prions will be discussed.
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Affiliation(s)
- Hiroshi Kurahashi
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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196
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Sagle LB, Ruvuna LK, Ruemmele JA, Van Duyne RP. Advances in localized surface plasmon resonance spectroscopy biosensing. Nanomedicine (Lond) 2011; 6:1447-62. [DOI: 10.2217/nnm.11.117] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In recent years, localized surface plasmon resonance (LSPR) spectroscopy advancements have made it a sensitive, flexible tool for probing biological interactions. Here, we describe the basic principles of this nanoparticle-based sensing technique, the ways nanoparticles can be tailored to optimize sensing, and examples of novel LSPR spectroscopy applications. These include detecting small molecules via protein conformational changes and resonance LSPR spectroscopy, as well as coupling LSPR with mass spectrometry to identify bound analytes. The last few sections highlight the advantages of single nanoparticle LSPR, in that it lowers limits of detection, allows multiplexing on the nanometer scale, and enables free diffusion of sensors in solution. The cases discussed herein illustrate creative ways that LSPR spectroscopy has been improved to achieve new sensing capabilities.
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Affiliation(s)
- Laura B Sagle
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, Evanston, IL 60208-3113 USA
| | - Laura K Ruvuna
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, Evanston, IL 60208-3113 USA
| | - Julia A Ruemmele
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, Evanston, IL 60208-3113 USA
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197
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Melo AM, Prieto M, Coutinho A. The effect of variable liposome brightness on quantifying lipid–protein interactions using fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2559-68. [DOI: 10.1016/j.bbamem.2011.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/01/2011] [Accepted: 06/01/2011] [Indexed: 11/17/2022]
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198
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McCann JJ, Zheng L, Chiantia S, Bowen ME. Domain orientation in the N-Terminal PDZ tandem from PSD-95 is maintained in the full-length protein. Structure 2011; 19:810-20. [PMID: 21645852 DOI: 10.1016/j.str.2011.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/24/2011] [Accepted: 02/21/2011] [Indexed: 12/19/2022]
Abstract
Tandem PDZ domains have been suggested to form structurally independent supramodules. However, dissimilarity between crystallography and NMR models emphasize their malleable conformation. Studies in full-length scaffold proteins are needed to examine the effect of tertiary interactions within their native context. Using single-molecule fluorescence to characterize the N-terminal PDZ tandem in PSD-95, we provide the first direct evidence that PDZ tandems can be structurally independent within a full-length scaffold protein. Molecular refinement using our data converged on a single structure with an antiparallel alignment of the ligand-binding sites. Devoid of interaction partners, single-molecule conditions captured PSD-95 in its unbound, ground state. Interactions between PDZ domains could not be detected while fluctuation correlation spectroscopy showed that other conformations are dynamically sampled. We conclude that ultra-weak interactions stabilize the conformation providing a "low-relief" energy landscape that allows the domain orientation to be flipped by environmental interactions.
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Affiliation(s)
- James J McCann
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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199
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Perevoshchikova IV, Kotova EA, Antonenko YN. Fluorescence correlation spectroscopy in biology, chemistry, and medicine. BIOCHEMISTRY (MOSCOW) 2011; 76:497-516. [PMID: 21639831 DOI: 10.1134/s0006297911050014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.
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Affiliation(s)
- I V Perevoshchikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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200
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Bollmann S, Burgert A, Plattner C, Nagel L, Sewald N, Löllmann M, Sauer M, Doose S. Conformational Flexibility of Glycosylated Peptides. Chemphyschem 2011; 12:2907-11. [DOI: 10.1002/cphc.201100650] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Indexed: 11/08/2022]
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