1
|
Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
Collapse
Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| |
Collapse
|
2
|
Kleinherbers E, Stegmann P, Kurzmann A, Geller M, Lorke A, König J. Pushing the Limits in Real-Time Measurements of Quantum Dynamics. PHYSICAL REVIEW LETTERS 2022; 128:087701. [PMID: 35275653 DOI: 10.1103/physrevlett.128.087701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Time-resolved studies of quantum systems are the key to understanding quantum dynamics at its core. The real-time measurement of individual quantum numbers as they switch between certain discrete values, well known as a "random telegraph signal," is expected to yield maximal physical insight. However, the signal suffers from both systematic errors, such as a limited time resolution and noise from the measurement apparatus, as well as statistical errors due to a limited amount of data. Here we demonstrate that an evaluation scheme based on factorial cumulants can reduce the influence of such errors by orders of magnitude. The error resilience is supported by a general theory for the detection errors as well as experimental data of single-electron tunneling through a self-assembled quantum dot. Thus, factorial cumulants push the limits in the analysis of random telegraph data, which represent a wide class of experiments in physics, chemistry, engineering, and life sciences.
Collapse
Affiliation(s)
- E Kleinherbers
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - P Stegmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - A Kurzmann
- 2nd Institute of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - M Geller
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - A Lorke
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - J König
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| |
Collapse
|
3
|
Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
| |
Collapse
|
4
|
Single-Molecule FRET Detection of Sub-Nanometer Distance Changes in the Range below a 3-Nanometer Scale. BIOSENSORS-BASEL 2020; 10:bios10110168. [PMID: 33171642 PMCID: PMC7695202 DOI: 10.3390/bios10110168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/24/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
Single-molecule fluorescence energy transfer (FRET) detection has become a key technique to monitor intra- and intermolecular distance changes in biological processes. As the sensitive detection range of conventional FRET pairs is limited to 3-8 nm, complement probes are necessary for extending this typical working range. Here, we realized a single-molecule FRET assay for a short distance range of below 3 nm by using a Cy2-Cy7 pair having extremely small spectral overlap. Using two DNA duplexes with a small difference in the labeling position, we demonstrated that our assay can observe subtle changes at a short distance range. High sensitivity in the range of 1-3 nm and compatibility with the conventional FRET assay make this approach useful for understanding dynamics at a short distance.
Collapse
|
5
|
Gilburt JAH, Girvan P, Blagg J, Ying L, Dodson CA. Ligand discrimination between active and inactive activation loop conformations of Aurora-A kinase is unmodified by phosphorylation. Chem Sci 2019; 10:4069-4076. [PMID: 31015948 PMCID: PMC6461105 DOI: 10.1039/c8sc03669a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/01/2019] [Indexed: 01/14/2023] Open
Abstract
Activation loop phosphorylation changes the position of equilibrium between DFG-in-like and DFG-out-like conformations but not the conformational preference of inhibitors.
Structure-based drug design is commonly used to guide the development of potent and specific enzyme inhibitors. Many enzymes – such as protein kinases – adopt multiple conformations, and conformational interconversion is expected to impact on the design of small molecule inhibitors. We measured the dynamic equilibrium between DFG-in-like active and DFG-out-like inactive conformations of the activation loop of unphosphorylated Aurora-A alone, in the presence of the activator TPX2, and in the presence of kinase inhibitors. The unphosphorylated kinase had a shorter residence time of the activation loop in the active conformation and a shift in the position of equilibrium towards the inactive conformation compared with phosphorylated kinase for all conditions measured. Ligand binding was associated with a change in the position of conformational equilibrium which was specific to each ligand and independent of the kinase phosphorylation state. As a consequence of this, the ability of a ligand to discriminate between active and inactive activation loop conformations was also independent of phosphorylation. Importantly, we discovered that the presence of multiple enzyme conformations can lead to a plateau in the overall ligand Kd, despite increasing affinity for the chosen target conformation, and modelled the conformational discrimination necessary for a conformation-promoting ligand.
Collapse
Affiliation(s)
- James A H Gilburt
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Paul Girvan
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , 15 Cotswold Road , Sutton , Surrey SM2 5NG , UK
| | - Liming Ying
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Charlotte A Dodson
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK.,Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK .
| |
Collapse
|
6
|
Schröder T, Scheible MB, Steiner F, Vogelsang J, Tinnefeld P. Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures. NANO LETTERS 2019; 19:1275-1281. [PMID: 30681342 DOI: 10.1021/acs.nanolett.8b04845] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An ideal point light source is as small and as bright as possible. For fluorescent point light sources, homogeneity of the light sources is important as well as that the fluorescent units inside the light source maintain their photophysical properties, which is compromised by dye aggregation. Here we propose DNA origami as a rigid scaffold to arrange dye molecules in a dense pixel array with high control of stoichiometry and dye-dye interactions. In order to find the highest labeling density in a DNA origami structure without influencing dye photophysics, we alter the distance of two ATTO647N dyes in single base pair steps and probe the dye-dye interactions on the single-molecule level. For small distances strong quenching in terms of intensity and fluorescence lifetime is observed. With increasing distance, we observe reduced quenching and molecular dynamics. However, energy transfer processes in the weak coupling regime still have a significant impact and can lead to quenching by singlet-dark-state-annihilation. Our study fills a gap of studying the interactions of dyes relevant for superresolution microscopy with dense labeling and for single-molecule biophysics. Incorporating these findings in a 3D DNA origami object will pave the way to bright and homogeneous DNA origami nanobeads.
Collapse
Affiliation(s)
- Tim Schröder
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| | - Max B Scheible
- GATTAquant GmbH , Am Schlosshof 8 , 91355 Hiltpoltstein , Germany
| | - Florian Steiner
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| | - Jan Vogelsang
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| |
Collapse
|
7
|
Donaphon B, Bloom LB, Levitus M. Photophysical characterization of interchromophoric interactions between rhodamine dyes conjugated to proteins. Methods Appl Fluoresc 2018; 6:045004. [PMID: 29985159 DOI: 10.1088/2050-6120/aad20f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rhodamine dyes in aqueous solution form non-fluorescent dimers with a plane-to-plane stacking geometry (H-dimers). The self-quenching properties of these dimers have been exploited to probe the conformation and dynamics of proteins using a variety of fluorescence approaches that require the interpretation of fluorescence intensities, lifetimes and fluctuations. Here, we report on a systematic study of the photophysical properties of three rhodamine dyes (tetramethylrhodamine, Alexa 488 and Alexa 546) covalently bound to the E. coli sliding clamp (β clamp) with emphasis on the properties of the H-dimers that form when the dimeric protein is labeled with one dye at each side of the dimer interface. Overall, results are consistent with an equilibrium between non-emissive dimers and unstacked monomers that experience efficient dynamic quenching Protein constructs labeled with tetramethylrhodamine show the characteristic features of H-dimers in their absorption spectra and a c.a. 40-fold quenching of fluorescence intensity. The degree of quenching decreases when samples are labeled with a tetramethylrhodamine derivative bearing a six-carbon linker. H-dimers do not form in samples labeled with Alexa 488 and A546, but fluorescence is still quenched in these samples through a dynamic mechanism. These results should help researchers design and interpret fluorescence experiments that take advantage of the properties of rhodamine dimers in protein research.
Collapse
Affiliation(s)
- Bryan Donaphon
- School of Molecular Sciences and Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States of America
| | | | | |
Collapse
|
8
|
Xu Z, Gakhar L, Bain FE, Spies M, Fuentes EJ. The Tiam1 guanine nucleotide exchange factor is auto-inhibited by its pleckstrin homology coiled-coil extension domain. J Biol Chem 2017; 292:17777-17793. [PMID: 28882897 PMCID: PMC5663878 DOI: 10.1074/jbc.m117.799114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/25/2017] [Indexed: 12/22/2022] Open
Abstract
T-cell lymphoma invasion and metastasis 1 (Tiam1) is a Dbl-family guanine nucleotide exchange factor (GEF) that specifically activates the Rho-family GTPase Rac1 in response to upstream signals, thereby regulating cellular processes including cell adhesion and migration. Tiam1 contains multiple domains, including an N-terminal pleckstrin homology coiled-coiled extension (PHn-CC-Ex) and catalytic Dbl homology and C-terminal pleckstrin homology (DH-PHc) domain. Previous studies indicate that larger fragments of Tiam1, such as the region encompassing the N-terminal to C-terminal pleckstrin homology domains (PHn-PHc), are auto-inhibited. However, the domains in this region responsible for inhibition remain unknown. Here, we show that the PHn-CC-Ex domain inhibits Tiam1 GEF activity by directly interacting with the catalytic DH-PHc domain, preventing Rac1 binding and activation. Enzyme kinetics experiments suggested that Tiam1 is auto-inhibited through occlusion of the catalytic site rather than by allostery. Small angle X-ray scattering and ensemble modeling yielded models of the PHn-PHc fragment that indicate it is in equilibrium between "open" and "closed" conformational states. Finally, single-molecule experiments support a model in which conformational sampling between the open and closed states of Tiam1 contributes to Rac1 dissociation. Our results highlight the role of the PHn-CC-Ex domain in Tiam1 GEF regulation and suggest a combinatorial model for GEF inhibition and activation of the Rac1 signaling pathway.
Collapse
Affiliation(s)
- Zhen Xu
- From the Department of Biochemistry
| | - Lokesh Gakhar
- From the Department of Biochemistry
- Protein Crystallography Facility, and
| | | | - Maria Spies
- From the Department of Biochemistry
- Holden Comprehensive Cancer Center, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Ernesto J Fuentes
- From the Department of Biochemistry,
- Holden Comprehensive Cancer Center, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| |
Collapse
|
9
|
Gilburt JAH, Sarkar H, Sheldrake P, Blagg J, Ying L, Dodson CA. Dynamic Equilibrium of the Aurora A Kinase Activation Loop Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- James A. H. Gilburt
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| | - Hajrah Sarkar
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| | - Peter Sheldrake
- Cancer Research UK Cancer Therapeutics Unit; The Institute of Cancer Research; 15 Cotswold Road Sutton Surrey SM2 5NG UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit; The Institute of Cancer Research; 15 Cotswold Road Sutton Surrey SM2 5NG UK
| | - Liming Ying
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| | - Charlotte A. Dodson
- National Heart & Lung Institute; SAF Building; Imperial College London; London SW7 2AZ UK
| |
Collapse
|
10
|
Gilburt JAH, Sarkar H, Sheldrake P, Blagg J, Ying L, Dodson CA. Dynamic Equilibrium of the Aurora A Kinase Activation Loop Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017; 56:11409-11414. [PMID: 28700101 PMCID: PMC5601181 DOI: 10.1002/anie.201704654] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Indexed: 12/14/2022]
Abstract
The conformation of the activation loop (T-loop) of protein kinases underlies enzymatic activity and influences the binding of small-molecule inhibitors. By using single-molecule fluorescence spectroscopy, we have determined that phosphorylated Aurora A kinase is in dynamic equilibrium between a DFG-in-like active T-loop conformation and a DFG-out-like inactive conformation, and have measured the rate constants of interconversion. Addition of the Aurora A activating protein TPX2 shifts the equilibrium towards an active T-loop conformation whereas addition of the inhibitors MLN8054 and CD532 favors an inactive T-loop. We show that Aurora A binds TPX2 and MLN8054 simultaneously and provide a new model for kinase conformational behavior. Our approach will enable conformation-specific effects to be integrated into inhibitor discovery across the kinome, and we outline some immediate consequences for structure-based drug discovery.
Collapse
Affiliation(s)
- James A. H. Gilburt
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| | - Hajrah Sarkar
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| | - Peter Sheldrake
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadSuttonSurreySM2 5NGUK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadSuttonSurreySM2 5NGUK
| | - Liming Ying
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| | - Charlotte A. Dodson
- National Heart & Lung InstituteSAF BuildingImperial College LondonLondonSW7 2AZUK
| |
Collapse
|
11
|
Tutkus M, Marciulionis T, Sasnauskas G, Rutkauskas D. DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field. Biophys J 2017; 112:850-858. [PMID: 28297644 DOI: 10.1016/j.bpj.2017.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/06/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
The single-molecule Förster resonance energy transfer (FRET) is a powerful tool to study interactions and conformational changes of biological molecules in the distance range from a few to 10 nm. In this study, we demonstrate a method to augment this range with longer distances. The method is based on the intensity changes of a tethered fluorophore, diffusing in the exponentially decaying evanescent excitation field. In combination with FRET it allowed us to reveal and characterize the dynamics of what had been inaccessible conformations of the DNA-protein complex. Our model system, restriction enzyme Ecl18kI, interacts with a FRET pair-labeled DNA fragment to form two different DNA loop conformations. The DNA-protein interaction geometry is such that the efficient FRET is expected for one of these conformations-"antiparallel" loop. In the alternative "parallel" loop, the expected distance between the dyes is outside the range accessible by FRET. Therefore, "antiparallel" looping is observed in a single-molecule time trajectory as discrete transitions to a state of high FRET efficiency. At the same time, transitions to a high-intensity state of the directly excited acceptor fluorophore on a DNA tether are due to a change of its average position in the evanescent field of excitation and can be associated with a loop of either "parallel" or "antiparallel" configuration. Simultaneous analysis of FRET and acceptor intensity trajectories then allows us to discriminate different DNA loop conformations and access the average lifetimes of different states.
Collapse
Affiliation(s)
- Marijonas Tutkus
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Tomas Marciulionis
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | | | - Danielis Rutkauskas
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania.
| |
Collapse
|
12
|
Daly S, Choi CM, Chirot F, MacAleese L, Antoine R, Dugourd P. Action-Self Quenching: Dimer-Induced Fluorescence Quenching of Chromophores as a Probe for Biomolecular Structure. Anal Chem 2017; 89:4604-4610. [DOI: 10.1021/acs.analchem.7b00152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven Daly
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Chang Min Choi
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Fabien Chirot
- Université Lyon, Université Claude Bernard Lyon 1, Ens de Lyon, CNRS, Institut des Sciences Analytiques UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Luke MacAleese
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Rodolphe Antoine
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| | - Philippe Dugourd
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière UMR 5306, F-69100, Villeurbanne, France
| |
Collapse
|
13
|
Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Sci Rep 2016; 6:33257. [PMID: 27641327 PMCID: PMC5027553 DOI: 10.1038/srep33257] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 01/24/2023] Open
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
Collapse
|
14
|
Farooq S, Hohlbein J. Camera-based single-molecule FRET detection with improved time resolution. Phys Chem Chem Phys 2016; 17:27862-72. [PMID: 26439729 DOI: 10.1039/c5cp04137f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The achievable time resolution of camera-based single-molecule detection is often limited by the frame rate of the camera. Especially in experiments utilizing single-molecule Förster resonance energy transfer (smFRET) to probe conformational dynamics of biomolecules, increasing the frame rate by either pixel-binning or cropping the field of view decreases the number of molecules that can be monitored simultaneously. Here, we present a generalised excitation scheme termed stroboscopic alternating-laser excitation (sALEX) that significantly improves the time resolution without sacrificing highly parallelised detection in total internal reflection fluorescence (TIRF) microscopy. In addition, we adapt a technique known from diffusion-based confocal microscopy to analyse the complex shape of FRET efficiency histograms. We apply both sALEX and dynamic probability distribution analysis (dPDA) to resolve conformational dynamics of interconverting DNA hairpins in the millisecond time range.
Collapse
Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
| | | |
Collapse
|
15
|
Boehm EM, Spies M, Washington MT. PCNA tool belts and polymerase bridges form during translesion synthesis. Nucleic Acids Res 2016; 44:8250-60. [PMID: 27325737 PMCID: PMC5041468 DOI: 10.1093/nar/gkw563] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022] Open
Abstract
Large multi-protein complexes play important roles in many biological processes, including DNA replication and repair, transcription, and signal transduction. One of the challenges in studying such complexes is to understand their mechanisms of assembly and disassembly and their architectures. Using single-molecule total internal reflection (TIRF) microscopy, we have examined the assembly and disassembly of the multi-protein complex that carries out translesion synthesis, the error-prone replication of damaged DNA. We show that the ternary complexes containing proliferating cell nuclear antigen (PCNA) and two non-classical DNA polymerases, Rev1 and DNA polymerase η, have two architectures: PCNA tool belts and Rev1 bridges. Moreover, these complexes are dynamic and their architectures can interconvert without dissociation. The formation of PCNA tool belts and Rev1 bridges and the ability of these complexes to change architectures are likely means of facilitating selection of the appropriate non-classical polymerase and polymerase-switching events.
Collapse
Affiliation(s)
- Elizabeth M Boehm
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| |
Collapse
|
16
|
Boehm EM, Powers KT, Kondratick CM, Spies M, Houtman JCD, Washington MT. The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase η Mediates Its Interaction with the C-terminal Domain of Rev1. J Biol Chem 2016; 291:8735-44. [PMID: 26903512 DOI: 10.1074/jbc.m115.697938] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Indexed: 11/06/2022] Open
Abstract
Y-family DNA polymerases, such as polymerase η, polymerase ι, and polymerase κ, catalyze the bypass of DNA damage during translesion synthesis. These enzymes are recruited to sites of DNA damage by interacting with the essential replication accessory protein proliferating cell nuclear antigen (PCNA) and the scaffold protein Rev1. In most Y-family polymerases, these interactions are mediated by one or more conserved PCNA-interacting protein (PIP) motifs that bind in a hydrophobic pocket on the front side of PCNA as well as by conserved Rev1-interacting region (RIR) motifs that bind in a hydrophobic pocket on the C-terminal domain of Rev1. Yeast polymerase η, a prototypical translesion synthesis polymerase, binds both PCNA and Rev1. It possesses a single PIP motif but not an RIR motif. Here we show that the PIP motif of yeast polymerase η mediates its interactions both with PCNA and with Rev1. Moreover, the PIP motif of polymerase η binds in the hydrophobic pocket on the Rev1 C-terminal domain. We also show that the RIR motif of human polymerase κ and the PIP motif of yeast Msh6 bind both PCNA and Rev1. Overall, these findings demonstrate that PIP motifs and RIR motifs have overlapping specificities and can interact with both PCNA and Rev1 in structurally similar ways. These findings also suggest that PIP motifs are a more versatile protein interaction motif than previously believed.
Collapse
Affiliation(s)
| | | | | | | | - Jon C D Houtman
- Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | | |
Collapse
|
17
|
Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2016; 581:105-145. [PMID: 27793278 PMCID: PMC5403009 DOI: 10.1016/bs.mie.2016.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today.
Collapse
|
18
|
Morten MJ, Peregrina JR, Figueira-Gonzalez M, Ackermann K, Bode BE, White MF, Penedo JC. Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach. Nucleic Acids Res 2015; 43:10907-24. [PMID: 26578575 PMCID: PMC4678828 DOI: 10.1093/nar/gkv1225] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/29/2015] [Indexed: 01/28/2023] Open
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all organisms and are characterized by the presence of an OB (oligonucleotide/oligosaccharide/oligopeptide) binding motif to recognize single-stranded DNA (ssDNA). Despite their critical role in genome maintenance, our knowledge about SSB function is limited to proteins containing multiple OB-domains and little is known about single OB-folds interacting with ssDNA. Sulfolobus solfataricus SSB (SsoSSB) contains a single OB-fold and being the simplest representative of the SSB-family may serve as a model to understand fundamental aspects of SSB:DNA interactions. Here, we introduce a novel approach based on the competition between Förster resonance energy transfer (FRET), protein-induced fluorescence enhancement (PIFE) and quenching to dissect SsoSSB binding dynamics at single-monomer resolution. We demonstrate that SsoSSB follows a monomer-by-monomer binding mechanism that involves a positive-cooperativity component between adjacent monomers. We found that SsoSSB dynamic behaviour is closer to that of Replication Protein A than to Escherichia coli SSB; a feature that might be inherited from the structural analogies of their DNA-binding domains. We hypothesize that SsoSSB has developed a balance between high-density binding and a highly dynamic interaction with ssDNA to ensure efficient protection of the genome but still allow access to ssDNA during vital cellular processes.
Collapse
Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Jose R Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Maria Figueira-Gonzalez
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| |
Collapse
|
19
|
Kahlscheuer ML, Widom J, Walter NG. Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines. Methods Enzymol 2015; 558:539-570. [PMID: 26068753 PMCID: PMC4886477 DOI: 10.1016/bs.mie.2015.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Spliceosomes are multimegadalton RNA-protein complexes responsible for the faithful removal of noncoding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition, and versatile structural dynamics. Single-molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues toward studying the mechanisms of biomolecular machines isolated directly from complex biological specimens, such as cell extracts. Here, we detail the general steps for using prism-based total internal reflection fluorescence microscopy in exemplary single-molecule pull-down FRET studies of the yeast spliceosome and discuss the broad application potential of this technique.
Collapse
Affiliation(s)
- Matthew L Kahlscheuer
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| |
Collapse
|
20
|
Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
Collapse
Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
| |
Collapse
|
21
|
Ghoneim M, Spies M. Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. NANO LETTERS 2014; 14:5920-31. [PMID: 25204359 PMCID: PMC4189620 DOI: 10.1021/nl502890g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report a dual illumination, single-molecule imaging strategy to dissect directly and in real-time the correlation between nanometer-scale domain motion of a DNA repair protein and its interaction with individual DNA substrates. The strategy was applied to XPD, an FeS cluster-containing DNA repair helicase. Conformational dynamics was assessed via FeS-mediated quenching of a fluorophore site-specifically incorporated into XPD. Simultaneously, binding of DNA molecules labeled with a spectrally distinct fluorophore was detected by colocalization of the DNA- and protein-derived signals. We show that XPD undergoes thermally driven conformational transitions that manifest in spatial separation of its two auxiliary domains. DNA binding does not strictly enforce a specific conformation. Interaction with a cognate DNA damage, however, stabilizes the compact conformation of XPD by increasing the weighted average lifetime of this state by 140% relative to an undamaged DNA. Our imaging strategy will be a valuable tool to study other FeS-containing nucleic acid processing enzymes.
Collapse
Affiliation(s)
- Mohamed Ghoneim
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Maria Spies
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
- E-mail: . Phone +1-319-335-3221
| |
Collapse
|
22
|
Hohlbein J, Craggs TD, Cordes T. Alternating-laser excitation: single-molecule FRET and beyond. Chem Soc Rev 2014; 43:1156-71. [PMID: 24037326 DOI: 10.1039/c3cs60233h] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.
Collapse
Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands.
| | | | | |
Collapse
|
23
|
Lee KS, Marciel AB, Kozlov AG, Schroeder CM, Lohman TM, Ha T. Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer. J Mol Biol 2014; 426:2413-21. [PMID: 24792418 DOI: 10.1016/j.jmb.2014.04.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/08/2014] [Accepted: 04/28/2014] [Indexed: 11/19/2022]
Abstract
Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of additional proteins and enzymes to their sites of action on DNA. SSB can also locally diffuse on ssDNA, which allows it to quickly reposition itself while remaining bound to ssDNA. In this work, we used a hybrid instrument that combines single-molecule fluorescence and force spectroscopy to directly visualize the movement of Escherichia coli SSB on long polymeric ssDNA. Long ssDNA was synthesized without secondary structure that can hinder quantitative analysis of SSB movement. The apparent diffusion coefficient of E. coli SSB thus determined ranged from 70,000 to 170,000nt(2)/s, which is at least 600 times higher than that determined from SSB diffusion on short ssDNA oligomers, and is within the range of values reported for protein diffusion on double-stranded DNA. Our work suggests that SSB can also migrate via a long-range intersegment transfer on long ssDNA. The force dependence of SSB movement on ssDNA further supports this interpretation.
Collapse
Affiliation(s)
- Kyung Suk Lee
- Department of Physics, Center for Physics in Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA
| | - Amanda B Marciel
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Box 8231, St. Louis, MO 63110-1093, USA
| | - Charles M Schroeder
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Box 8231, St. Louis, MO 63110-1093, USA
| | - Taekjip Ha
- Department of Physics, Center for Physics in Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA.
| |
Collapse
|
24
|
RUEDAS-RAMA MJ, ALVAREZ-PEZ JM, ORTE A. SOLVING SINGLE BIOMOLECULES BY ADVANCED FRET-BASED SINGLE-MOLECULE FLUORESCENCE TECHNIQUES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The use of Förster resonance energy transfer (FRET) has undergone a renaissance in the last two decades, especially in the study of structure of biomolecules, biomolecular interactions, and dynamics. Thanks to powerful advances in single-molecule fluorescence (SMF) techniques, seeing molecules at work is a reality, which has helped to build up the mindset of molecular machines. In the last few years, many technical developments have broadened the applications of SMF-FRET, expanding the amount of information that can be recovered from individual molecules. Here, we focus on the non-standard SMF-FRET techniques, such as two-color coincidence detection (TCCD), alternating laser excitation (ALEX), multiparameter fluorescence detection (MFD); the addition of fluorescence lifetime as an orthogonal dimension in single-molecule experiments; or the development of novel and improved methods of analysis constituting to a set of advanced methodologies that may become routine tools in a close future. [Formula: see text]Special Issue Comment: This review about advanced single-molecule FRET techniques is specially related to the review by Jørgensen and Hatzakis,6 who detail experimetal strategies to solve the activity of single enzymes. The advanced techniques described in our paper may serve as interesting alternatives when applied to enzyme studies. Our manuscript is also related to the reviews in this Special Issue that deal with model solving.22,130
Collapse
Affiliation(s)
- M. J. RUEDAS-RAMA
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, Granada, 18071, Spain
| | - J. M. ALVAREZ-PEZ
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, Granada, 18071, Spain
| | - A. ORTE
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, Granada, 18071, Spain
| |
Collapse
|
25
|
Lin CY, Huang JY, Lo LW. Deciphering the catalysis-associated conformational changes of human adenylate kinase 1 with single-molecule spectroscopy. J Phys Chem B 2013; 117:13947-55. [PMID: 24134437 DOI: 10.1021/jp4019537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human adenylate kinase isoenzyme 1 (AK1) is the key enzyme in maintaining the cellular energy homeostasis. The catalysis-associated conformational changes of AK1 involve large-amplitude rearrangements. To decipher the conformational changes of AK1 at the single-molecule level, we tagged AK1 with two identical fluorophores, one near the substrate-binding site and the other at the boundary of the core domain. We found that magnesium ion binding to AK1 increases the structural heterogeneity of AK1, whereas ADP binding reduces the structural heterogeneity. We exploited the hidden Markov model to extract the underlying catalysis-associated conformational dynamics and determined thermodynamic parameters of the multiple catalytic pathways. The third-order correlation difference calculated from photon fluctuation traces reveals the irreversible nature of the conformational motions, suggesting that single-molecule AK1 is in a nonequilibrium steady state. This discovery offers a fresh viewpoint to look into the molecular mechanisms of cellular biochemistry.
Collapse
Affiliation(s)
- Chien Y Lin
- Department of Photonics, Chiao Tung University , Hsinchu, Taiwan
| | | | | |
Collapse
|
26
|
Stinson BM, Nager AR, Glynn SE, Schmitz KR, Baker TA, Sauer RT. Nucleotide binding and conformational switching in the hexameric ring of a AAA+ machine. Cell 2013; 153:628-39. [PMID: 23622246 DOI: 10.1016/j.cell.2013.03.029] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/07/2013] [Accepted: 03/20/2013] [Indexed: 10/26/2022]
Abstract
ClpX, a AAA+ ring homohexamer, uses the energy of ATP binding and hydrolysis to power conformational changes that unfold and translocate target proteins into the ClpP peptidase for degradation. In multiple crystal structures, some ClpX subunits adopt nucleotide-loadable conformations, others adopt unloadable conformations, and each conformational class exhibits substantial variability. Using mutagenesis of individual subunits in covalently tethered hexamers together with fluorescence methods to assay the conformations and nucleotide-binding properties of these subunits, we demonstrate that dynamic interconversion between loadable and unloadable conformations is required to couple ATP hydrolysis by ClpX to mechanical work. ATP binding to different classes of subunits initially drives staged allosteric changes, which set the conformation of the ring to allow hydrolysis and linked mechanical steps. Subunit switching between loadable and unloadable conformations subsequently isomerizes or resets the configuration of the nucleotide-loaded ring and is required for mechanical function.
Collapse
Affiliation(s)
- Benjamin M Stinson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | | | |
Collapse
|
27
|
Beerens N, Jepsen MD, Nechyporuk-Zloy V, Krüger AC, Darlix JL, Kjems J, Birkedal V. Role of the primer activation signal in tRNA annealing onto the HIV-1 genome studied by single-molecule FRET microscopy. RNA (NEW YORK, N.Y.) 2013; 19:517-526. [PMID: 23404895 PMCID: PMC3677262 DOI: 10.1261/rna.035733.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
HIV-1 reverse transcription is primed by a cellular tRNAlys3 molecule that binds to the primer binding site (PBS) in the genomic RNA. An additional interaction between the tRNA molecule and the primer activation signal (PAS) is thought to regulate the initiation of reverse transcription. The mechanism of tRNA annealing onto the HIV-1 genome was examined using ensemble and single-molecule Förster Resonance Energy Transfer (FRET) assays, in which fluorescent donor and acceptor molecules were covalently attached to an RNA template mimicking the PBS region. The role of the viral nucleocapsid (NC) protein in tRNA annealing was studied. Both heat annealing and NC-mediated annealing of tRNAlys3 were found to change the FRET efficiency, and thus the conformation of the HIV-1 RNA template. The results are consistent with a model for tRNA annealing that involves an interaction between the tRNAlys3 molecule and the PAS sequence in the HIV-1 genome. The NC protein may stimulate the interaction of the tRNA molecule with the PAS, thereby regulating the initiation of reverse transcription.
Collapse
Affiliation(s)
- Nancy Beerens
- Department of Molecular Biology, Aarhus University, Aarhus 8000, Denmark
| | - Mette D.E. Jepsen
- Department of Molecular Biology, Aarhus University, Aarhus 8000, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | | | - Asger C. Krüger
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | - Jean-Luc Darlix
- UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, Illkirch 67401, France
| | - Jørgen Kjems
- Department of Molecular Biology, Aarhus University, Aarhus 8000, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| |
Collapse
|
28
|
Ren R, Wang H, Liu R, Zhang S. Direct visualization of the reaction transformation and signal amplification in a DNA molecular machine with total internal reflection fluorescence microscopy. Front Chem 2013; 1:23. [PMID: 24790951 PMCID: PMC3982516 DOI: 10.3389/fchem.2013.00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/26/2013] [Indexed: 11/13/2022] Open
Abstract
In this study, as a proof of concept, the signal amplification in an artificial DNA molecular machine was directly visualized via total internal reflection fluorescence microscopy (TIRFM). The molecular machine brought about obvious morphology change in DNA nanostructures as well as signal amplifications. On one hand, through a triggered and autonomically repeated RCA, a DNA nano-complex featuring a "locked" circular DNA template (serving as raw feed) was converted into a long periodically repeated strand, i.e., the RCA products. On the other hand, this RCA was repeated in three controllable reaction phases, bring about progressive signal amplification. It was testified that the RCA products (presented as long thread-like fluorescent objects) can be easily distinguished from the inputted DNA probes (presented as fluorescent dots), thus the transformation in reaction can be visualized. Also, by quantitive counting of the aforementioned fluorescence objects, the progress of the reaction through the phases, along with time, and over the lysozyme concentration can be demonstrated through TIRFM visualization. Overall, it was demonstrated that TIRFM is an efficient approach to quantitatively visualize the biochemical processes at single-molecule level.
Collapse
Affiliation(s)
- Rui Ren
- School of Chemistry and Chemical Engineering, Linyi University , Linyi, China ; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| | - Haiyan Wang
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| | - Rui Liu
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| | - Shusheng Zhang
- School of Chemistry and Chemical Engineering, Linyi University , Linyi, China ; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| |
Collapse
|
29
|
Kim H, Ha T. Single-molecule nanometry for biological physics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:016601. [PMID: 23249673 PMCID: PMC3549428 DOI: 10.1088/0034-4885/76/1/016601] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precision measurement is a hallmark of physics but the small length scale (∼nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ∼0.3 nm precision at ∼1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics.
Collapse
Affiliation(s)
- Hajin Kim
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
| | | |
Collapse
|
30
|
Lyu ZX, Shao Q, Gao YQ, Zhao XS. Direct observation of the uptake of outer membrane proteins by the periplasmic chaperone Skp. PLoS One 2012; 7:e46068. [PMID: 23049938 PMCID: PMC3458824 DOI: 10.1371/journal.pone.0046068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/28/2012] [Indexed: 11/18/2022] Open
Abstract
The transportation of membrane proteins through the aqueous subcellular space is an important and challenging process. Its molecular mechanism and the associated structural change are poorly understood. Periplasmic chaperones, such as Skp in Escherichia coli, play key roles in the transportation and protection of outer membrane proteins (OMPs) in Gram-negative bacteria. The molecular mechanism through which Skp interacts with and protects OMPs remains mysterious. Here, a combined experimental and molecular dynamics simulation study was performed to gain the structural and dynamical information in the process of OMPs and Skp binding. Stopped-flow experiments on site specific mutated and labeled Skp and several OMPs, namely OmpC, the transmembrane domain of OmpA, and OmpF, allowed us to obtain the mechanism of OMP entering the Skp cavity, and molecular dynamics simulations yielded detailed molecular interactions responsible for this process. Both experiment and simulation show that the entrance of OMP into Skp is a highly directional process, which is initiated by the interaction between the N-terminus of OMP and the bottom “tentacle” domain of Skp. The opening of the more flexible tentacle of Skp, the non-specific electrostatic interactions between OMP and Skp, and the constant formation and breaking of salt bridges between Skp and its substrate together allow OMP to enter Skp and gradually “climb” into the Skp cavity in the absence of an external energy supply.
Collapse
Affiliation(s)
- Zhi-Xin Lyu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, Biodynamic Optical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Qiang Shao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- * E-mail: (YQG); (XSZ)
| | - Xin Sheng Zhao
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, Biodynamic Optical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- * E-mail: (YQG); (XSZ)
| |
Collapse
|
31
|
Swoboda M, Henig J, Cheng HM, Brugger D, Haltrich D, Plumeré N, Schlierf M. Enzymatic oxygen scavenging for photostability without pH drop in single-molecule experiments. ACS NANO 2012; 6:6364-9. [PMID: 22703450 PMCID: PMC3403312 DOI: 10.1021/nn301895c] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/17/2012] [Indexed: 05/18/2023]
Abstract
Over the past years, bottom-up bionanotechnology has been developed as a promising tool for future technological applications. Many of these biomolecule-based assemblies are characterized using various single-molecule techniques that require strict anaerobic conditions. The most common oxygen scavengers for single-molecule experiments are glucose oxidase and catalase (GOC) or protocatechuate dioxygenase (PCD). One of the pitfalls of these systems, however, is the production of carboxylic acids. These acids can result in a significant pH drop over the course of experiments and must thus be compensated by an increased buffer strength. Here, we present pyranose oxidase and catalase (POC) as a novel enzymatic system to perform single-molecule experiments in pH-stable conditions at arbitrary buffer strength. We show that POC keeps the pH stable over hours, while GOC and PCD cause an increasing acidity of the buffer system. We further verify in single-molecule fluorescence experiments that POC performs as good as the common oxygen-scavenging systems, but offers long-term pH stability and more freedom in buffer conditions. This enhanced stability allows the observation of bionanotechnological assemblies in aqueous environments under well-defined conditions for an extended time.
Collapse
Affiliation(s)
- Marko Swoboda
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Jörg Henig
- Center for Electrochemical Sciences, CES, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Hsin-Mei Cheng
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Dagmar Brugger
- Food Biotechnology Laboratory, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Nicolas Plumeré
- Center for Electrochemical Sciences, CES, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
- E-mail: ,
| | - Michael Schlierf
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
- E-mail: ,
| |
Collapse
|
32
|
Hatzakis NS, Wei L, Jorgensen SK, Kunding AH, Bolinger PY, Ehrlich N, Makarov I, Skjot M, Svendsen A, Hedegård P, Stamou D. Single enzyme studies reveal the existence of discrete functional states for monomeric enzymes and how they are "selected" upon allosteric regulation. J Am Chem Soc 2012; 134:9296-302. [PMID: 22489643 DOI: 10.1021/ja3011429] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate with the enzyme's major conformational states and are redistributed in the presence of the regulatory effector. Thus, our data support allosteric regulation of monomeric enzymes to operate via selection of preexisting functional states and not via induction of new ones.
Collapse
Affiliation(s)
- Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, University of Copenhagen, Denmark.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|