101
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Schrimpf W, Lemmens V, Smisdom N, Ameloot M, Lamb DC, Hendrix J. Crosstalk-free multicolor RICS using spectral weighting. Methods 2018; 140-141:97-111. [DOI: 10.1016/j.ymeth.2018.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 11/16/2022] Open
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102
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Rigler R, Widengren J. Fluorescence-based monitoring of electronic state and ion exchange kinetics with FCS and related techniques: from T-jump measurements to fluorescence fluctuations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2018; 47:479-492. [PMID: 29260269 PMCID: PMC5982452 DOI: 10.1007/s00249-017-1271-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/30/2017] [Accepted: 12/03/2017] [Indexed: 11/01/2022]
Abstract
In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later. FCS can be used for monitoring reaction kinetics, based on fluctuations at thermodynamic equilibrium, rather than on relaxation measurements following perturbations. In this review, we more specifically discuss FCS measurements on photodynamic, electronic state transitions in fluorophore molecules, and on proton exchange dynamics in solution and on biomembranes. In the latter case, FCS measurements have proven capable of casting new light on the mechanisms of proton exchange at biological membranes, of central importance to bioenergetics and signal transduction. Finally, we describe the transient-state (TRAST) spectroscopy/imaging technique, sharing features with both relaxation (T-jump) and equilibrium fluctuation (FCS) techniques. TRAST is broadly applicable for cellular and molecular studies, and we briefly outline how TRAST can provide unique information from fluorophore blinking kinetics, reflecting e.g., cellular metabolism, rare molecular encounters, and molecular stoichiometries.
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Affiliation(s)
- Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jerker Widengren
- Experimental Biomolecular Physics/ Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden.
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103
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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104
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Schrimpf W, Barth A, Hendrix J, Lamb DC. PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data. Biophys J 2018; 114:1518-1528. [PMID: 29642023 PMCID: PMC5954487 DOI: 10.1016/j.bpj.2018.02.035] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/15/2018] [Accepted: 02/12/2018] [Indexed: 11/24/2022] Open
Abstract
Fluorescence microscopy and spectroscopy data hold a wealth of information on the investigated molecules, structures, or organisms. Nowadays, the same fluorescence data set can be analyzed in many ways to extract different properties of the measured sample. Yet, doing so remains slow and cumbersome, often requiring incompatible software packages. Here, we present PAM (pulsed interleaved excitation analysis with MATLAB), an open-source software package written in MATLAB that offers a simple and efficient workflow through its graphical user interface. PAM is a framework for integrated and robust analysis of fluorescence ensemble, single-molecule, and imaging data. Although it was originally developed for the analysis of pulsed interleaved excitation experiments, PAM has since been extended to support most types of data collection modalities. It combines a multitude of powerful analysis algorithms, ranging from time- and space-correlation analysis, over single-molecule burst analysis, to lifetime imaging microscopy, while offering intrinsic support for multicolor experiments. We illustrate the key concepts and workflow of the software by discussing data handling and sorting and provide step-by-step descriptions for the individual usage cases.
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Affiliation(s)
- Waldemar Schrimpf
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Anders Barth
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Biomedical Research Institute (BIOMED), Advanced Optical Microscopy Centre, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, KU Leuven, Heverlee, Belgium
| | - Don C Lamb
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
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105
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Schwille P. There and back again: from the origin of life to single molecules. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:493-498. [PMID: 29569181 PMCID: PMC5982444 DOI: 10.1007/s00249-018-1295-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/08/2018] [Accepted: 03/13/2018] [Indexed: 11/27/2022]
Abstract
What is life? There is hardly a more fundamental question raised by aspiring researchers, and one less prone to ever be answered in a scientifically satisfying way. In the long, productive and highly influential period of research following his Nobel-recognised work on relaxation kinetics, Manfred Eigen made seminal contributions towards a quantifiable definition of life, with a strong focus on its evolutionary character. In the last years of his time as an active researcher, however, he devoted himself to another, purely experimental topic: the detection and analysis of single biomolecules in aqueous solution. In this short review, I will give an overview of the groundbreaking contributions to the field of single molecule research made by Eigen and coworkers, and show that both, in its intrinsic motivation, and in its consequences, single molecule research strongly relates to the question of the physical-chemical essence of life. In fact, research on living systems with single molecule sensitivity will always refer the researcher to the question of the simplest possible representation, and thus the origin, of any biological phenomenon.
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Affiliation(s)
- Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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106
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Hoischen C, Yavas S, Wohland T, Diekmann S. CENP-C/H/I/K/M/T/W/N/L and hMis12 but not CENP-S/X participate in complex formation in the nucleoplasm of living human interphase cells outside centromeres. PLoS One 2018; 13:e0192572. [PMID: 29509805 PMCID: PMC5839545 DOI: 10.1371/journal.pone.0192572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 01/25/2018] [Indexed: 12/25/2022] Open
Abstract
Kinetochore proteins assemble onto centromeric chromatin and regulate DNA segregation during cell division. The inner kinetochore proteins bind centromeres while most outer kinetochore proteins assemble at centromeres during mitosis, connecting the complex to microtubules. Here, we measured the co-migration between protein pairs of the constitutive centromere associated network (CCAN) and hMis12 complexes by fluorescence cross-correlation spectroscopy (FCCS) in the nucleoplasm outside centromeres in living human interphase cells. FCCS is a method that can tell if in living cells two differently fluorescently labelled molecules migrate independently, or co-migrate and thus are part of one and the same soluble complex. We also determined the apparent dissociation constants (Kd) of the hetero-dimers CENP-T/W and CENP-S/X. We measured co-migration between CENP-K and CENP-T as well as between CENP-M and CENP-T but not between CENP-T/W and CENP-S/X. Furthermore, CENP-C co-migrated with CENP-H, and CENP-K with CENP-N as well as with CENP-L. Thus, in the nucleoplasm outside centromeres, a large fraction of the CENP-H/I/K/M proteins interact with CENP-C, CENP-N/L and CENP-T/W but not with CENP-S/X. Our FCCS analysis of the Mis12 complex showed that hMis12, Nsl1, Dsn1 and Nnf1 also form a complex outside centromeres of which at least hMis12 associated with the CENP-C/H/I/K/M/T/W/N/L complex.
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Affiliation(s)
- Christian Hoischen
- Molecular Biology, Leibniz Institute on Aging-Friz-Lipmann-Institute (FLI), Jena, Germany
| | - Sibel Yavas
- Departments of Biological Sciences and Chemistry and Centre of Bioimaging Sciences, Lee Wee Kheng Buildung, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry and Centre of Bioimaging Sciences, Lee Wee Kheng Buildung, National University of Singapore, Singapore, Singapore
| | - Stephan Diekmann
- Molecular Biology, Leibniz Institute on Aging-Friz-Lipmann-Institute (FLI), Jena, Germany
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107
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Kaliszewski MJ, Shi X, Hou Y, Lingerak R, Kim S, Mallory P, Smith AW. Quantifying membrane protein oligomerization with fluorescence cross-correlation spectroscopy. Methods 2018; 140-141:40-51. [PMID: 29448037 DOI: 10.1016/j.ymeth.2018.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/17/2017] [Accepted: 02/07/2018] [Indexed: 01/27/2023] Open
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is an advanced fluorescence technique that can quantify protein-protein interactions in vivo. Due to the dynamic, heterogeneous nature of the membrane, special considerations must be made to interpret FCCS data accurately. In this study, we describe a method to quantify the oligomerization of membrane proteins tagged with two commonly used fluorescent probes, mCherry (mCH) and enhanced green (eGFP) fluorescent proteins. A mathematical model is described that relates the relative cross-correlation value (fc) to the degree of oligomerization. This treatment accounts for mismatch in the confocal volumes, combinatoric effects of using two fluorescent probes, and the presence of non-fluorescent probes. Using this model, we calculate a ladder of fc values which can be used to determine the oligomer state of membrane proteins from live-cell experimental data. Additionally, a probabilistic mathematical simulation is described to resolve the affinity of different dimeric and oligomeric protein controls.
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Affiliation(s)
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Yixuan Hou
- Food Animal Health Research Program, Ohio Agriculture Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Ryan Lingerak
- Department of Biology, University of Akron, Akron, OH 44325, USA
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Paul Mallory
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA.
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108
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Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
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Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
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109
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Papini C, Royer CA. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks. Biophys Rev 2018; 10:87-96. [PMID: 29383593 DOI: 10.1007/s12551-017-0394-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/29/2017] [Indexed: 12/27/2022] Open
Abstract
Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.
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Affiliation(s)
- Christina Papini
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Catherine A Royer
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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110
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Zhang Y, Bao D, Wang S, Dong Y, Wu F, Li H, Liu D. A Modularly Designable Vesicle for Sequentially Multiple Loading. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:1703259. [PMID: 29282879 DOI: 10.1002/smll.201703259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/19/2017] [Indexed: 06/07/2023]
Abstract
The vesicle is one of the most intriguing platforms for drug delivery, which is believed to improve drug efficacy. In the past few decades, a great deal of materials have been explored to make vesicles, including lipids, block copolymers, dendrons, erythrocyte membranes, and even DNA. Other than shape and size control, most efforts are focused on achieving certain functions, for example, an abundance of stimuli-responsive features are introduced to vesicles, which can be applied to controllable release, such as pH, redox, light, radiation, enzyme etc. Besides, crosslinking or pegylation is used to increase vesicles' stability and elongate circulation time. By incorporating affinity ligands, vesicles can further accumulate to diseased cells or tissues to achieve targeting properties. Recently, multidrug delivery is believed to show a synergy effect in cancer therapy and has become a new direction in this field. However, coloading hydrophilic-hydrophobic small molecules, oligonucleotides, and peptides in the same size- and shape-controlled vesicle through a stepwise manner with high efficiency is still challenging. Herein, a modularly designable vesicle is reported for sequential multiple loading based on frame-guided assembly, which is believed to be an outstanding platform for drug delivery in the future.
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Affiliation(s)
- Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Dandan Bao
- School of Chemistry and Material Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Shuo Wang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuancheng Dong
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Fen Wu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, China
| | - Haitao Li
- School of Chemistry and Material Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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111
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Voith von Voithenberg L, Lamb DC. Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics. Bioessays 2018; 40. [DOI: 10.1002/bies.201700078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 12/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lena Voith von Voithenberg
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
- BIOSS Centre for Signalling Studies; Schänzlestr. 18 79104 Freiburg Germany
| | - Don C. Lamb
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
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112
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Meng L, He S, Zhao XS. Determination of Equilibrium Constant and Relative Brightness in FRET-FCS by Including the Third-Order Correlations. J Phys Chem B 2017; 121:11262-11272. [PMID: 29155588 DOI: 10.1021/acs.jpcb.7b09229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) encodes the information on the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k+ and k-) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence autocorrelation spectroscopy (FACS). Here, we extend the method to fluorescence cross-correlation spectroscopy (FCCS), which appears when FCS is coupled with fluorescence resonance energy transfer (FRET). Among 12 total second-order and third-order pre-exponential factors in a relaxation process probed by the FRET-FCS technique, 3 are independent. We presented and discussed 3 sets of explicit solutions to use these pre-exponential factors to calculate K and Q. Together with the relaxation time, the acquired K will allow people to obtain k+ and k-, so that the goal of deciphering the FRET-FCS data will be fully reached. The theory is verified by extensive computer simulations and tested experimentally on a system of oligonucleotide hybridization.
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Affiliation(s)
- Lingyi Meng
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,School of Life Sciences, Peking University , Beijing 100871, China
| | - Shanshan He
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Xin Sheng Zhao
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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113
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Toplak T, Palmieri B, Juanes-García A, Vicente-Manzanares M, Grant M, Wiseman PW. Wavelet Imaging on Multiple Scales (WIMS) reveals focal adhesion distributions, dynamics and coupling between actomyosin bundle stability. PLoS One 2017; 12:e0186058. [PMID: 29049414 PMCID: PMC5648137 DOI: 10.1371/journal.pone.0186058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 09/25/2017] [Indexed: 11/22/2022] Open
Abstract
We introduce and use Wavelet Imaging on Multiple Scales (WIMS) as an improvement to fluorescence correlation spectroscopy to measure physical processes and features that occur across multiple length scales. In this study, wavelet transforms of cell images are used to characterize molecular dynamics at the cellular and subcellular levels (i.e. focal adhesions). We show the usefulness of the technique by applying WIMS to an image time series of a migrating osteosarcoma cell expressing fluorescently labelled adhesion proteins, which allows us to characterize different components of the cell ranging from optical resolution scale through to focal adhesion and whole cell size scales. Using WIMS we measured focal adhesion numbers, orientation and cell boundary velocities for retraction and protrusion. We also determine the internal dynamics of individual focal adhesions undergoing assembly, disassembly or elongation. Thus confirming as previously shown, WIMS reveals that the number of adhesions and the area of the protruding region of the cell are strongly correlated, establishing a correlation between protrusion size and adhesion dynamics. We also apply this technique to characterize the behavior of adhesions, actin and myosin in Chinese hamster ovary cells expressing a mutant form of myosin IIB (1935D) that displays decreased filament stability and impairs front-back cell polarity. We find separate populations of actin and myosin at each adhesion pole for both the mutant and wild type form. However, we find these populations move rapidly inwards toward one another in the mutant case in contrast to the cells that express wild type myosin IIB where those populations remain stationary. Results obtained with these two systems demonstrate how WIMS has the potential to reveal novel correlations between chosen parameters that belong to different scales.
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Affiliation(s)
- Tim Toplak
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Benoit Palmieri
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Alba Juanes-García
- Universidad Autonoma de Madrid School of Medicine/IIS-Princesa Diego de Leon, Madrid, Spain
| | | | - Martin Grant
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Paul W. Wiseman
- Department of Physics, McGill University, Montréal, Québec, Canada
- Department of Chemistry, McGill University, Montréal, Québec, Canada
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114
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Dunsing V, Mayer M, Liebsch F, Multhaup G, Chiantia S. Direct evidence of amyloid precursor-like protein 1 trans interactions in cell-cell adhesion platforms investigated via fluorescence fluctuation spectroscopy. Mol Biol Cell 2017; 28:3609-3620. [PMID: 29021345 PMCID: PMC5706989 DOI: 10.1091/mbc.e17-07-0459] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 01/25/2023] Open
Abstract
The amyloid precursor–like protein 1 (APLP1) plays a role in synaptic adhesion and synaptogenesis. In this work, we use quantitative fluorescence microscopy to demonstrate the existence of APLP1–APLP1 trans interaction across cell–cell junctions and propose a model explaining the molecular mechanism driving APLP1 multimerization. The amyloid precursor–like protein 1 (APLP1) is a type I transmembrane protein that plays a role in synaptic adhesion and synaptogenesis. Past investigations indicated that APLP1 is involved in the formation of protein–protein complexes that bridge the junctions between neighboring cells. Nevertheless, APLP1–APLP1 trans interactions have never been directly observed in higher eukaryotic cells. Here, we investigated APLP1 interactions and dynamics directly in living human embryonic kidney cells using fluorescence fluctuation spectroscopy techniques, namely cross-correlation scanning fluorescence correlation spectroscopy and number and brightness analysis. Our results show that APLP1 forms homotypic trans complexes at cell–cell contacts. In the presence of zinc ions, the protein forms macroscopic clusters, exhibiting an even higher degree of trans binding and strongly reduced dynamics. Further evidence from giant plasma membrane vesicles suggests that the presence of an intact cortical cytoskeleton is required for zinc-induced cis multimerization. Subsequently, large adhesion platforms bridging interacting cells are formed through APLP1–APLP1 trans interactions. Taken together, our results provide direct evidence that APLP1 functions as a neuronal zinc-dependent adhesion protein and allow a more detailed understanding of the molecular mechanisms driving the formation of APLP1 adhesion platforms.
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Affiliation(s)
- Valentin Dunsing
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Magnus Mayer
- Institute of Chemistry and Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Filip Liebsch
- Department of Pharmacology and Therapeutics/Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y63, Canada
| | - Gerhard Multhaup
- Department of Pharmacology and Therapeutics/Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y63, Canada
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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115
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Silvestri A, Di Silvio D, Llarena I, Murray RA, Marelli M, Lay L, Polito L, Moya SE. Influence of surface coating on the intracellular behaviour of gold nanoparticles: a fluorescence correlation spectroscopy study. NANOSCALE 2017; 9:14730-14739. [PMID: 28948261 DOI: 10.1039/c7nr04640e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the biomedical applications of nanoparticles (NPs), the proper choice of surface chemistry is a crucial aspect in their design. The nature of the coating can heavily impact the interaction of NPs with biomolecules, affect the state of aggregation, and ultimately determine their biological fate. As such, protein corona formation and the aggregation behaviour of gold NPs (Au NPs) are studied here. Au NPs are prepared with four distinct surface functionalisations, namely mercaptosuccinic acid (MSA), N-4-thiobutyroil glucosamine, HS-PEG5000 and HS-alkyl-PEG600. Corona formation, aggregation, and the intracellular behaviour of the Au NPs are then investigated by means of Fluorescence Correlation Spectroscopy (FCS) in cell culture media and in live cells. To evaluate the state of aggregation and the formation of a protein corona, the Au NPs are incubated in cell media and the diffusion coefficient is determined via FCS. The in vitro behaviour is compared with the level of aggregation of the NPs in cells. Diffusion times of the NPs are estimated at different positions in the cell after a one hour incubation period. It is found that the majority of MSA and glucose-Au NPs are present inside the cell as slowly diffusing species with diffusion times (τD) greater than 6000 μs (hydrodynamic diameter >250 nm). PEGylated Au NPs adsorb a small amount of protein and manifest low agglomeration both in media and in living cells. In particular, the HS-alkyl-PEG600 coating shows an excellent correlation between lower protein adsorption, 4-fold lower compared to the MSA coated NPs, and limited intracellular aggregation. In the case of single HS-alkyl-PEG600 coated NPs, it is found that typical intracellular τD values range from 500 to 1500 μs, indicating that these particles display reduced aggregation in the intracellular environment.
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Affiliation(s)
- A Silvestri
- CNR - ISTM, Nanotechnology Lab., Via G. Fantoli 16/15, 20138, Milan, Italy.
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116
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Borodavka A, Dykeman EC, Schrimpf W, Lamb DC. Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments. eLife 2017; 6:27453. [PMID: 28922109 PMCID: PMC5621836 DOI: 10.7554/elife.27453] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/03/2017] [Indexed: 01/06/2023] Open
Abstract
Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. A major challenge in understanding their assembly is the combinatorial problem of a non-random selection of a full genomic set of distinct RNAs. This process involves complex RNA-RNA and protein-RNA interactions, which are often obscured by non-specific binding at concentrations approaching in vivo assembly conditions. Here, we present direct experimental evidence of sequence-specific inter-segment interactions between rotavirus RNAs, taking place in a complex RNA- and protein-rich milieu. We show that binding of the rotavirus-encoded non-structural protein NSP2 to viral ssRNAs results in the remodeling of RNA, which is conducive to formation of stable inter-segment contacts. To identify the sites of these interactions, we have developed an RNA-RNA SELEX approach for mapping the sequences involved in inter-segment base-pairing. Our findings elucidate the molecular basis underlying inter-segment interactions in rotaviruses, paving the way for delineating similar RNA-RNA interactions that govern assembly of other segmented RNA viruses. Rotavirus is a highly infectious virus that affects children worldwide, causing severe diarrhoea. Despite the introduction of several highly effective vaccines, more than 200,000 children still die from rotavirus each year. There are currently no drugs that can combat this disease once a child has been infected. Viruses carry the instructions that determine their properties and behavior in molecules of DNA or RNA. Unlike many other viruses, which typically have a single molecule of DNA or RNA, rotavirus has 11 distinct “RNA segments”. After invading a cell the virus begins to replicate itself. During replication, the RNA segments (which consist of two strands of RNA paired together) are copied many times. It is not clear how rotaviruses ‘count’ up to 11 so that each new virus acquires a single copy of each segment. Previous biochemical and structural studies of rotavirus replication suggest that selecting 11 distinct RNA segments must involve the RNAs forming complex interactions with proteins and other RNA molecules. Using a highly sensitive fluorescence-based approach, termed fluorescence cross-correlation spectroscopy, Borodavka et al. now present direct experimental evidence of interactions between the RNA segments that occur via single strands of the rotavirus RNA. These RNA-RNA interactions require the binding of a rotavirus protein NSP2 to the RNA strands, which results in the remodeling of the RNA; this remodeling is required to form stable contacts between different RNA segments. Furthermore, a new experimental approach (called RNA-RNA SELEX) developed by Borodavka et al. identified the parts of the RNA segments that may take part in these interactions. The results presented by Borodavka et al. pave the way for identifying the RNA-RNA interactions that govern how other segmented RNA viruses can package their genetic material. Further work to uncover the entire RNA interaction network in rotaviruses would also accelerate the design of new vaccines and may help us to develop antiviral drugs to treat infections.
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Affiliation(s)
- Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.,Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Waldemar Schrimpf
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
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117
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Gopal AA, Ricoult SG, Harris SN, Juncker D, Kennedy TE, Wiseman PW. Spatially Selective Dissection of Signal Transduction in Neurons Grown on Netrin-1 Printed Nanoarrays via Segmented Fluorescence Fluctuation Analysis. ACS NANO 2017; 11:8131-8143. [PMID: 28679208 DOI: 10.1021/acsnano.7b03004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Axonal growth cones extend during neural development in response to precise distributions of extracellular cues. Deleted in colorectal cancer (DCC), a receptor for the chemotropic guidance cue netrin-1, directs F-actin reorganization, and is essential for mammalian neural development. To elucidate how the extracellular distribution of netrin-1 influences the distribution of DCC and F-actin within axonal growth cones, we patterned nanoarrays of substrate bound netrin-1 using lift-off nanocontact printing. The distribution of DCC and F-actin in embryonic rat cortical neuron growth cones was then imaged using total internal reflection fluorescence (TIRF) microscopy. Fluorescence fluctuation analysis via image cross-correlation spectroscopy (ICCS) was applied to extract the molecular density and aggregation state of DCC and F-actin, identifying the fraction of DCC and F-actin colocalizing with the patterned netrin-1 substrate. ICCS measurement of spatially segmented images based on the substrate nanodot patterns revealed distinct molecular distributions of F-actin and DCC in regions directly overlying the nanodots compared to over the reference surface surrounding the nanodots. Quantifiable variations between the populations of DCC and F-actin on and off the nanodots reveal specific responses to the printed protein substrate. We report that nanodots of substrate-bound netrin-1 locally recruit and aggregate DCC and direct F-actin organization. These effects were blocked by tetanus toxin, consistent with netrin-1 locally recruiting DCC to the plasma membrane via a VAMP2-dependent mechanism. Our findings demonstrate the utility of segmented ICCS image analysis, combined with precisely patterned immobilized ligands, to reveal local receptor distribution and signaling within specialized subcellular compartments.
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Affiliation(s)
- Angelica A Gopal
- Department of Chemistry, ‡Department of Neurology and Neurosurgery, Montreal Neurological Institute, §Department of Biomedical Engineering, Genome Quebec Innovation Centre, and ∥Department of Physics, McGill University , Montreal, Quebec H3A 0G4 Canada
| | - Sebastien G Ricoult
- Department of Chemistry, ‡Department of Neurology and Neurosurgery, Montreal Neurological Institute, §Department of Biomedical Engineering, Genome Quebec Innovation Centre, and ∥Department of Physics, McGill University , Montreal, Quebec H3A 0G4 Canada
| | - Stephanie N Harris
- Department of Chemistry, ‡Department of Neurology and Neurosurgery, Montreal Neurological Institute, §Department of Biomedical Engineering, Genome Quebec Innovation Centre, and ∥Department of Physics, McGill University , Montreal, Quebec H3A 0G4 Canada
| | - David Juncker
- Department of Chemistry, ‡Department of Neurology and Neurosurgery, Montreal Neurological Institute, §Department of Biomedical Engineering, Genome Quebec Innovation Centre, and ∥Department of Physics, McGill University , Montreal, Quebec H3A 0G4 Canada
| | - Timothy E Kennedy
- Department of Chemistry, ‡Department of Neurology and Neurosurgery, Montreal Neurological Institute, §Department of Biomedical Engineering, Genome Quebec Innovation Centre, and ∥Department of Physics, McGill University , Montreal, Quebec H3A 0G4 Canada
| | - Paul W Wiseman
- Department of Chemistry, ‡Department of Neurology and Neurosurgery, Montreal Neurological Institute, §Department of Biomedical Engineering, Genome Quebec Innovation Centre, and ∥Department of Physics, McGill University , Montreal, Quebec H3A 0G4 Canada
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118
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Krüger D, Ebenhan J, Werner S, Bacia K. Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Correlation Spectroscopy. Biophys J 2017; 113:1311-1320. [PMID: 28697897 DOI: 10.1016/j.bpj.2017.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/21/2017] [Accepted: 06/08/2017] [Indexed: 11/26/2022] Open
Abstract
Fluorescence correlation spectroscopy has been previously used to investigate peptide and protein binding to lipid membranes, as it allows for very low amounts of sample, short measurement times and equilibrium binding conditions. Labeling only one of the binding partners, however, comes with certain drawbacks, as it relies on identifying binding events by a change in diffusion coefficient. Since peptide and protein aggregation can obscure specific binding, and since non-stoichiometric binding necessitates the explicit choice of a statistical distribution for the number of bound ligands, we additionally label the liposomes and perform dual-color fluorescence cross-correlation spectroscopy (dcFCCS). We develop a theoretical framework showing that dcFCCS amplitudes allow calculation of the degree of ligand binding and the concentration of unbound ligand, leading to a model-independent binding curve. As the degree of labeling of the ligands does not factor into the measured quantities, it is permissible to mix labeled and unlabeled ligand, thereby extending the range of usable protein concentrations and accessible dissociation constants, KD. The total protein concentration, but not the fraction of labeled protein, needs to be known. In this work, we apply our dcFCCS analysis scheme to Sar1p, a protein of the COPII complex, which binds "major-minor-mix" liposomes. A Langmuir isotherm model yields KD=(2.1±1.1)μM as the single-site dissociation constant. The dcFCCS framework presented here is highly versatile for biophysical analysis of binding interactions. It may be applied to many types of fluorescently labeled ligands and small diffusing particles, including nanodiscs and liposomes containing membrane protein receptors.
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Affiliation(s)
- Daniela Krüger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Ebenhan
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Werner
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Kirsten Bacia
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
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119
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Adjusting the size of multicompartmental containers made of anionic liposomes and polycations by introducing branching and PEO moieties. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.05.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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120
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Dopamine Receptor Signaling in MIN6 β-Cells Revealed by Fluorescence Fluctuation Spectroscopy. Biophys J 2017; 111:609-618. [PMID: 27508444 DOI: 10.1016/j.bpj.2016.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 11/22/2022] Open
Abstract
Insulin secretion defects are central to the development of type II diabetes mellitus. Glucose stimulation of insulin secretion has been extensively studied, but its regulation by other stimuli such as incretins and neurotransmitters is not as well understood. We investigated the mechanisms underlying the inhibition of insulin secretion by dopamine, which is synthesized in pancreatic β-cells from circulating L-dopa. Previous research has shown that this inhibition is mediated primarily by activation of the dopamine receptor D3 subtype (DRD3), even though both DRD2 and DRD3 are expressed in β-cells. To understand this dichotomy, we investigated the dynamic interactions between the dopamine receptor subtypes and their G-proteins using two-color fluorescence fluctuation spectroscopy (FFS) of mouse MIN6 β-cells. We show that proper membrane localization of exogenous G-proteins depends on both the Gβ and Gγ subunits being overexpressed in the cell. Triple transfections of the dopamine receptor subtype and Gβ and Gγ subunits, each labeled with a different-colored fluorescent protein (FP), yielded plasma membrane expression of all three FPs and permitted an FFS evaluation of interactions between the dopamine receptors and the Gβγ complex. Upon dopamine stimulation, we measured a significant decrease in interactions between DRD3 and the Gβγ complex, which is consistent with receptor activation. In contrast, dopamine stimulation did not cause significant changes in the interactions between DRD2 and the Gβγ complex. These results demonstrate that two-color FFS is a powerful tool for measuring dynamic protein interactions in living cells, and show that preferential DRD3 signaling in β-cells occurs at the level of G-protein release.
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121
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Jafari F, Samadi S, Nowroozi A, Sadrjavadi K, Moradi S, Ashrafi-Kooshk MR, Shahlaei M. Experimental and computational studies on the binding of diazinon to human serum albumin. J Biomol Struct Dyn 2017; 36:1490-1510. [DOI: 10.1080/07391102.2017.1329096] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Fataneh Jafari
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Setareh Samadi
- Department of Toxicology, Shahreza Branch, Islamic Azad University, Shaahreza, Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Komail Sadrjavadi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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122
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Wang J, Huang X, Liu H, Dong C, Ren J. Fluorescence and Scattering Light Cross Correlation Spectroscopy and Its Applications in Homogeneous Immunoassay. Anal Chem 2017; 89:5230-5237. [PMID: 28436659 DOI: 10.1021/acs.analchem.6b04547] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, we propose fluorescence and scattering light cross-correlation spectroscopy (FSCCS) based on laser confocal configuration using silver nanoparticle (SNPs) and Alexa Fluor 488 (Alexa) as probe pairs. FSCCS is a single molecule (particle) method, and its principle is similar to that of fluorescence cross-correlation spectroscopy (FCCS). We established the setup of FSCCS using single wavelength laser and developed an immunoassay model of FSCCS. The reliability and adaptability of FSCCS method were evaluated by homogeneous sandwich immunoassay mode. In the study, liver cancer biomarker alpha-fetoprotein (AFP) was used as an assay model, two different antibodies were labeled with SNPs and fluorophore Alexa Fluor 488, respectively. In the optimal conditions, the linear range of AFP covers 5 pM to 580 pM and the detection limit is 3.1 pM. This method was successfully applied for direct determination of AFP levels in human serum samples, and the obtained results were in good agreement with data obtained via ELISAs. The advantage of this method lies in its simplicity, attractive SNPs probes, high sensitivity and selectivity and high efficiency. We believe that FSCCS method exhibits promising potential applications in homogeneous bioassays and study on the molecular interaction and nanoparticle-molecule interaction.
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Affiliation(s)
- Jinjie Wang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China.,College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science , 333 Longteng Road, Shanghai, 201620, P.R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Heng Liu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
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123
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Das KK, Shalaby R, García-Sáez AJ. Determinants of BH3 Sequence Specificity for the Disruption of Bcl-xL/cBid Complexes in Membranes. ACS Chem Biol 2017; 12:989-1000. [PMID: 28170214 DOI: 10.1021/acschembio.6b01084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The prosurvival Bcl-2 proteins exhibit a specific pattern of interactions with BH3-only proteins that determines the cellular dependence on apoptotic stress. This specificity is crucial for the development of BH3 mimetics, a class of anticancer molecules based on the BH3 domain with promising activity in clinical trials. Although complex formation mainly takes place in the mitochondrial outer membrane, most studies so far addressed the interaction between BH3 peptides and truncated Bcl-2 proteins in solution. As a consequence, quantitative understanding of the sequence specificity determinants of BH3 peptides in the membrane environment is missing. Here, we tackle this issue by systematically quantifying the ability of BH3 peptides to compete for the complexes between cBid and Bcl-xL in giant unilamellar vesicles and compare it with solution and mitochondria. We show that the BH3 peptides derived from Hrk, Bim, Bid, and Bad are the most efficient in disrupting cBid/Bcl-xL complexes in the membrane, which correlates with their activity in mitochondria. Our findings support the targeting to the membrane of small molecules that bind Bcl-2 proteins as a strategy to improve their efficiency.
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Affiliation(s)
- Kushal Kumar Das
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Raed Shalaby
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Ana J. García-Sáez
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
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124
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Li J, Dong C, Ren J. Strategies to reduce detection volume of fluorescence correlation spectroscopy (FCS) to realize physiological concentration measurements. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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125
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Marouzi S, Sharifi Rad A, Beigoli S, Teimoori Baghaee P, Assaran Darban R, Chamani J. Study on effect of lomefloxacin on human holo-transferrin in the presence of essential and nonessential amino acids: Spectroscopic and molecular modeling approaches. Int J Biol Macromol 2017; 97:688-699. [DOI: 10.1016/j.ijbiomac.2017.01.047] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/08/2023]
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126
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Sigaut L, Villarruel C, Ponce Dawson S. FCS experiments to quantify Ca 2+ diffusion and its interaction with buffers. J Chem Phys 2017; 146:104203. [PMID: 28298094 DOI: 10.1063/1.4977586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ca2+ signals are ubiquitous. One of the key factors for their versatility is the variety of spatio-temporal distributions that the cytosolic Ca2+ can display. In most cell types Ca2+ signals not only depend on Ca2+ entry from the extracellular medium but also on Ca2+ release from internal stores, a process which is in turn regulated by cytosolic Ca2+ itself. The rate at which Ca2+ is transported, the fraction that is trapped by intracellular buffers, and with what kinetics are thus key features that affect the time and spatial range of action of Ca2+ signals. The quantification of Ca2+ diffusion in intact cells is quite challenging because the transport rates that can be inferred using optical techniques are intricately related to the interaction of Ca2+ with the dye that is used for its observation and with the cellular buffers. In this paper, we introduce an approach that uses Fluorescence Correlation Spectroscopy (FCS) experiments performed at different conditions that in principle allows the quantification of Ca2+ diffusion and of its reaction rates with unobservable (non-fluorescent) Ca2+ buffers. To this end, we develop the necessary theory to interpret the experimental results and then apply it to FCS experiments performed in a set of solutions containing Ca2+, a single wavelength Ca2+ dye, and a non-fluorescent Ca2+ buffer. We show that a judicious choice of the experimental conditions and an adequate interpretation of the fitting parameters can be combined to extract information on the free diffusion coefficient of Ca2+ and of some of the properties of the unobservable buffer. We think that this approach can be applied to other situations, particularly to experiments performed in intact cells.
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Affiliation(s)
- Lorena Sigaut
- Departamento de Física, FCEN-UBA, and IFIBA, CONICET, Ciudad Universitaria, Pabellón I, 1428 Buenos Aires, Argentina
| | - Cecilia Villarruel
- Departamento de Física, FCEN-UBA, and IFIBA, CONICET, Ciudad Universitaria, Pabellón I, 1428 Buenos Aires, Argentina
| | - Silvina Ponce Dawson
- Departamento de Física, FCEN-UBA, and IFIBA, CONICET, Ciudad Universitaria, Pabellón I, 1428 Buenos Aires, Argentina
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127
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Neubauer R, Höhn S, Dulle M, Lapp A, Schulreich C, Hellweg T. Protein diffusion in a bicontinuous microemulsion: inducing sub-diffusion by tuning the water domain size. SOFT MATTER 2017; 13:1998-2003. [PMID: 28197579 DOI: 10.1039/c6sm02107g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We study the diffusion of an enhanced green fluorescent protein (GFP+) in bicontinuous sugar-surfactant based microemulsions. The size of the water domains in such systems is controlled by changes of the oil-to-water ratio. Hence, microemulsions allow to produce confinement effects in a controlled way. At high water content the protein is found to exhibit Fickian diffusion. Decreasing the water domain size leads to a slowing down of the protein diffusion and sub-diffusive behavior is obtained on the scale observed by fluorescence correlation spectroscopy. Further decrease of the water domain size finally nearly fixes the GFP+ in these domains and forces it to increasingly follow the breathing mode of the microemulsion matrix.
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Affiliation(s)
- Ralph Neubauer
- Universität Bayreuth, Physikalische Chemie I, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Sebastian Höhn
- Universität Bayreuth, Physikalische Chemie I, Universitätsstr. 30, D-95447 Bayreuth, Germany and Universität Bielefeld, Physikalische und Biophysikalische Chemie, Universitätsstr. 25, D-33615 Bielefeld, Germany.
| | - Martin Dulle
- Universität Bayreuth, Physikalische Chemie I, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Alain Lapp
- Laboratoire Léon Brillouin, CE Saclay, Gif sur Yvette, France
| | - Christoph Schulreich
- Universität Bielefeld, Physikalische und Biophysikalische Chemie, Universitätsstr. 25, D-33615 Bielefeld, Germany.
| | - Thomas Hellweg
- Universität Bielefeld, Physikalische und Biophysikalische Chemie, Universitätsstr. 25, D-33615 Bielefeld, Germany.
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128
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Lagerholm BC, Andrade DM, Clausen MP, Eggeling C. Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:063001. [PMID: 28458397 PMCID: PMC5390782 DOI: 10.1088/1361-6463/aa519e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 05/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.
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Affiliation(s)
- B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Débora M Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR, UK
| | - Mathias P Clausen
- MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Christian Eggeling
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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129
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Röder R, Preiß T, Hirschle P, Steinborn B, Zimpel A, Höhn M, Rädler JO, Bein T, Wagner E, Wuttke S, Lächelt U. Multifunctional Nanoparticles by Coordinative Self-Assembly of His-Tagged Units with Metal–Organic Frameworks. J Am Chem Soc 2017; 139:2359-2368. [DOI: 10.1021/jacs.6b11934] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ruth Röder
- Pharmaceutical
Biotechnology, Department of Pharmacy and Center for NanoScience
(CeNS), LMU Munich, 81377 Munich, Germany
| | - Tobias Preiß
- Department
of Physics and Center for NanoScience (CeNS), LMU Munich, 80539 Munich, Germany
| | - Patrick Hirschle
- Department
of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Benjamin Steinborn
- Pharmaceutical
Biotechnology, Department of Pharmacy and Center for NanoScience
(CeNS), LMU Munich, 81377 Munich, Germany
| | - Andreas Zimpel
- Department
of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Miriam Höhn
- Pharmaceutical
Biotechnology, Department of Pharmacy and Center for NanoScience
(CeNS), LMU Munich, 81377 Munich, Germany
| | - Joachim O. Rädler
- Department
of Physics and Center for NanoScience (CeNS), LMU Munich, 80539 Munich, Germany
| | - Thomas Bein
- Department
of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Ernst Wagner
- Pharmaceutical
Biotechnology, Department of Pharmacy and Center for NanoScience
(CeNS), LMU Munich, 81377 Munich, Germany
| | - Stefan Wuttke
- Department
of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Ulrich Lächelt
- Pharmaceutical
Biotechnology, Department of Pharmacy and Center for NanoScience
(CeNS), LMU Munich, 81377 Munich, Germany
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130
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Gao S, Cui M, Li R, Liang L, Liu Y, Xie L. Quantitative deconvolution of autocorrelations and cross correlations from two-dimensional lifetime decay maps in fluorescence lifetime correlation spectroscopy. Sci Bull (Beijing) 2017; 62:9-15. [PMID: 36718073 DOI: 10.1016/j.scib.2016.11.006] [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: 10/08/2016] [Revised: 11/05/2016] [Accepted: 11/11/2016] [Indexed: 02/01/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a widely used method for measuring molecular diffusion and chemical kinetics. However, when a mixture of fluorescent species is taken into account, the conventional FCS method has limitations in extracting autocorrelations for different species and cross correlations between different species. Recently developed fluorescence lifetime correlation spectroscopy (FLCS) based on time-tagged time-resolved (TTTR) photon recording, which can record the global and micro arrival time for each individual photon, has been used to discriminate different species according to fluorescence lifetime. Here, based on two-dimensional lifetime decay maps constructed from TTTR photon stream, we have developed a quantitative lifetime-deconvolution FCS model (LDFCS) to extract precise chemical rates for chemical conversions in multi-species systems. The key point of LDFCS model is separation of different species according to the global distribution of fluorescence lifetime and then deconvolution of autocorrelations and cross-correlations from the two-dimensional lifetime decay maps constructed by the micro arrival times of photon pairs at each delay time.
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Affiliation(s)
- Shanshan Gao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Menghua Cui
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Ruiru Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Ling Liang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Ying Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Liming Xie
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
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131
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Gopal AA, Rappaz B, Rouger V, Martyn IB, Dahlberg PD, Meland RJ, Beamish IV, Kennedy TE, Wiseman PW. Netrin-1-Regulated Distribution of UNC5B and DCC in Live Cells Revealed by TICCS. Biophys J 2017; 110:623-634. [PMID: 26840727 DOI: 10.1016/j.bpj.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023] Open
Abstract
Netrins are secreted proteins that direct cell migration and adhesion during development. Netrin-1 binds its receptors deleted in colorectal cancer (DCC) and the UNC5 homologs (UNC5A-D) to activate downstream signaling that ultimately directs cytoskeletal reorganization. To investigate how netrin-1 regulates the dynamic distribution of DCC and UNC5 homologs, we applied fluorescence confocal and total internal reflection fluorescence microscopy, and sliding window temporal image cross correlation spectroscopy, to measure time profiles of the plasma membrane distribution, aggregation state, and interaction fractions of fluorescently tagged netrin receptors expressed in HEK293T cells. Our measurements reveal changes in receptor aggregation that are consistent with netrin-1-induced recruitment of DCC-enhanced green fluorescent protein (EGFP) from intracellular vesicles to the plasma membrane. Netrin-1 also induced colocalization of coexpressed full-length DCC-EGFP with DCC-T-mCherry, a putative DCC dominant negative that replaces the DCC intracellular domain with mCherry, consistent with netrin-1-induced receptor oligomerization, but with no change in aggregation state with time, providing evidence that signaling via the DCC intracellular domain triggers DCC recruitment to the plasma membrane. UNC5B expressed alone was also recruited by netrin-1 to the plasma membrane. Coexpressed DCC and UNC5 homologs are proposed to form a heteromeric netrin-receptor complex to mediate a chemorepellent response. Application of temporal image cross correlation spectroscopy to image series of cells coexpressing UNC5B-mCherry and DCC-EGFP revealed a netrin-1-induced increase in colocalization, with both receptors recruited to the plasma membrane from preexisting clusters, consistent with vesicular recruitment and receptor heterooligomerization. Plasma membrane recruitment of DCC or UNC5B was blocked by application of the netrin-1 VI-V peptide, which fails to activate chemoattraction, or by pharmacological block of Src family kinase signaling, consistent with receptor recruitment requiring netrin-1-activated signaling. Our findings reveal a mechanism activated by netrin-1 that recruits DCC and UNC5B to the plasma membrane.
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Affiliation(s)
- Angelica A Gopal
- Department of Chemistry, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada; McGill Program in Neuroengineering, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Benjamin Rappaz
- McGill Program in Neuroengineering, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada; Department of Physics, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Vincent Rouger
- Department of Chemistry, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Iain B Martyn
- Department of Physics, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Peter D Dahlberg
- Department of Physics, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Rachel J Meland
- Department of Chemistry, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Ian V Beamish
- McGill Program in Neuroengineering, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Timothy E Kennedy
- McGill Program in Neuroengineering, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Paul W Wiseman
- Department of Chemistry, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada; McGill Program in Neuroengineering, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada; Department of Physics, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
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132
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Klima M, Chalupska D, Różycki B, Humpolickova J, Rezabkova L, Silhan J, Baumlova A, Dubankova A, Boura E. Kobuviral Non-structural 3A Proteins Act as Molecular Harnesses to Hijack the Host ACBD3 Protein. Structure 2017; 25:219-230. [PMID: 28065508 DOI: 10.1016/j.str.2016.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/08/2016] [Accepted: 11/28/2016] [Indexed: 10/20/2022]
Abstract
Picornaviruses are small positive-sense single-stranded RNA viruses that include many important human pathogens. Within the host cell, they replicate at specific replication sites called replication organelles. To create this membrane platform, they hijack several host factors including the acyl-CoA-binding domain-containing protein-3 (ACBD3). Here, we present a structural characterization of the molecular complexes formed by the non-structural 3A proteins from two species of the Kobuvirus genus of the Picornaviridae family and the 3A-binding domain of the host ACBD3 protein. Specifically, we present a series of crystal structures as well as a molecular dynamics simulation of the 3A:ACBD3 complex at the membrane, which reveals that the viral 3A proteins act as molecular harnesses to enslave the ACBD3 protein leading to its stabilization at target membranes. Our data provide a structural rationale for understanding how these viral-host protein complexes assemble at the atomic level and identify new potential targets for antiviral therapies.
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Affiliation(s)
- Martin Klima
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic.
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Adriana Baumlova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Anna Dubankova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic.
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133
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González Bardeci N, Angiolini JF, De Rossi MC, Bruno L, Levi V. Dynamics of intracellular processes in live-cell systems unveiled by fluorescence correlation microscopy. IUBMB Life 2016; 69:8-15. [PMID: 27896901 DOI: 10.1002/iub.1589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/07/2016] [Indexed: 11/12/2022]
Abstract
Fluorescence fluctuation-based methods are non-invasive microscopy tools especially suited for the study of dynamical aspects of biological processes. These methods examine spontaneous intensity fluctuations produced by fluorescent molecules moving through the small, femtoliter-sized observation volume defined in confocal and multiphoton microscopes. The quantitative analysis of the intensity trace provides information on the processes producing the fluctuations that include diffusion, binding interactions, chemical reactions and photophysical phenomena. In this review, we present the basic principles of the most widespread fluctuation-based methods, discuss their implementation in standard confocal microscopes and briefly revise some examples of their applications to address relevant questions in living cells. The ultimate goal of these methods in the Cell Biology field is to observe biomolecules as they move, interact with targets and perform their biological action in the natural context. © 2016 IUBMB Life, 69(1):8-15, 2017.
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Affiliation(s)
- Nicolás González Bardeci
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
| | - Juan Francisco Angiolini
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
| | - María Cecilia De Rossi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
| | | | - Valeria Levi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
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134
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Sanchez SR, Bachilo SM, Kadria-Vili Y, Lin CW, Weisman RB. (n,m)-Specific Absorption Cross Sections of Single-Walled Carbon Nanotubes Measured by Variance Spectroscopy. NANO LETTERS 2016; 16:6903-6909. [PMID: 27760291 DOI: 10.1021/acs.nanolett.6b02819] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new method based on variance spectroscopy has enabled the determination of absolute absorption cross sections for the first electronic transition of 12 (n,m) structural species of semiconducting single-walled carbon nanotubes (SWCNTs). Spectrally resolved measurements of fluorescence variance in dilute bulk samples provided particle number concentrations of specific SWCNT species. These values were converted to carbon concentrations and correlated with resonant components in the absorbance spectrum to deduce (n,m)-specific absorption cross sections (absorptivities) for nanotubes ranging in diameter from 0.69 to 1.03 nm. The measured cross sections per atom tend to vary inversely with nanotube diameter and are slightly greater for structures of mod 1 type than for mod 2. Directly measured and extrapolated values are now available to support quantitative analysis of SWCNT samples through absorption spectroscopy.
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Affiliation(s)
- Stephen R Sanchez
- Department of Chemistry and the Smalley-Curl Institute and ‡Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Sergei M Bachilo
- Department of Chemistry and the Smalley-Curl Institute and ‡Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Yara Kadria-Vili
- Department of Chemistry and the Smalley-Curl Institute and ‡Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Ching-Wei Lin
- Department of Chemistry and the Smalley-Curl Institute and ‡Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - R Bruce Weisman
- Department of Chemistry and the Smalley-Curl Institute and ‡Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, Houston, Texas 77005, United States
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135
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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136
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Ingargiola A, Laurence T, Boutelle R, Weiss S, Michalet X. Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments. Biophys J 2016; 110:26-33. [PMID: 26745406 DOI: 10.1016/j.bpj.2015.11.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/04/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022] Open
Abstract
We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.
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Affiliation(s)
- Antonino Ingargiola
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California.
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Robert Boutelle
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California
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137
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An Intermittent Model for Intracellular Motions of Gold Nanostars by k-Space Scattering Image Correlation. Biophys J 2016; 109:2246-58. [PMID: 26636936 DOI: 10.1016/j.bpj.2015.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022] Open
Abstract
Anisotropic metallic nanoparticles have been devised as powerful potential tools for in vivo imaging, photothermal therapy, and drug delivery thanks to plasmon-enhanced absorption and scattering cross sections, ease in synthesis and functionalization, and controlled cytotoxicity. The rational design of all these applications requires the characterization of the nanoparticles intracellular trafficking pathways. In this work, we exploit live-cell time-lapse confocal reflectance microscopy and image correlation in both direct and reciprocal space to investigate the intracellular transport of branched gold nanostars (GNSs). Different transport mechanisms, spanning from pure Brownian diffusion to (sub-)ballistic superdiffusion, are revealed by temporal and spatio-temporal image correlation spectroscopy on the tens-of-seconds timescale. According to these findings, combined with numerical simulations and with a Bayesian (hidden Markov model-based) analysis of single particle tracking data, we ascribe the superdiffusive, subballistic behavior characterizing the GNSs dynamics to a two-state switching between Brownian diffusion in the cytoplasm and molecular motor-mediated active transport. For the investigation of intermittent-type transport phenomena, we derive an analytical theoretical framework for Fourier-space image correlation spectroscopy (kICS). At first, we evaluate the influence of all the dynamic and kinetic parameters (the diffusion coefficient, the drift velocity, and the transition rates between the diffusive and the active transport regimes) on simulated kICS correlation functions. Then we outline a protocol for data analysis and employ it to derive whole-cell maps for each parameter underlying the GNSs intracellular dynamics. Capable of identifying even simpler transport phenomena, whether purely diffusive or ballistic, our intermittent kICS approach allows an exhaustive investigation of the dynamics of GNSs and biological macromolecules.
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138
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Wuttke S, Braig S, Preiß T, Zimpel A, Sicklinger J, Bellomo C, Rädler JO, Vollmar AM, Bein T. MOF nanoparticles coated by lipid bilayers and their uptake by cancer cells. Chem Commun (Camb) 2016; 51:15752-5. [PMID: 26359316 DOI: 10.1039/c5cc06767g] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report the synthesis of MOF@lipid nanoparticles as a versatile and powerful novel class of nanocarriers based on metal-organic frameworks (MOFs). We show that the MOF@lipid system can effectively store dye molecules inside the porous scaffold of the MOF while the lipid bilayer prevents their premature release. Efficient uptake of the MOF@lipid nanoparticles by cancer cells makes these nanocarriers promising for drug delivery and diagnostic purposes.
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Affiliation(s)
- Stefan Wuttke
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11 (E), 81377 München, Germany.
| | - Simone Braig
- Department of Pharmacy University of Munich (LMU), Butenandtstraße 5, 81377 München, Germany
| | - Tobias Preiß
- Faculty of Physics and Center for NanoScience (CeNS), University of Munich (LMU), Geschwister Scholl Platz 1, 80539 München, Germany
| | - Andreas Zimpel
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11 (E), 81377 München, Germany.
| | - Johannes Sicklinger
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11 (E), 81377 München, Germany.
| | - Claudia Bellomo
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11 (E), 81377 München, Germany.
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience (CeNS), University of Munich (LMU), Geschwister Scholl Platz 1, 80539 München, Germany
| | - Angelika M Vollmar
- Department of Pharmacy University of Munich (LMU), Butenandtstraße 5, 81377 München, Germany
| | - Thomas Bein
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11 (E), 81377 München, Germany.
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139
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Ozgen H, Baron W, Hoekstra D, Kahya N. Oligodendroglial membrane dynamics in relation to myelin biogenesis. Cell Mol Life Sci 2016; 73:3291-310. [PMID: 27141942 PMCID: PMC4967101 DOI: 10.1007/s00018-016-2228-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
In the central nervous system, oligodendrocytes synthesize a specialized membrane, the myelin membrane, which enwraps the axons in a multilamellar fashion to provide fast action potential conduction and to ensure axonal integrity. When compared to other membranes, the composition of myelin membranes is unique with its relatively high lipid to protein ratio. Their biogenesis is quite complex and requires a tight regulation of sequential events, which are deregulated in demyelinating diseases such as multiple sclerosis. To devise strategies for remedying such defects, it is crucial to understand molecular mechanisms that underlie myelin assembly and dynamics, including the ability of specific lipids to organize proteins and/or mediate protein-protein interactions in healthy versus diseased myelin membranes. The tight regulation of myelin membrane formation has been widely investigated with classical biochemical and cell biological techniques, both in vitro and in vivo. However, our knowledge about myelin membrane dynamics, such as membrane fluidity in conjunction with the movement/diffusion of proteins and lipids in the membrane and the specificity and role of distinct lipid-protein and protein-protein interactions, is limited. Here, we provide an overview of recent findings about the myelin structure in terms of myelin lipids, proteins and membrane microdomains. To give insight into myelin membrane dynamics, we will particularly highlight the application of model membranes and advanced biophysical techniques, i.e., approaches which clearly provide an added value to insight obtained by classical biochemical techniques.
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Affiliation(s)
- Hande Ozgen
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Wia Baron
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
| | - Dick Hoekstra
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nicoletta Kahya
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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140
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Marita M, Wang Y, Kaliszewski MJ, Skinner KC, Comar WD, Shi X, Dasari P, Zhang X, Smith AW. Class A Plexins Are Organized as Preformed Inactive Dimers on the Cell Surface. Biophys J 2016; 109:1937-45. [PMID: 26536270 DOI: 10.1016/j.bpj.2015.04.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 04/10/2015] [Accepted: 04/27/2015] [Indexed: 01/08/2023] Open
Abstract
Plexins are single-pass transmembrane receptors that bind the axon guidance molecules semaphorins. Single-pass transmembrane proteins are an important class of receptors that display a wide variety of activation mechanisms, often involving ligand-dependent dimerization or conformational changes. Resolving the activation mechanism and dimerization state of these receptors is extremely challenging, especially in a live-cell environment. Here, we report on the dimerization state of PlexinA4 and its response to activation by semaphorin binding. Semaphorins are dimeric molecules that activate plexin by binding two copies of plexin simultaneously and inducing formation of a specific active dimer of plexin. An open question is whether there are preexisting plexin dimers that could act as autoinhibitory complexes. We address these questions with pulsed interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS). PIE-FCCS is a two-color fluorescence microscopy method that is directly sensitive to protein dimerization in a live-cell environment. With PIE-FCCS, we show that inactive PlexinA4 is dimerized in the live-cell plasma membrane. By comparing the cross correlation of full-length PlexinA4 to control proteins and plexin mutants, we show that dimerization of inactive PlexinA4 requires the Sema domain, but not the cytoplasmic domain. Ligand stimulation with Sema6A does not change the degree of cross correlation, indicating that plexin activation does not lead to higher-order oligomerization. Together, the results suggest that semaphorin activates plexin by disrupting an inhibitory plexin dimer and inducing the active dimer.
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Affiliation(s)
- Morgan Marita
- Department of Chemistry, University of Akron, Akron, Ohio
| | - Yuxiao Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | | | | | | | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, Ohio
| | - Pranathi Dasari
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, Ohio.
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141
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Homogeneous time-resolved G protein-coupled receptor–ligand binding assay based on fluorescence cross-correlation spectroscopy. Anal Biochem 2016; 502:24-35. [DOI: 10.1016/j.ab.2016.02.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/19/2016] [Accepted: 02/25/2016] [Indexed: 12/13/2022]
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142
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Buntru A, Trepte P, Klockmeier K, Schnoegl S, Wanker EE. Current Approaches Toward Quantitative Mapping of the Interactome. Front Genet 2016; 7:74. [PMID: 27200083 PMCID: PMC4854875 DOI: 10.3389/fgene.2016.00074] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Protein–protein interactions (PPIs) play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as dual luminescence-based co-immunoprecipitation, Förster resonance energy transfer or luminescence-based mammalian interactome mapping with bait control. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research.
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Affiliation(s)
| | - Philipp Trepte
- Max Delbrueck Center for Molecular Medicine Berlin, Germany
| | | | | | - Erich E Wanker
- Max Delbrueck Center for Molecular Medicine Berlin, Germany
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143
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Pakulska MM, Miersch S, Shoichet MS. Designer protein delivery: From natural to engineered affinity-controlled release systems. Science 2016; 351:aac4750. [PMID: 26989257 DOI: 10.1126/science.aac4750] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploiting binding affinities between molecules is an established practice in many fields, including biochemical separations, diagnostics, and drug development; however, using these affinities to control biomolecule release is a more recent strategy. Affinity-controlled release takes advantage of the reversible nature of noncovalent interactions between a therapeutic protein and a binding partner to slow the diffusive release of the protein from a vehicle. This process, in contrast to degradation-controlled sustained-release formulations such as poly(lactic-co-glycolic acid) microspheres, is controlled through the strength of the binding interaction, the binding kinetics, and the concentration of binding partners. In the context of affinity-controlled release--and specifically the discovery or design of binding partners--we review advances in in vitro selection and directed evolution of proteins, peptides, and oligonucleotides (aptamers), aided by computational design.
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Affiliation(s)
- Malgosia M Pakulska
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shane Miersch
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Molly S Shoichet
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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144
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Vester M, Grueter A, Finkler B, Becker R, Jung G. Biexponential photon antibunching: recombination kinetics within the Förster-cycle in DMSO. Phys Chem Chem Phys 2016; 18:10281-8. [PMID: 27020473 DOI: 10.1039/c6cp00718j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Time-resolved experiments with pulsed-laser excitation are the standard approach to map the dynamic evolution of excited states, but ground-state kinetics remain hidden or require pump-dump-probe schemes. Here, we exploit the so-called photon antibunching, a purely quantum-optical effect related to single molecule detection to assess the rate constants for a chemical reaction in the electronic ground state. The measurement of the second-order correlation function g((2)), i.e. the evaluation of inter-photon arrival times, is applied to the reprotonation in a Förster-cycle. We find that the antibunching of three different photoacids in the aprotic solvent DMSO significantly differs from the behavior in water. The longer decay constant of the biexponential antibunching tl is linked to the bimolecular reprotonation kinetics of the fully separated ion-pair, independent of the acidic additives. The value of the corresponding bimolecular rate constant, kp = 4 × 10(9) M(-1) s(-1), indicates diffusion-controlled reprotonation. The analysis of tl also allows for the extraction of the separation yield of proton and the conjugated base after excitation and amounts to approximately 15%. The shorter time component ts is connected to the decay of the solvent-separated ion pair. The associated time constant for geminate reprotonation is approximately 3 ± 1 ns in agreement with independent tcspc experiments. These experiments verify that the transfer of quantum-optical experiments to problems in chemistry enables mechanistic conclusions which are hardly accessible by other methods.
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Affiliation(s)
- Michael Vester
- Biophysical Chemistry, Saarland University, 66123 Saarbrücken, Germany.
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145
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Zheng Y, Tian S, Peng X, Yang J, Fu Y, Jiao Y, Zhao J, He J, Hong T. Kinesin-1 inhibits the aggregation of amyloid-β peptide as detected by fluorescence cross-correlation spectroscopy. FEBS Lett 2016; 590:1028-37. [DOI: 10.1002/1873-3468.12137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 02/04/2016] [Accepted: 03/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Yanpeng Zheng
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Shijun Tian
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Xianglei Peng
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Jingfa Yang
- Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Yuanhui Fu
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Yueying Jiao
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Jiang Zhao
- Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Jinsheng He
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Tao Hong
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
- Institute for Viral Disease Control and Prevention; Chinese Centre for Disease Control and Prevention; Beijing China
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146
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Navarro JRG, Wennmalm S, Godfrey J, Breitholtz M, Edlund U. Luminescent Nanocellulose Platform: From Controlled Graft Block Copolymerization to Biomarker Sensing. Biomacromolecules 2016; 17:1101-9. [DOI: 10.1021/acs.biomac.5b01716] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julien R. G. Navarro
- Fiber
and Polymer Technology, Royal Institute of Technology (KTH), Teknikringen 56, SE-100 44 Stockholm, Sweden
| | - Stefan Wennmalm
- Science
for Life Laboratory, Department of Applied Physics, KTH-Royal Institute of Technology, SE-171 65 Solna, Sweden
| | - Jamie Godfrey
- Fiber
and Polymer Technology, Royal Institute of Technology (KTH), Teknikringen 56, SE-100 44 Stockholm, Sweden
| | - Magnus Breitholtz
- Department
of Environmental Science and Analytical Chemistry, Stockholm University, SE-114
18 Stockholm, Sweden
| | - Ulrica Edlund
- Fiber
and Polymer Technology, Royal Institute of Technology (KTH), Teknikringen 56, SE-100 44 Stockholm, Sweden
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147
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Homogeneous immunoassay for the cancer marker alpha-fetoprotein using single wavelength excitation fluorescence cross-correlation spectroscopy and CdSe/ZnS quantum dots and fluorescent dyes as labels. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1694-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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148
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Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 2015; 350:823-6. [PMID: 26564855 DOI: 10.1126/science.aac6572] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA-guided CRISPR-associated protein Cas9 is used for genome editing, transcriptional modulation, and live-cell imaging. Cas9-guide RNA complexes recognize and cleave double-stranded DNA sequences on the basis of 20-nucleotide RNA-DNA complementarity, but the mechanism of target searching in mammalian cells is unknown. Here, we use single-particle tracking to visualize diffusion and chromatin binding of Cas9 in living cells. We show that three-dimensional diffusion dominates Cas9 searching in vivo, and off-target binding events are, on average, short-lived (<1 second). Searching is dependent on the local chromatin environment, with less sampling and slower movement within heterochromatin. These results reveal how the bacterial Cas9 protein interrogates mammalian genomes and navigates eukaryotic chromatin structure.
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Affiliation(s)
- Spencer C Knight
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Liangqi Xie
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Wulan Deng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. Transcriptional Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Benjamin Guglielmi
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lea B Witkowsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lana Bosanac
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Elisa T Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Mohamed El Beheiry
- Laboratoire Physico-Chimie Curie, Institut Curie, Centre National de la Recherche Scientifique UMR 168, Paris, France
| | | | - Maxime Dahan
- Transcriptional Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. Laboratoire Physico-Chimie Curie, Institut Curie, Centre National de la Recherche Scientifique UMR 168, Paris, France
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. Transcriptional Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, CA, USA. Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. Innovative Genomics Initiative, University of California, Berkeley, CA, USA.
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. Transcriptional Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. Li Ka Shing Biomedical and Health Sciences Center, University of California, Berkeley, CA, USA.
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149
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Nepal M, Oyler-Yaniv A, Krichevsky O. Scanning fluorescence correlation spectroscopy as a versatile tool to measure static and dynamic properties of soft matter systems. SOFT MATTER 2015; 11:8939-8947. [PMID: 26406382 DOI: 10.1039/c5sm01582k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present the formalism and experimental implementation of scanning fluorescence correlation spectroscopy (SFCS) for the measurements of soft matter system structure and dynamics. We relate the SFCS function Fourier transform to the system intermediate scattering function and demonstrate how SFCS can be combined with specific labelling to measure the desired statistical and kinetic features of the system. Using DNA as a model polymer, we demonstrate the application of SFCS to measure (1) the static structure factor of the system, (2) polymer end-to-end distance distribution, and (3) polymer segmental dynamics in dilute and in dense solutions. The measured DNA end-to-end distance distributions are close to Gaussian. Implementing SFCS we obtain reliable data on segmental mean-square displacement kinetics in dense solutions, where the static FCS approach fails because of dye photobleaching. For moderate concentrations in the semidilute regime (at ∼7 overlap concentrations) segmental dynamics exhibit only weak entanglements. Both of these experimental findings are consistent with theoretical predictions of the weakness of excluded interactions in semiflexible polymers.
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Affiliation(s)
- Manish Nepal
- Physics Department, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Alon Oyler-Yaniv
- Physics Department, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Oleg Krichevsky
- Physics Department, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel. and Ilse Kats Centre for Nanoscience, Ben-Gurion University, Beer-Sheva 84105, Israel
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150
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Abstract
The local structure and composition of the outer membrane of an animal cell are important factors in the control of many membrane processes and mechanisms. These include signaling, sorting, and exo- and endocytic processes that are occurring all the time in a living cell. Paradoxically, not only are the local structure and composition of the membrane matters of much debate and discussion, the mechanisms that govern its genesis remain highly controversial. Here, we discuss a swathe of new technological advances that may be applied to understand the local structure and composition of the membrane of a living cell from the molecular scale to the scale of the whole membrane.
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Affiliation(s)
- Thomas S van Zanten
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
| | - Satyajit Mayor
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
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