1
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Zangi R. Breakdown of Langmuir Adsorption Isotherm in Small Closed Systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38315174 PMCID: PMC10883037 DOI: 10.1021/acs.langmuir.3c03894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
For more than a century, monolayer adsorptions in which adsorbate molecules and adsorbing sites behave ideally have been successfully described by Langmuir's adsorption isotherm. For example, the amount of adsorbed material, as a function of concentration of the material which is not adsorbed, obeys Langmuir's equation. In this paper, we argue that this relation is valid only for macroscopic systems. However, when particle numbers of adsorbate molecules and/or adsorbing sites are small, Langmuir's model fails to describe the chemical equilibrium of the system. This is because the kinetics of forming, or the probability of observing, occupied sites arises from two-body interactions, and as such, ought to include cross-correlations between particle numbers of the adsorbate and adsorbing sites. The effect of these correlations, as reflected by deviations in predicting composition when correlations are ignored, increases with decreasing particle numbers and becomes substantial when only few adsorbate molecules, or adsorbing sites, are present in the system. In addition, any change that augments the fraction of occupied sites at equilibrium (e.g., smaller volume, lower temperature, or stronger adsorption energy) further increases the discrepancy between observed properties of small systems and those predicted by Langmuir's theory. In contrast, for large systems, these cross-correlations become negligible, and therefore when expressing properties involving two-body processes, it is possible to consider independently the concentration of each component. By applying statistical mechanics concepts, we derive a general expression of the equilibrium constant for adsorption. It is also demonstrated that in ensembles in which total numbers of particles are fixed, the magnitudes of fluctuations in particle numbers alone can predict the average chemical composition of the system. Moreover, an alternative adsorption equation, predicting the average fraction of occupied sites from the value of the equilibrium constant, is proposed. All derived relations were tested against results obtained by Monte Carlo simulations.
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Affiliation(s)
- Ronen Zangi
- Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastián, Spain
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, 20018 Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
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2
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White D, Smith MA, Chanda B, Goldsmith RH. Strategies for Overcoming the Single-Molecule Concentration Barrier. ACS MEASUREMENT SCIENCE AU 2023; 3:239-257. [PMID: 37600457 PMCID: PMC10436376 DOI: 10.1021/acsmeasuresciau.3c00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 08/22/2023]
Abstract
Fluorescence-based single-molecule approaches have helped revolutionize our understanding of chemical and biological mechanisms. Unfortunately, these methods are only suitable at low concentrations of fluorescent molecules so that single fluorescent species of interest can be successfully resolved beyond background signal. The application of these techniques has therefore been limited to high-affinity interactions despite most biological and chemical processes occurring at much higher reactant concentrations. Fortunately, recent methodological advances have demonstrated that this concentration barrier can indeed be broken, with techniques reaching concentrations as high as 1 mM. The goal of this Review is to discuss the challenges in performing single-molecule fluorescence techniques at high-concentration, offer applications in both biology and chemistry, and highlight the major milestones that shatter the concentration barrier. We also hope to inspire the widespread use of these techniques so we can begin exploring the new physical phenomena lying beyond this barrier.
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Affiliation(s)
- David
S. White
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Mackinsey A. Smith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Baron Chanda
- Center
for
Investigation of Membrane Excitability Diseases, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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3
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Buholzer KJ, McIvor J, Zosel F, Teppich C, Nettels D, Mercadante D, Schuler B. Multilayered allosteric modulation of coupled folding and binding by phosphorylation, peptidyl-prolyl cis/trans isomerization, and diversity of interaction partners. J Chem Phys 2022; 157:235102. [PMID: 36550025 DOI: 10.1063/5.0128273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) play key roles in cellular regulation, including signal transduction, transcription, and cell-cycle control. Accordingly, IDPs can commonly interact with numerous different target proteins, and their interaction networks are expected to be highly regulated. However, many of the underlying regulatory mechanisms have remained unclear. Here, we examine the representative case of the nuclear coactivator binding domain (NCBD) of the large multidomain protein CBP, a hub in transcriptional regulation, and the interaction with several of its binding partners. Single-molecule Förster resonance energy transfer measurements show that phosphorylation of NCBD reduces its binding affinity, with effects that vary depending on the binding partner and the site and number of modifications. The complexity of the interaction is further increased by the dependence of the affinities on peptidyl-prolyl cis/trans isomerization in NCBD. Overall, our results reveal the potential for allosteric regulation on at least three levels: the different affinities of NCBD for its different binding partners, the differential modulation of these affinities by phosphorylation, and the effect of peptidyl-prolyl cis/trans isomerization on binding.
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Affiliation(s)
- Karin J Buholzer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Jordan McIvor
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Franziska Zosel
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Christian Teppich
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Davide Mercadante
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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4
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Zelger-Paulus S, Hadzic MCAS, Sigel RKO, Börner R. Encapsulation of Fluorescently Labeled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF Microscopy. Methods Mol Biol 2020; 2113:1-16. [PMID: 32006303 DOI: 10.1007/978-1-0716-0278-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Imaging fluorescently labeled biomolecules on a single-molecule level is a well-established technique to follow intra- and intermolecular processes in time, usually hidden in the ensemble average. The classical approach comprises surface immobilization of the molecule of interest, which increases the risk of restricting the natural behavior due to surface interactions. Encapsulation of such biomolecules into surface-tethered phospholipid vesicles enables to follow one molecule at a time, freely diffusing and without disturbing surface interactions. Further, the encapsulation allows to keep reaction partners (reactants and products) in close proximity and enables higher temperatures otherwise leading to desorption of the direct immobilized biomolecules.Here, we describe a detailed protocol for the encapsulation of a catalytically active RNA starting from surface passivation over RNA encapsulation to data evaluation of single-molecule FRET experiments in TIRF microscopy. We present an optimized procedure that preserves RNA functionality and applies to investigations of, e.g., large ribozymes and RNAs, where direct immobilization is structurally not possible.
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Affiliation(s)
| | | | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
| | - Richard Börner
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
- Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, Mittweida, Germany.
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5
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Johnston CL, Marzano NR, van Oijen AM, Ecroyd H. Using Single-Molecule Approaches to Understand the Molecular Mechanisms of Heat-Shock Protein Chaperone Function. J Mol Biol 2018; 430:4525-4546. [PMID: 29787765 DOI: 10.1016/j.jmb.2018.05.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 02/01/2023]
Abstract
The heat-shock proteins (Hsp) are a family of molecular chaperones, which collectively form a network that is critical for the maintenance of protein homeostasis. Traditional ensemble-based measurements have provided a wealth of knowledge on the function of individual Hsps and the Hsp network; however, such techniques are limited in their ability to resolve the heterogeneous, dynamic and transient interactions that molecular chaperones make with their client proteins. Single-molecule techniques have emerged as a powerful tool to study dynamic biological systems, as they enable rare and transient populations to be identified that would usually be masked in ensemble measurements. Thus, single-molecule techniques are particularly amenable for the study of Hsps and have begun to be used to reveal novel mechanistic details of their function. In this review, we discuss the current understanding of the chaperone action of Hsps and how gaps in the field can be addressed using single-molecule methods. Specifically, this review focuses on the ATP-independent small Hsps and the broader Hsp network and describes how these dynamic systems are amenable to single-molecule techniques.
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Affiliation(s)
- Caitlin L Johnston
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Nicholas R Marzano
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Heath Ecroyd
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
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6
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Keller AM, DeVore MS, Stich DG, Vu DM, Causgrove T, Werner JH. Multicolor Three-Dimensional Tracking for Single-Molecule Fluorescence Resonance Energy Transfer Measurements. Anal Chem 2018; 90:6109-6115. [DOI: 10.1021/acs.analchem.8b00244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Aaron M. Keller
- Department of Chemistry, William Jewell College, Liberty, Missouri 64068, United States
| | - Matthew S. DeVore
- Department of Natural & Applied Sciences, Evangel University, Springfield, Missouri 65802, United States
| | - Dominik G. Stich
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado 80045, United States
| | - Dung M. Vu
- Physical Chemistry & Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Timothy Causgrove
- Department of Physical & Environmental Sciences, Texas A&M University—Corpus Christi, Corpus Christi, Texas 78412, United States
| | - James H. Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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7
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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8
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Zhang Z, Yomo D, Gradinaru C. Choosing the right fluorophore for single-molecule fluorescence studies in a lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1242-1253. [PMID: 28392350 DOI: 10.1016/j.bbamem.2017.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/14/2017] [Accepted: 04/05/2017] [Indexed: 10/19/2022]
Abstract
Nonspecific interactions between lipids and fluorophores can alter the outcomes of single-molecule spectroscopy of membrane proteins in live cells, liposomes or lipid nanodiscs and of cytosolic proteins encapsulated in liposomes or tethered to supported lipid bilayers. To gain insight into these effects, we examined interactions between 9 dyes that are commonly used as labels for single-molecule fluorescence (SMF) and 6 standard lipids including cationic, zwitterionic and anionic types. The diffusion coefficients of dyes in the absence and presence of set amounts of lipid vesicles were measured by fluorescence correlation spectroscopy (FCS). The partition coefficients and the free energies of partitioning for different fluorophore-lipid pairs were obtained by global fitting of the titration FCS curves. Lipids with different charges, head groups and degrees of chain saturation were investigated, and interactions with dyes are discussed in terms of hydrophobic, electrostatic and steric contributions. Fluorescence imaging of individual fluorophores adsorbed on supported lipid bilayers provides visualization and additional quantification of the strength of dye-lipid interaction in the context of single-molecule measurements. By dissecting fluorophore-lipid interactions, our study provides new insights into setting up single-molecule fluorescence spectroscopy experiments with minimal interference from interactions between fluorescent labels and lipids in the environment.
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Affiliation(s)
- Zhenfu Zhang
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Dan Yomo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Claudiu Gradinaru
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada.
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9
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Chen YC, Jablonski AE, Issaeva I, Bourassa D, Hsiang JC, Fahrni CJ, Dickson RM. Optically Modulated Photoswitchable Fluorescent Proteins Yield Improved Biological Imaging Sensitivity. J Am Chem Soc 2015; 137:12764-7. [PMID: 26402244 DOI: 10.1021/jacs.5b07871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photoswitchable fluorescent proteins (PS-FPs) open grand new opportunities in biological imaging. Through optical manipulation of FP emission, we demonstrate that dual-laser modulated synchronously amplified fluorescence image recovery (DM-SAFIRe) improves signal contrast in high background through unambiguous demodulation and is linear in relative fluorophore abundance at different points in the cell. The unique bright-to-dark state interconversion rates of each PS-FP not only enables discrimination of different, yet spectrally indistinguishable FPs, but also allows signal rejection of diffusing relative to bound forms of the same PS-FP, rsFastLime. Adding to the sensitivity gains realized from rejecting non-modulatable background, the selective signal recovery of immobilized vs diffusing intracellular rsFastLime suggests that DM-SAFIRe can detect weak protein-protein interactions that are normally obscured by large fractions of unbound FPs.
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Affiliation(s)
- Yen-Cheng Chen
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Amy E Jablonski
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Irina Issaeva
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Daisy Bourassa
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Jung-Cheng Hsiang
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Christoph J Fahrni
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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10
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Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
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Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
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11
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Abstract
The Michaelis-Menten equation provides a hundred-year-old prediction by which any increase in the rate of substrate unbinding will decrease the rate of enzymatic turnover. Surprisingly, this prediction was never tested experimentally nor was it scrutinized using modern theoretical tools. Here we show that unbinding may also speed up enzymatic turnover--turning a spotlight to the fact that its actual role in enzymatic catalysis remains to be determined experimentally. Analytically constructing the unbinding phase space, we identify four distinct categories of unbinding: inhibitory, excitatory, superexcitatory, and restorative. A transition in which the effect of unbinding changes from inhibitory to excitatory as substrate concentrations increase, and an overlooked tradeoff between the speed and efficiency of enzymatic reactions, are naturally unveiled as a result. The theory presented herein motivates, and allows the interpretation of, groundbreaking experiments in which existing single-molecule manipulation techniques will be adapted for the purpose of measuring enzymatic turnover under a controlled variation of unbinding rates. As we hereby show, these experiments will not only shed first light on the role of unbinding but will also allow one to determine the time distribution required for the completion of the catalytic step in isolation from the rest of the enzymatic turnover cycle.
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12
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Chen P, Keller AM, Joshi CP, Martell DJ, Andoy NM, Benítez JJ, Chen TY, Santiago AG, Yang F. Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones. Biochemistry 2013; 52:7170-83. [PMID: 24053279 DOI: 10.1021/bi400597v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.
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Affiliation(s)
- Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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13
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Christensen AL, Lohr C, Christensen SM, Stamou D. Single vesicle biochips for ultra-miniaturized nanoscale fluidics and single molecule bioscience. LAB ON A CHIP 2013; 13:3613-3625. [PMID: 23856986 DOI: 10.1039/c3lc50492a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
One of the major bottlenecks in the development of biochips is maintaining the structure and function of biomolecules when interfacing them with hard matter (glass, plastics, metals, etc.), a challenge that is exacerbated during miniaturization that inevitably increases the interface to volume ratio of these devices. Biochips based on immobilized vesicles circumvent this problem by encapsulating biomolecules in the protective environment of a lipid bilayer, thus minimizing interactions with hard surfaces. Here we review the development of biochips based on arrays of single nanoscale vesicles, their fabrication via controlled self-assembly, and their characterization using fluorescence microscopy. We also highlight their applications in selected fields such as nanofluidics and single molecule bioscience. Despite their great potential for improved biocompatibility, extreme miniaturization and high throughput, single vesicle biochips are still a niche technology that has yet to establish its commercial relevance.
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Affiliation(s)
- Andreas L Christensen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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14
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Elting MW, Leslie SR, Churchman LS, Korlach J, McFaul CMJ, Leith JS, Levene MJ, Cohen AE, Spudich JA. Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC). OPTICS EXPRESS 2013; 21:1189-202. [PMID: 23389011 PMCID: PMC3632498 DOI: 10.1364/oe.21.001189] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/14/2012] [Accepted: 12/15/2012] [Indexed: 05/22/2023]
Abstract
Resolving single fluorescent molecules in the presence of high fluorophore concentrations remains a challenge in single-molecule biophysics that limits our understanding of weak molecular interactions. Total internal reflection fluorescence (TIRF) imaging, the workhorse of single-molecule fluorescence microscopy, enables experiments at concentrations up to about 100 nM, but many biological interactions have considerably weaker affinities, and thus require at least one species to be at micromolar or higher concentration. Current alternatives to TIRF often require three-dimensional confinement, and thus can be problematic for extended substrates, such as cytoskeletal filaments. To address this challenge, we have demonstrated and applied two new single-molecule fluorescence microscopy techniques, linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC), for imaging the processive motion of molecular motors myosin V and VI along actin filaments. Both technologies will allow imaging in the presence of higher fluorophore concentrations than TIRF microscopy. They will enable new biophysical measurements of a wide range of processive molecular motors that move along filamentous tracks, such as other myosins, dynein, and kinesin. A particularly salient application of these technologies will be to examine chemomechanical coupling by directly imaging fluorescent nucleotide molecules interacting with processive motors as they traverse their actin or microtubule tracks.
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Affiliation(s)
- Mary Williard Elting
- Department of Applied Physics, Stanford University, Stanford, California 94305,
USA
- Department of Biochemistry, Stanford University, Stanford, California 94305,
USA
- Current Address: Department of Cell and Tissue Biology, University of California, San Francisco, California 94143,
USA
| | - Sabrina R. Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2TA,
Canada
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, Massachusetts 02138,
USA
| | - L. Stirling Churchman
- Department of Biochemistry, Stanford University, Stanford, California 94305,
USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115,
USA
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025,
USA
| | | | - Jason S. Leith
- Department of Physics, McGill University, Montreal, QC H3A 2TA,
Canada
| | - Michael J. Levene
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520,
USA
| | - Adam E. Cohen
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, Massachusetts 02138,
USA
| | - James A. Spudich
- Department of Biochemistry, Stanford University, Stanford, California 94305,
USA
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15
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Keller AM, Benítez JJ, Klarin D, Zhong L, Goldfogel M, Yang F, Chen TY, Chen P. Dynamic multibody protein interactions suggest versatile pathways for copper trafficking. J Am Chem Soc 2012; 134:8934-43. [PMID: 22578168 DOI: 10.1021/ja3018835] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As part of intracellular copper trafficking pathways, the human copper chaperone Hah1 delivers Cu(+) to the Wilson's Disease Protein (WDP) via weak and dynamic protein-protein interactions. WDP contains six homologous metal binding domains (MBDs) connected by flexible linkers, and these MBDs all can receive Cu(+) from Hah1. The functional roles of the MBD multiplicity in Cu(+) trafficking are not well understood. Building on our previous study of the dynamic interactions between Hah1 and the isolated fourth MBD of WDP, here we study how Hah1 interacts with MBD34, a double-domain WDP construct, using single-molecule fluorescence resonance energy transfer (smFRET) combined with vesicle trapping. By alternating the positions of the smFRET donor and acceptor, we systematically probed Hah1-MBD3, Hah1-MBD4, and MBD3-MBD4 interaction dynamics within the multidomain system. We found that the two interconverting interaction geometries were conserved in both intermolecular Hah1-MBD and intramolecular MBD-MBD interactions. The Hah1-MBD interactions within MBD34 are stabilized by an order of magnitude relative to the isolated single-MBDs, and thermodynamic and kinetic evidence suggest that Hah1 can interact with both MBDs simultaneously. The enhanced interaction stability of Hah1 with the multi-MBD system, the dynamic intramolecular MBD-MBD interactions, and the ability of Hah1 to interact with multiple MBDs simultaneously suggest an efficient and versatile mechanism for the Hah1-to-WDP pathway to transport Cu(+).
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Affiliation(s)
- Aaron M Keller
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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Chen YF, Serey X, Sarkar R, Chen P, Erickson D. Controlled photonic manipulation of proteins and other nanomaterials. NANO LETTERS 2012; 12:1633-7. [PMID: 22283484 PMCID: PMC3461583 DOI: 10.1021/nl204561r] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The ability to controllably handle the smallest materials is a fundamental enabling technology for nanoscience. Conventional optical tweezers have proven useful for manipulating microscale objects but cannot exert enough force to manipulate dielectric materials smaller than about 100 nm. Recently, several near-field optical trapping techniques have been developed that can provide higher trapping stiffness, but they tend to be limited in their ability to reversibly trap and release smaller materials due to a combination of the extremely high electromagnetic fields and the resulting local temperature rise. Here, we have developed a new form of photonic crystal "nanotweezer" that can trap and release on-command Wilson disease proteins, quantum dots, and 22 nm polymer particles with a temperature rise less than ~0.3 K, which is below the point where unwanted fluid mechanical effects will prevent trapping or damage biological targets.
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Affiliation(s)
- Yih-Fan Chen
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, USA
- Medical Device Innovation Center and Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Xavier Serey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Rupa Sarkar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - David Erickson
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, USA
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McCann JJ, Zheng L, Chiantia S, Bowen ME. Domain orientation in the N-Terminal PDZ tandem from PSD-95 is maintained in the full-length protein. Structure 2011; 19:810-20. [PMID: 21645852 DOI: 10.1016/j.str.2011.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/24/2011] [Accepted: 02/21/2011] [Indexed: 12/19/2022]
Abstract
Tandem PDZ domains have been suggested to form structurally independent supramodules. However, dissimilarity between crystallography and NMR models emphasize their malleable conformation. Studies in full-length scaffold proteins are needed to examine the effect of tertiary interactions within their native context. Using single-molecule fluorescence to characterize the N-terminal PDZ tandem in PSD-95, we provide the first direct evidence that PDZ tandems can be structurally independent within a full-length scaffold protein. Molecular refinement using our data converged on a single structure with an antiparallel alignment of the ligand-binding sites. Devoid of interaction partners, single-molecule conditions captured PSD-95 in its unbound, ground state. Interactions between PDZ domains could not be detected while fluctuation correlation spectroscopy showed that other conformations are dynamically sampled. We conclude that ultra-weak interactions stabilize the conformation providing a "low-relief" energy landscape that allows the domain orientation to be flipped by environmental interactions.
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Affiliation(s)
- James J McCann
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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Benítez JJ, Keller AM, Huffman DL, Yatsunyk LA, Rosenzweig AC, Chen P. Relating dynamic protein interactions of metallochaperones with metal transfer at the single-molecule level. Faraday Discuss 2011; 148:71-82; discussion 97-108. [PMID: 21322478 DOI: 10.1039/c004913a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Metallochaperones undertake specific interactions with their target proteins to deliver metal ions inside cells. Understanding how these protein interactions are coupled with the underlying metal transfer process is important, but challenging because they are weak and dynamic. Here we use a nanovesicle trapping scheme to enable single-molecule FRET measurements of the weak, dynamic interactions between the copper chaperone Hahl and the fourth metal binding domain (MBD4) of WDP. By monitoring the behaviors of single interacting pairs, we visualize their interactions in real time in both the absence and the presence of various equivalents of Cu(1+). Regardless of the proteins' metallation state, we observe multiple, interconverting interaction complexes between Hah1 and MBD4. Within our experimental limit, the overall interaction geometries of these complexes appear invariable, but their stabilities are dependent on the proteins' metallation state. In apo-holo Hah1-MBD4 interactions, the complexes are stabilized relative to that observed in the apo-apo interactions. This stabilization is indiscernible when Hah1's Cu(1+)-binding is eliminated or when both proteins have Cu(1+) loaded. The nature of this Cu(1+)-induced complex stabilization and of the interaction complexes are discussed. These Cu(1+)-induced effects on the Hah1-MBD4 interactions provide a step toward understanding how the dynamic protein interactions of copper chaperones are coupled with their metal transfer function.
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Affiliation(s)
- Jaime J Benítez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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van Oijen AM. Single-molecule approaches to characterizing kinetics of biomolecular interactions. Curr Opin Biotechnol 2011; 22:75-80. [DOI: 10.1016/j.copbio.2010.10.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/06/2010] [Indexed: 12/01/2022]
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