1
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Morales-Inostroza L, Folz J, Kühnemuth R, Felekyan S, Wieser FF, Seidel CAM, Götzinger S, Sandoghdar V. An optofluidic antenna for enhancing the sensitivity of single-emitter measurements. Nat Commun 2024; 15:2545. [PMID: 38514627 PMCID: PMC10957926 DOI: 10.1038/s41467-024-46730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Many single-molecule investigations are performed in fluidic environments, for example, to avoid unwanted consequences of contact with surfaces. Diffusion of molecules in this arrangement limits the observation time and the number of collected photons, thus, compromising studies of processes with fast or slow dynamics. Here, we introduce a planar optofluidic antenna (OFA), which enhances the fluorescence signal from molecules by about 5 times per passage, leads to about 7-fold more frequent returns to the observation volume, and significantly lengthens the diffusion time within one passage. We use single-molecule multi-parameter fluorescence detection (sm-MFD), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) measurements to characterize our OFAs. The antenna advantages are showcased by examining both the slow (ms) and fast (50 μs) dynamics of DNA four-way (Holliday) junctions with real-time resolution. The FRET trajectories provide evidence for the absence of an intermediate conformational state and introduce an upper bound for its lifetime. The ease of implementation and compatibility with various microscopy modalities make OFAs broadly applicable to a diverse range of studies.
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Affiliation(s)
- Luis Morales-Inostroza
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Julian Folz
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Ralf Kühnemuth
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Suren Felekyan
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Claus A M Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Stephan Götzinger
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91052, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany.
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany.
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2
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Kolimi N, Ballard J, Peulen T, Goutam R, Duffy FX, Ramírez-Sarmiento CA, Babul J, Medina E, Sanabria H. DNA controls the dimerization of the human FoxP1 forkhead domain. Cell Rep Phys Sci 2024; 5:101854. [PMID: 38585429 PMCID: PMC10997372 DOI: 10.1016/j.xcrp.2024.101854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences and gating access to genes. Even when the binding of TFs and their cofactors to DNA is reversible, indicating a reversible control of gene expression, there is little knowledge about the molecular effect DNA has on TFs. Using single-molecule multiparameter fluorescence spectroscopy, molecular dynamics simulations, and biochemical assays, we find that the monomeric form of the forkhead (FKH) domain of the human FoxP1 behaves as a disordered protein and increases its folded population when it dimerizes. Notably, DNA binding promotes a disordered FKH dimer bound to DNA, negatively controlling the stability of the dimeric FoxP1:DNA complex. The DNA-mediated reversible regulation on FKH dimers suggests that FoxP1-dependent gene suppression is unstable, and it must require the presence of other dimerization domains or cofactors to revert the negative impact exerted by the DNA.
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Affiliation(s)
- Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Jake Ballard
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Thomas Peulen
- Rudolf-Virchow-Zentrum – Center for Integrative and Translational Bioimaging, Haus D15, Josef-Schneider-Straße 2, 97080 Würzburg Germany
| | - Rajen Goutam
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Francis X. Duffy
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Exequiel Medina
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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3
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Agam G, Barth A, Lamb DC. Folding pathway of a discontinuous two-domain protein. Nat Commun 2024; 15:690. [PMID: 38263337 PMCID: PMC10805907 DOI: 10.1038/s41467-024-44901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments. We observe a dynamic folding intermediate population in the N-terminal domain (NTD), C-terminal domain (CTD), and at the domain interface. The dynamic intermediate fluctuates rapidly between unfolded states and compact states, which have a similar FRET efficiency to the folded conformation. Our data reveals that the delayed folding of the NTD in DM-MBP is imposed by an entropic barrier with subsequent folding of the highly dynamic CTD. Notably, accelerated DM-MBP folding is routed through the same dynamic intermediate within the cavity of the GroEL/ES chaperone system, suggesting that the chaperonin limits the conformational space to overcome the entropic folding barrier. Our study highlights the subtle tuning and co-dependency in the folding of a discontinuous multi-domain protein.
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Affiliation(s)
- Ganesh Agam
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Anders Barth
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629HZ, Delft, The Netherlands
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany.
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany.
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4
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Luginina A, Maslov I, Khorn P, Volkov O, Khnykin A, Kuzmichev P, Shevtsov M, Belousov A, Kapranov I, Dashevskii D, Kornilov D, Bestsennaia E, Hofkens J, Hendrix J, Gensch T, Cherezov V, Ivanovich V, Mishin A, Borshchevskiy V. Functional GPCR Expression in Eukaryotic LEXSY System. J Mol Biol 2023; 435:168310. [PMID: 37806553 DOI: 10.1016/j.jmb.2023.168310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
G protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins in the human genome, and represent one of the most important classes of drug targets. Their structural studies facilitate rational drug discovery. However, atomic structures of only about 20% of human GPCRs have been solved to date. Recombinant production of GPCRs for structural studies at a large scale is challenging due to their low expression levels and stability. Therefore, in this study, we explored the efficacy of the eukaryotic system LEXSY (Leishmania tarentolae) for GPCR production. We selected the human A2A adenosine receptor (A2AAR), as a model protein, expressed it in LEXSY, purified it, and compared with the same receptor produced in insect cells, which is the most popular expression system for structural studies of GPCRs. The A2AAR purified from both expression systems showed similar purity, stability, ligand-induced conformational changes and structural dynamics, with a remarkably higher protein yield in the case of LEXSY expression. Overall, our results suggest that LEXSY is a promising platform for large-scale production of GPCRs for structural studies.
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Affiliation(s)
- Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | | | - Andrey Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Anatoliy Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Dmitrii Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Daniil Kornilov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ekaterina Bestsennaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium; Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Valentin Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Joint Institute for Nuclear Research, Dubna, Russia.
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5
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Terterov I, Nettels D, Makarov DE, Hofmann H. Time-resolved burst variance analysis. Biophys Rep (N Y) 2023; 3:100116. [PMID: 37559939 PMCID: PMC10406964 DOI: 10.1016/j.bpr.2023.100116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023]
Abstract
Quantifying biomolecular dynamics has become a major task of single-molecule fluorescence spectroscopy methods. In single-molecule Förster resonance energy transfer (smFRET), kinetic information is extracted from the stream of photons emitted by attached donor and acceptor fluorophores. Here, we describe a time-resolved version of burst variance analysis that can quantify kinetic rates at microsecond to millisecond timescales in smFRET experiments of diffusing molecules. Bursts are partitioned into segments with a fixed number of photons. The FRET variance is computed from these segments and compared with the variance expected from shot noise. By systematically varying the segment size, dynamics at different timescales can be captured. We provide a theoretical framework to extract kinetic rates from the decay of the FRET variance with increasing segment size. Compared to other methods such as filtered fluorescence correlation spectroscopy, recurrence analysis of single particles, and two-dimensional lifetime correlation spectroscopy, fewer photons are needed to obtain reliable timescale estimates, which reduces the required measurement time.
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Affiliation(s)
- Ivan Terterov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of Zurich, Zurich, Switzerland
| | - Dmitrii E. Makarov
- Department of Chemistry and Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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6
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Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
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7
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Maslov I, Volkov O, Khorn P, Orekhov P, Gusach A, Kuzmichev P, Gerasimov A, Luginina A, Coucke Q, Bogorodskiy A, Gordeliy V, Wanninger S, Barth A, Mishin A, Hofkens J, Cherezov V, Gensch T, Hendrix J, Borshchevskiy V. Sub-millisecond conformational dynamics of the A 2A adenosine receptor revealed by single-molecule FRET. Commun Biol 2023; 6:362. [PMID: 37012383 PMCID: PMC10070357 DOI: 10.1038/s42003-023-04727-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
The complex pharmacology of G-protein-coupled receptors (GPCRs) is defined by their multi-state conformational dynamics. Single-molecule Förster Resonance Energy Transfer (smFRET) is well suited to quantify dynamics for individual protein molecules; however, its application to GPCRs is challenging. Therefore, smFRET has been limited to studies of inter-receptor interactions in cellular membranes and receptors in detergent environments. Here, we performed smFRET experiments on functionally active human A2A adenosine receptor (A2AAR) molecules embedded in freely diffusing lipid nanodiscs to study their intramolecular conformational dynamics. We propose a dynamic model of A2AAR activation that involves a slow (>2 ms) exchange between the active-like and inactive-like conformations in both apo and antagonist-bound A2AAR, explaining the receptor's constitutive activity. For the agonist-bound A2AAR, we detected faster (390 ± 80 µs) ligand efficacy-dependent dynamics. Our work establishes a general smFRET platform for GPCR investigations that can potentially be used for drug screening and/or mechanism-of-action studies.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | | | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Anastasiia Gusach
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Andrey Gerasimov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Vyatka State University, Kirov, Russia
| | - Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Quinten Coucke
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Simon Wanninger
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, HZ, Delft, The Netherlands
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium.
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium.
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
- Joint Institute for Nuclear Research, Dubna, Russian Federation.
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8
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Agam G, Gebhardt C, Popara M, Mächtel R, Folz J, Ambrose B, Chamachi N, Chung SY, Craggs TD, de Boer M, Grohmann D, Ha T, Hartmann A, Hendrix J, Hirschfeld V, Hübner CG, Hugel T, Kammerer D, Kang HS, Kapanidis AN, Krainer G, Kramm K, Lemke EA, Lerner E, Margeat E, Martens K, Michaelis J, Mitra J, Moya Muñoz GG, Quast RB, Robb NC, Sattler M, Schlierf M, Schneider J, Schröder T, Sefer A, Tan PS, Thurn J, Tinnefeld P, van Noort J, Weiss S, Wendler N, Zijlstra N, Barth A, Seidel CAM, Lamb DC, Cordes T. Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nat Methods 2023; 20:523-535. [PMID: 36973549 PMCID: PMC10089922 DOI: 10.1038/s41592-023-01807-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/31/2023] [Indexed: 03/29/2023]
Abstract
Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.
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Affiliation(s)
- Ganesh Agam
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Milana Popara
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Julian Folz
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Neharika Chamachi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Sang Yoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | | | - Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, the Netherlands
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Laboratory, University of Regensburg, Regensburg, Germany
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine and Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Laboratory, Advanced Optical Microscopy Center and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Hasselt, Belgium
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | | | | | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Dominik Kammerer
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Hyun-Seo Kang
- Bayerisches NMR Zentrum, Department of Bioscience, School of Natural Sciences, Technical University of München, Garching, Germany
| | - Achillefs N Kapanidis
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Laboratory, University of Regensburg, Regensburg, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics and Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Kirsten Martens
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | | | - Jaba Mitra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine and Howard Hughes Medical Institute, Baltimore, MD, USA
- Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Robert B Quast
- Centre de Biologie Structurale (CBS), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Nicole C Robb
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford, UK
- Warwick Medical School, The University of Warwick, Coventry, UK
| | - Michael Sattler
- Bayerisches NMR Zentrum, Department of Bioscience, School of Natural Sciences, Technical University of München, Garching, Germany
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Munich, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Jonathan Schneider
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Tim Schröder
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany
| | - Anna Sefer
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Piau Siong Tan
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Johann Thurn
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Institute of Technical Physics, German Aerospace Center (DLR), Stuttgart, Germany
| | - Philip Tinnefeld
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Nicolas Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Anders Barth
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany.
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany.
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9
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Abstract
A quantitative understanding of the forces controlling the assembly and functioning of biomolecular condensates requires the identification of phase boundaries at which condensates form as well as the determination of tie-lines. Here, we describe in detail how Fluorescence Correlation Spectroscopy (FCS) provides a versatile approach to estimate phase boundaries of single-component and multicomponent solutions as well as insights about the transport properties of the condensate.
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Affiliation(s)
- Juan Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St Louis, St. Louis, MO, USA
| | - Debjit Roy
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St Louis, St. Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St Louis, St. Louis, MO, USA.
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10
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Sefer A, Kallis E, Eilert T, Röcker C, Kolesnikova O, Neuhaus D, Eustermann S, Michaelis J. Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level. Nat Commun 2022; 13:6569. [PMID: 36323657 PMCID: PMC9630430 DOI: 10.1038/s41467-022-34148-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.
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Affiliation(s)
- Anna Sefer
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Eleni Kallis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tobias Eilert
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Boehringer Ingelheim, CoC CMC Statistics & Data Science, Birkendorfer Str. 65, 88400, Biberach, Germany
| | - Carlheinz Röcker
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Olga Kolesnikova
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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11
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Götz M, Barth A, Bohr SSR, Börner R, Chen J, Cordes T, Erie DA, Gebhardt C, Hadzic MCAS, Hamilton GL, Hatzakis NS, Hugel T, Kisley L, Lamb DC, de Lannoy C, Mahn C, Dunukara D, de Ridder D, Sanabria H, Schimpf J, Seidel CAM, Sigel RKO, Sletfjerding MB, Thomsen J, Vollmar L, Wanninger S, Weninger KR, Xu P, Schmid S. A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories. Nat Commun 2022. [PMID: 36104339 DOI: 10.1101/2021.11.23.469671v2.article-info] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We test them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise levels, varied model complexity, non-equilibrium dynamics, and kinetic heterogeneity. Our results highlight the current strengths and limitations in inferring kinetic information from smFRET trajectories. In addition, we formulate concrete recommendations and identify key targets for future developments, aimed to advance our understanding of biomolecular dynamics through quantitative experiment-derived models.
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Affiliation(s)
- Markus Götz
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
- PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany.
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Richard Börner
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
- Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, 09648, Mittweida, Germany
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, USA
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | | | - George L Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Don C Lamb
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Carlos de Lannoy
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Chelsea Mahn
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dushani Dunukara
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Julia Schimpf
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Magnus Berg Sletfjerding
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Leonie Vollmar
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Simon Wanninger
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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12
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Götz M, Barth A, Bohr SSR, Börner R, Chen J, Cordes T, Erie DA, Gebhardt C, Hadzic MCAS, Hamilton GL, Hatzakis NS, Hugel T, Kisley L, Lamb DC, de Lannoy C, Mahn C, Dunukara D, de Ridder D, Sanabria H, Schimpf J, Seidel CAM, Sigel RKO, Sletfjerding MB, Thomsen J, Vollmar L, Wanninger S, Weninger KR, Xu P, Schmid S. A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories. Nat Commun 2022; 13:5402. [PMID: 36104339 PMCID: PMC9474500 DOI: 10.1038/s41467-022-33023-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/30/2022] [Indexed: 01/04/2023] Open
Abstract
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We test them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise levels, varied model complexity, non-equilibrium dynamics, and kinetic heterogeneity. Our results highlight the current strengths and limitations in inferring kinetic information from smFRET trajectories. In addition, we formulate concrete recommendations and identify key targets for future developments, aimed to advance our understanding of biomolecular dynamics through quantitative experiment-derived models.
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Affiliation(s)
- Markus Götz
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
- PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany.
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Richard Börner
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
- Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, 09648, Mittweida, Germany
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, USA
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | | | - George L Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Don C Lamb
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Carlos de Lannoy
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Chelsea Mahn
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dushani Dunukara
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Julia Schimpf
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Magnus Berg Sletfjerding
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Leonie Vollmar
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Simon Wanninger
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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13
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Hamilton GL, Saikia N, Basak S, Welcome FS, Wu F, Kubiak J, Zhang C, Hao Y, Seidel CAM, Ding F, Sanabria H, Bowen ME. Fuzzy supertertiary interactions within PSD-95 enable ligand binding. eLife 2022; 11:e77242. [PMID: 36069777 PMCID: PMC9581536 DOI: 10.7554/elife.77242] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
The scaffold protein PSD-95 links postsynaptic receptors to sites of presynaptic neurotransmitter release. Flexible linkers between folded domains in PSD-95 enable a dynamic supertertiary structure. Interdomain interactions within the PSG supramodule, formed by PDZ3, SH3, and Guanylate Kinase domains, regulate PSD-95 activity. Here we combined discrete molecular dynamics and single molecule Förster resonance energy transfer (FRET) to characterize the PSG supramodule, with time resolution spanning picoseconds to seconds. We used a FRET network to measure distances in full-length PSD-95 and model the conformational ensemble. We found that PDZ3 samples two conformational basins, which we confirmed with disulfide mapping. To understand effects on activity, we measured binding of the synaptic adhesion protein neuroligin. We found that PSD-95 bound neuroligin well at physiological pH while truncated PDZ3 bound poorly. Our hybrid structural models reveal how the supertertiary context of PDZ3 enables recognition of this critical synaptic ligand.
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Affiliation(s)
- George L Hamilton
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Nabanita Saikia
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Sujit Basak
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Franceine S Welcome
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Fang Wu
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Jakub Kubiak
- Molecular Physical Chemistry, Heinrich Heine UniversityDüsseldorfGermany
| | - Changcheng Zhang
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Yan Hao
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
| | - Claus AM Seidel
- Molecular Physical Chemistry, Heinrich Heine UniversityDüsseldorfGermany
| | - Feng Ding
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson UniversityClemsonUnited States
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook UniversityStony BrookUnited States
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14
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Chinnaraj M, Flaumenhaft R, Pozzi N. Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles. J Biol Chem 2022; 298:102217. [PMID: 35780832 PMCID: PMC9352907 DOI: 10.1016/j.jbc.2022.102217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Human protein disulfide isomerase (PDI) is an essential redox-regulated enzyme required for oxidative protein folding. It comprises four thioredoxin domains, two catalytically active (a, a’) and two inactive (b, b’), organized to form a flexible abb’a’ U-shape. Snapshots of unbound oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure changes in response to the redox environment and inhibitor binding remains controversial. Here, we used multiparameter confocal single-molecule FRET to track the movements of the two catalytic domains with high temporal resolution. We found that at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O1 and O2) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O1, O2, and C more evenly and in a slower fashion, reduced PDI predominantly populates O1 and O2 and exchanges between them more rapidly, on the submillisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the R300-W396 cation-π interaction and active site cysteines dictate, in unexpected ways, how the catalytic domains relocate. Finally, we show that irreversible inhibitors targeting the active sites of reduced PDI did not abolish these protein dynamics but rather shifted the equilibrium toward the closed ensemble. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize its multifaceted role in biology, and should be considered when designing PDI-targeted therapeutics.
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Affiliation(s)
- Mathivanan Chinnaraj
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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15
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Opanasyuk O, Barth A, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CA. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks. J Chem Phys 2022; 157:031501. [DOI: 10.1063/5.0095754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) experiments are ideally suited to resolve the structural dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly when these dynamics occur on the sub-millisecond timescale. Many methods for quantitative analysis are challenged if more than two states are involved, and the appropriate choice of the number of states in the kinetic network is difficult. An additional complication arises if dynamically active molecules coexist with pseudo-static molecules in similar conformational states with undistinguishable FRET efficiencies. To address these problems, we developed a quantitative integrative analysis framework that combines the information from FRET-lines that relate average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms, fluorescence decays obtained by time-correlated single photon counting, photon distribution analysis of the intensities and fluorescence correlation spectroscopy. Individually, these methodologies provide ambiguous results for the characterization of dynamics in complex kinetic networks. However, the global analysis approach enables accurate determination of the number of states, their kinetic connectivity, the transition rate constants, and species fractions. To challenge the potential of smFRET experiments studying multi-state kinetic networks, we apply our integrative framework using a set of synthetic data for three-state systems with different kinetic connectivity and exchange rates. Our methodology paves the way towards an integrated analysis of multiparameter smFRET experiments that spans all dimensions of the experimental data. Finally, we propose a workflow for the analysis and show examples that demonstrate the usefulness of this toolkit for dynamic structural biology.
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Affiliation(s)
| | | | | | - Suren Felekyan
- PC-II, Heinrich Heine University Düsseldorf Department of Chemistry, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
| | | | - Claus A.M. Seidel
- Institut fuer Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
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16
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Barth A, Opanasyuk O, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CAM. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines. J Chem Phys 2022; 156:141501. [PMID: 35428384 PMCID: PMC9014241 DOI: 10.1063/5.0089134] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E–τD diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.
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Affiliation(s)
- Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Oleg Opanasyuk
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Thomas-Otavio Peulen
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, USA
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
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17
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Abstract
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Motions in biomolecules
are critical for biochemical reactions.
In cells, many biochemical reactions are executed inside of biomolecular
condensates formed by ultradynamic intrinsically disordered proteins.
A deep understanding of the conformational dynamics of intrinsically
disordered proteins in biomolecular condensates is therefore of utmost
importance but is complicated by diverse obstacles. Here we review
emerging data on the motions of intrinsically disordered proteins
inside of liquidlike condensates. We discuss how liquid–liquid
phase separation modulates internal motions across a wide range of
time and length scales. We further highlight the importance of intermolecular
interactions that not only drive liquid–liquid phase separation
but appear as key determinants for changes in biomolecular motions
and the aging of condensates in human diseases. The review provides
a framework for future studies to reveal the conformational dynamics
of intrinsically disordered proteins in the regulation of biomolecular
condensate chemistry.
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Affiliation(s)
- Anton Abyzov
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Martin Blackledge
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.,CEA, DSV, IBS, 38044 Grenoble, France.,CNRS, IBS, 38044 Grenoble, France
| | - Markus Zweckstetter
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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18
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Naudi-Fabra S, Blackledge M, Milles S. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins. Biomolecules 2021; 12:biom12010027. [PMID: 35053175 PMCID: PMC8773649 DOI: 10.3390/biom12010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
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19
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Kay TM, Aplin CP, Simonet R, Beenken J, Miller RC, Libal C, Boersma AJ, Sheets ED, Heikal AA. Molecular Brightness Approach for FRET Analysis of Donor-Linker-Acceptor Constructs at the Single Molecule Level: A Concept. Front Mol Biosci 2021; 8:730394. [PMID: 34595208 PMCID: PMC8476790 DOI: 10.3389/fmolb.2021.730394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In this report, we have developed a simple approach using single-detector fluorescence autocorrelation spectroscopy (FCS) to investigate the Förster resonance energy transfer (FRET) of genetically encoded, freely diffusing crTC2.1 (mTurquoise2.1-linker-mCitrine) at the single molecule level. We hypothesize that the molecular brightness of the freely diffusing donor (mTurquoise2.1) in the presence of the acceptor (mCitrine) is lower than that of the donor alone due to FRET. To test this hypothesis, the fluorescence fluctuation signal and number of molecules of freely diffusing construct were measured using FCS to calculate the molecular brightness of the donor, excited at 405 nm and detected at 475/50 nm, in the presence and absence of the acceptor. Our results indicate that the molecular brightness of cleaved crTC2.1 in a buffer is larger than that of the intact counterpart under 405-nm excitation. The energy transfer efficiency at the single molecule level is larger and more spread in values as compared with the ensemble-averaging time-resolved fluorescence measurements. In contrast, the molecular brightness of the intact crTC2.1, under 488 nm excitation of the acceptor (531/40 nm detection), is the same or slightly larger than that of the cleaved counterpart. These FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of the precise time constants associated with autocorrelation curves due to the presence of potential photophysical processes. Ultimately, when used in living cells, the proposed approach would only require a low expression level of these genetically encoded constructs, helping to limit potential interference with the cell machinery.
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Affiliation(s)
- Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN, United States
| | - Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Rowan Simonet
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Julie Beenken
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Christin Libal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
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20
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Kolimi N, Pabbathi A, Saikia N, Ding F, Sanabria H, Alper J. Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches. J Phys Chem B 2021; 125:10404-10418. [PMID: 34506140 PMCID: PMC8474109 DOI: 10.1021/acs.jpcb.1c02424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Out-of-equilibrium
processes are ubiquitous across living organisms
and all structural hierarchies of life. At the molecular scale, out-of-equilibrium
processes (for example, enzyme catalysis, gene regulation, and motor
protein functions) cause biological macromolecules to sample an ensemble
of conformations over a wide range of time scales. Quantifying and
conceptualizing the structure–dynamics to function relationship
is challenging because continuously evolving multidimensional energy
landscapes are necessary to describe nonequilibrium biological processes
in biological macromolecules. In this perspective, we explore the
challenges associated with state-of-the-art experimental techniques
to understanding biological macromolecular function. We argue that
it is time to revisit how we probe and model functional out-of-equilibrium
biomolecular dynamics. We suggest that developing integrated single-molecule
multiparametric force–fluorescence instruments and using advanced
molecular dynamics simulations to study out-of-equilibrium biomolecules
will provide a path towards understanding the principles of and mechanisms
behind the structure–dynamics to function paradigm in biological
macromolecules.
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Affiliation(s)
- Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Ashok Pabbathi
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Nabanita Saikia
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Joshua Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States.,Department of Biological Sciences, Clemson University, Clemson, South Carolina 29634, United States
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21
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Ghosh A, Enderlein J. Advanced fluorescence correlation spectroscopy for studying biomolecular conformation. Curr Opin Struct Biol 2021; 70:123-131. [PMID: 34371261 DOI: 10.1016/j.sbi.2021.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 10/20/2022]
Abstract
We present the recent developments and advances in fluorescence correlation spectroscopy (FCS) and their application to the investigation of biomolecular conformations. In particular, we present and discuss three techniques: multichannel nanosecond FCS, photo-induced electron transfer FCS, and fluorescence lifetime correlation spectroscopy. We briefly describe each method and discuss recent applications to diverse biophysical studies of biomolecular conformation.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics, Biophysics, University of Göttingen, Friedrich Hund Platz 1 Göttingen, 37077, Germany
| | - Jörg Enderlein
- Third Institute of Physics, Biophysics, University of Göttingen, Friedrich Hund Platz 1 Göttingen, 37077, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen, 37077, Germany.
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22
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Sarkar B, Ishii K, Tahara T. Microsecond Folding of preQ 1 Riboswitch and Its Biological Significance Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Am Chem Soc 2021; 143:7968-7978. [PMID: 34013733 DOI: 10.1021/jacs.1c01077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Riboswitches are regulatory elements of bacterial mRNA which function with conformational switching upon binding of specific cellular metabolites. In particular, transcriptional riboswitches regulate gene expression kinetically through the conformational change of the aptamer domain. In this study, we investigate the conformational dynamics and ligand binding mechanisms of the aptamer domain of a transcriptional prequeuosine (preQ1) riboswitch from Bacillus subtilis using two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS) with microsecond time resolution. The obtained time-resolved single-molecule data indicate that the aptamer domain undergoes folding/unfolding including three forms, which are attributed to hairpin (O), pseudoknot-like (pF), and H-type pseudoknot (fF) structures. It is found that a cofactor, Mg2+, binds only to the fF form with the conformational selection mechanism. In contrast, it is indicated that the ligand, preQ1, binds to the O form with the induced-fit mechanism and significantly accelerates the microsecond O → pF folding process. It is also shown that the binding with preQ1 substantially stabilizes the fF form that is generated from the pF form with a long time constant (>10 ms). Combining these results with the results of a former smFRET study on the slower time scale, we obtain an overall picture of the folding/unfolding dynamics of the aptamer domain as well as its energy landscape. On the basis of the picture obtained, we discuss the significance of the microsecond folding/unfolding of the aptamer domain for biological function of the riboswitch and propose the molecular mechanism of the gene expression controlled by the structural dynamics of the aptamer domain.
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Affiliation(s)
- Bidyut Sarkar
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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23
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Abstract
Fluorescence-based single-molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labeling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labeling sites, experimental setup, and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.
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Affiliation(s)
- Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Haiqi Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
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24
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Ma J, Saikia N, Godar S, Hamilton GL, Ding F, Alper J, Sanabria H. Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch. RNA 2021; 27:rna.075937.120. [PMID: 33863818 PMCID: PMC8208051 DOI: 10.1261/rna.075937.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 04/13/2021] [Indexed: 05/05/2023]
Abstract
Thiamine pyrophosphate (TPP) riboswitches regulate thiamine metabolism by inhibiting the translation of enzymes essential to thiamine synthesis pathways upon binding to thiamine pyrophosphate in cells across all domains of life. Recent work on the Arabidopsis thaliana TPP riboswitch suggests a multi-step TPP binding process involving multiple riboswitch configurational ensembles and that Mg2+ dependence underlies the mechanism of TPP recognition and subsequent transition to the expression-inhibiting state of the aptamer domain followed by changes in the expression platform. However, details of the relationship between TPP riboswitch conformational changes and interactions with TPP and Mg2+ ¬¬in the aptamer domain constituting this mechanism are unknown. Therefore, we integrated single-molecule multiparameter fluorescence and force spectroscopy with atomistic molecular dynamics simulations and found that conformational transitions within the aptamer domain's sensor helices associated with TPP and Mg2+ ligand binding occurred between at least five different ensembles on timescales ranging from µs to ms. These dynamics are orders of magnitude faster than the 10 second-timescale folding kinetics associated with expression-state switching in the switch sequence. Together, our results show that a TPP and Mg2+ dependent mechanism determines dynamic configurational state ensemble switching of the aptamer domain's sensor helices that regulates the stability of the switch helix, which ultimately may lead to the expression-inhibiting state of the riboswitch. Additionally, we propose that two pathways exist for ligand recognition and that this mechanism underlies a kinetic rheostat-like behavior of the Arabidopsis thaliana TPP riboswitch.
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Affiliation(s)
- Junyan Ma
- Department of Chemistry, Clemson University
| | | | - Subash Godar
- Department of Physics and Astronomy, Clemson University
| | | | - Feng Ding
- Department of Physics and Astronomy, Clemson University
| | - Joshua Alper
- Department of Physics and Astronomy, Clemson University
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University
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25
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Lira-Navarrete E, Pallarés MC, Castello F, Ruedas-Rama MJ, Orte A, Lostao A, Hurtado-Guerrero R. Protein O-Fucosyltransferase 1 Undergoes Interdomain Flexibility in Solution. Molecules 2021; 26:2105. [PMID: 33916911 PMCID: PMC8067585 DOI: 10.3390/molecules26082105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/25/2022] Open
Abstract
Protein O-fucosyltransferase 1 (PoFUT1) is a GT-B fold enzyme that fucosylates proteins containing EGF-like repeats. GT-B glycosyltransferases have shown a remarkable grade of plasticity adopting closed and open conformations as a way of tuning their catalytic cycle, a feature that has not been observed for PoFUT1. Here, we analyzed Caenorhabditis elegans PoFUT1 (CePoFUT1) conformational behavior in solution by atomic force microscopy (AFM) and single-molecule fluorescence resonance energy transfer (SMF-FRET). Our results show that this enzyme is very flexible and adopts mainly compact conformations and to a lesser extend a highly dynamic population that oscillates between compact and highly extended conformations. Overall, our experiments illustrate the inherent complexity of CePoFUT1 dynamics, which might play a role during its catalytic cycle.
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Affiliation(s)
- Erandi Lira-Navarrete
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain;
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain;
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Fabio Castello
- Departamento de Fisicoquímica, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; (F.C.); (M.J.R.-R.)
| | - Maria J. Ruedas-Rama
- Departamento de Fisicoquímica, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; (F.C.); (M.J.R.-R.)
| | - Angel Orte
- Departamento de Fisicoquímica, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; (F.C.); (M.J.R.-R.)
| | - Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain;
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain;
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
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26
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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27
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Cheng CH, Ishii K, Tahara T. Microsecond Equilibrium Dynamics of Hairpin-Forming Oligonucleotides Quantified by Two-Color Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem B 2020; 124:10673-10681. [PMID: 33200606 DOI: 10.1021/acs.jpcb.0c07600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA and DNA play distinct roles in biological systems. However, the underlying physicochemical difference has been poorly understood, in particular, that in dynamical aspects. In this paper, we report on a comparative study of the formation-dissociation dynamics of a hairpin structure of RNA and DNA with development of two-color two-dimensional fluorescence lifetime correlation spectroscopy (two-color 2D FLCS). In this extension of 2D FLCS, we newly introduce the two-color detection scheme to analyze not only donor fluorescence photons but also acceptor fluorescence photons from a doubly labeled Förster resonance energy transfer (FRET) pair. This new 2D FLCS is utilized to resolve multiple species present in an equilibrated condition with a microsecond time resolution and enhanced sensitivity, and the combined use with the filtered fluorescence correlation spectroscopy (FCS) method enables a quantitative discussion on microsecond structural dynamics occurring in the equilibrium. This integrated approach is applied to FRET-labeled RNA/DNA oligonucleotides having analogous hairpin-forming sequences, and it was revealed that the hairpin dissociation rate of RNA is an order of magnitude slower than that of DNA while their hairpin-forming rates are comparable. This marked difference is attributable to the distinct duplex structure of RNA and DNA. The present study demonstrates that the integrated approach combining two-color 2D FLCS and filtered FCS has a high potential for quantifying microsecond kinetics at the single-molecule level, which allows us to experimentally construct a free energy landscape.
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Affiliation(s)
- Chao-Han Cheng
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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28
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Štefl M, Herbst K, Rübsam M, Benda A, Knop M. Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo. Biophys J 2020; 119:1359-1370. [PMID: 32919495 DOI: 10.1016/j.bpj.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 01/18/2023] Open
Abstract
The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence-based methods like two-color fluorescence cross-correlation spectroscopy can provide this information, but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photostability, bleaching, and fluorescence brightness can have an impact. Here, we take advantage of previously published fluorescence lifetime correlation spectroscopy which relies on lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross talk. To establish sc-FLCCS, we first engineered and tested multiple green fluorescent protein (GFP)-like fluorescent proteins for their suitability. This identified a novel, to our knowledge, GFP variant termed short-lifetime monomeric GFP with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and short-lifetime monomeric GFP, were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color fluorescence cross-correlation spectroscopy measurements.
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Affiliation(s)
- Martin Štefl
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Prague, Czech Republic.
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Marc Rübsam
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Aleš Benda
- IMCF at BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.
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29
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Tsytlonok M, Hemmen K, Hamilton G, Kolimi N, Felekyan S, Seidel CAM, Tompa P, Sanabria H. Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A. J Mol Biol 2020; 432:2998-3017. [PMID: 32088186 PMCID: PMC7254055 DOI: 10.1016/j.jmb.2020.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/27/2020] [Accepted: 02/09/2020] [Indexed: 12/12/2022]
Abstract
The protein p27, a prominent regulatory protein in eukaryotes and an intrinsically disordered protein (IDP), regulates cell division by causing cell cycle arrest when bound in ternary complex with cyclin-dependent kinase (Cdk2) and cyclins (e.g., Cdk2/Cyclin A). We present an integrative study of p27 and its binding to Cdk2/Cyclin A complex by performing single-molecule multiparameter fluorescence spectroscopy, stopped-flow experiments, and molecular dynamics simulations. Our results suggest that unbound p27 adopts a compact conformation and undergoes conformational dynamics across several orders of magnitude in time (nano-to milliseconds), reflecting a multi-step mechanism for binding Cdk2/Cyclin A. Mutagenesis studies reveal that the region D1 in p27 plays a significant role in mediating the association kinetics, undergoing conformational rearrangement upon initial binding. Additionally, FRET experiments indicate an expansion of p27 throughout binding. The detected local and long-range structural dynamics suggest that p27 exhibits a limited binding surface in the unbound form, and stochastic conformational changes in D1 facilitate initial binding to Cdk2/Cyclin A complex. Furthermore, the post-kinase inhibitory domain (post-KID) region of p27 exchanges between distinct conformational ensembles: an extended regime exhibiting worm-like chain behavior, and a compact ensemble, which may protect p27 against nonspecific interactions. In summary, the binding interaction involves three steps: (i) D1 initiates binding, (ii) p27 wraps around Cdk2/Cyclin A and D2 binds, and (iii) the fully-formed fuzzy ternary complex is formed concomitantly with an extension of the post-KID region. An understanding of how the IDP nature of p27 underpins its functional interactions with Cdk2/Cyclin A provides insight into the complex binding mechanisms of IDPs and their regulatory mechanisms.
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Affiliation(s)
- Maksym Tsytlonok
- VIB-VUB Center for Structural Biology (CSB), Vrije Universiteit Brussel, Brussels, Belgium
| | - Katherina Hemmen
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany; Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97078, Würzburg, Germany
| | - George Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Suren Felekyan
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Claus A M Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Hugo Sanabria
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany; Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
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30
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Tang C, Gong Z. Integrating Non-NMR Distance Restraints to Augment NMR Depiction of Protein Structure and Dynamics. J Mol Biol 2020; 432:2913-29. [DOI: 10.1016/j.jmb.2020.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/24/2022]
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31
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Sanabria H, Rodnin D, Hemmen K, Peulen TO, Felekyan S, Fleissner MR, Dimura M, Koberling F, Kühnemuth R, Hubbell W, Gohlke H, Seidel CAM. Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun 2020; 11:1231. [PMID: 32144241 DOI: 10.1038/s41467-020-14886-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2020] [Indexed: 11/23/2022] Open
Abstract
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by combining single-molecule and ensemble multiparameter fluorescence detection, EPR spectroscopy, mutagenesis, and FRET-positioning and screening, and other biochemical and biophysical tools, we characterize three short-lived conformational states over the ns-ms timescale. The use of 33 FRET-derived distance sets, to screen available T4L structures, reveal that T4L in solution mainly adopts the known open and closed states in exchange at 4 µs. A newly found minor state, undisclosed by, at present, more than 500 crystal structures of T4L and sampled at 230 µs, may be actively involved in the product release step in catalysis. The presented fluorescence spectroscopic toolkit will likely accelerate the development of dynamic structural biology by identifying transient conformational states that are highly abundant in biology and critical in enzymatic reactions. T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.
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32
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Abstract
Integrative and hybrid methods have the potential to bridge long-standing knowledge gaps in structural biology. These methods will have a prominent role in the future of the field as we make advances toward a complete, unified representation of biology that spans the molecular and cellular scales. The Department of Physics and Astronomy at Clemson University hosted The Future of Integrative Structural Biology workshop on April 29, 2017 and partially sponsored by partially sponsored by a program of the Oak Ridge Associated Universities (ORAU). The workshop brought experts from multiple structural biology disciplines together to discuss near-term steps toward the goal of a molecular atlas of the cell. The discussion focused on the types of structural data that should be represented, how this data should be represented, and how the time domain might be incorporated into such an atlas. The consensus was that an explorable, map-like Virtual Cell, containing both spatial and temporal data bridging the atomic and cellular length scales obtained by multiple experimental methods, represents the best path toward a complete atlas of the cell.
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Affiliation(s)
- George L Hamilton
- Physics and Astronomy, Clemson University, 216 Kinard Lab, Clemson, S.C. USA
| | - Joshua Alper
- Physics and Astronomy, Clemson University, 302B Kinard Lab, Clemson, S.C. 29634-0978. USA
| | - Hugo Sanabria
- Physics and Astronomy, Clemson University, 214 Kinard Lab, Clemson, S.C. 29634-0978. USA,
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33
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Abstract
Feynman commented that "Everything that living things do can be understood in terms of the jiggling and wiggling of atoms". Proteins can jiggle and wiggle large structural elements such as domains and subunits as part of their functional cycles. Single-molecule fluorescence resonance energy transfer (smFRET) is an excellent tool to study conformational dynamics and decipher coordinated large-scale motions within proteins. smFRET methods introduced in recent years are geared toward understanding the time scales and amplitudes of function-related motions. This review discusses the methodology for obtaining and analyzing smFRET temporal trajectories that provide direct dynamic information on transitions between conformational states. It also introduces correlation methods that are useful for characterizing intramolecular motions. This arsenal of techniques has been used to study multiple molecular systems, from membrane proteins through molecular chaperones, and we examine some of these studies here. Recent exciting methodological novelties permit revealing very fast, submillisecond dynamics, whose relevance to protein function is yet to be fully grasped.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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34
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Affiliation(s)
- Takuhiro Otosu
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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35
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Abstract
Over the last decades, G protein coupled receptors (GPCRs) have experienced a tremendous amount of attention, which has led to a boost of structural and pharmacological insights on this large membrane protein superfamily involved in various essential physiological functions. Recently, evidence has emerged that, rather than being activated by ligands in an on/off manner switching from an inactive to an active state, GPCRs exhibit high structural flexibility in the absence and even in the presence of ligands. So far the physiological as well as pharmacological impact of this structural flexibility remains largely unexplored albeit its potential role in precisely fine-tuning receptor function and regulating the specificity of signal transduction into the cell. By complementing other biophysical approaches, single molecule fluorescence (SMF) offers the advantage of monitoring structural dynamics in biomolecules in real-time, with minimal structural invasiveness and in the context of complex biological environments. In this review a general introduction to GPCR structural dynamics is given followed by a presentation of SMF methods used to explore them. Particular attention is paid to single molecule Förster resonance energy transfer (smFRET), a key method to measure actual distance changes between two probes, and highlight conformational changes occurring at timescales relevant for protein conformational movements. The available literature reporting on GPCR structural dynamics by SMF is discussed with a focus on the newly gained biological insights on receptor activation and signaling, in particular for the β2 adrenergic and the metabotropic glutamate receptors.
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Affiliation(s)
- Robert B Quast
- CBS, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Emmanuel Margeat
- CBS, CNRS, INSERM, Université de Montpellier, Montpellier, France.
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36
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Tsytlonok M, Sanabria H, Wang Y, Felekyan S, Hemmen K, Phillips AH, Yun MK, Waddell MB, Park CG, Vaithiyalingam S, Iconaru L, White SW, Tompa P, Seidel CAM, Kriwacki R. Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation. Nat Commun 2019; 10:1676. [PMID: 30976006 PMCID: PMC6459857 DOI: 10.1038/s41467-019-09446-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/06/2019] [Indexed: 01/07/2023] Open
Abstract
p27Kip1 is an intrinsically disordered protein (IDP) that inhibits cyclin-dependent kinase (Cdk)/cyclin complexes (e.g., Cdk2/cyclin A), causing cell cycle arrest. Cell division progresses when stably Cdk2/cyclin A-bound p27 is phosphorylated on one or two structurally occluded tyrosine residues and a distal threonine residue (T187), triggering degradation of p27. Here, using an integrated biophysical approach, we show that Cdk2/cyclin A-bound p27 samples lowly-populated conformations that provide access to the non-receptor tyrosine kinases, BCR-ABL and Src, which phosphorylate Y88 or Y88 and Y74, respectively, thereby promoting intra-assembly phosphorylation (of p27) on distal T187. Even when tightly bound to Cdk2/cyclin A, intrinsic flexibility enables p27 to integrate and process signaling inputs, and generate outputs including altered Cdk2 activity, p27 stability, and, ultimately, cell cycle progression. Intrinsic dynamics within multi-component assemblies may be a general mechanism of signaling by regulatory IDPs, which can be subverted in human disease. The cyclin-dependent kinase (Cdk) inhibitor p27Kip1 (p27) folds upon binding to Cdk/cyclin complexes and during cell cycle progression p27 becomes phosphorylated, which triggers its ubiquitination and degradation. Here the authors use an integrated approach and show that Cdk2/cyclin A-bound p27 samples lowly-populated conformations that dynamically anticipate the sequential steps of the signaling cascade.
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Affiliation(s)
- Maksym Tsytlonok
- VIB Center for Structural Biology, Vrije Universiteit Brussel, Pleinlaan, 2 1050, Brussels, Belgium
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.,Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Yuefeng Wang
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,Department of Radiation Oncology, West Cancer Center and Research Institute, Memphis, TN, 38138, USA
| | - Suren Felekyan
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Katherina Hemmen
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38103, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38103, USA
| | - Luigi Iconaru
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Peter Tompa
- VIB Center for Structural Biology, Vrije Universiteit Brussel, Pleinlaan, 2 1050, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Claus A M Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany.
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. .,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
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37
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Barth A, Hendrix J, Fried D, Barak Y, Bayer EA, Lamb DC. Dynamic interactions of type I cohesin modules fine-tune the structure of the cellulosome of Clostridium thermocellum. Proc Natl Acad Sci U S A 2018; 115:E11274-E11283. [PMID: 30429330 PMCID: PMC6275499 DOI: 10.1073/pnas.1809283115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Efficient degradation of plant cell walls by selected anaerobic bacteria is performed by large extracellular multienzyme complexes termed cellulosomes. The spatial arrangement within the cellulosome is organized by a protein called scaffoldin, which recruits the cellulolytic subunits through interactions between cohesin modules on the scaffoldin and dockerin modules on the enzymes. Although many structural studies of the individual components of cellulosomal scaffoldins have been performed, the role of interactions between individual cohesin modules and the flexible linker regions between them are still not entirely understood. Here, we report single-molecule measurements using FRET to study the conformational dynamics of a bimodular cohesin segment of the scaffoldin protein CipA of Clostridium thermocellum We observe compacted structures in solution that persist on the timescale of milliseconds. The compacted conformation is found to be in dynamic equilibrium with an extended state that shows distance fluctuations on the microsecond timescale. Shortening of the intercohesin linker does not destabilize the interactions but reduces the rate of contact formation. Upon addition of dockerin-containing enzymes, an extension of the flexible state is observed, but the cohesin-cohesin interactions persist. Using all-atom molecular-dynamics simulations of the system, we further identify possible intercohesin binding modes. Beyond the view of scaffoldin as "beads on a string," we propose that cohesin-cohesin interactions are an important factor for the precise spatial arrangement of the enzymatic subunits in the cellulosome that leads to the high catalytic synergy in these assemblies and should be considered when designing cellulosomes for industrial applications.
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Affiliation(s)
- Anders Barth
- Physical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Nanosystems Initative Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Nanosystems Initative Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Daniel Fried
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Barak
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany;
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Nanosystems Initative Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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38
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Vandenberk N, Karamanou S, Portaliou AG, Zorzini V, Hofkens J, Hendrix J, Economou A. The Preprotein Binding Domain of SecA Displays Intrinsic Rotational Dynamics. Structure 2018; 27:90-101.e6. [PMID: 30471924 DOI: 10.1016/j.str.2018.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/27/2018] [Accepted: 10/10/2018] [Indexed: 11/26/2022]
Abstract
SecA converts ATP energy to protein translocation work. Together with the membrane-embedded SecY channel it forms the bacterial protein translocase. How secretory proteins bind to SecA and drive conformational cascades to promote their secretion remains unknown. To address this, we focus on the preprotein binding domain (PBD) of SecA. PBD crystalizes in three distinct states, swiveling around its narrow stem. Here, we examined whether PBD displays intrinsic dynamics in solution using single-molecule Förster resonance energy transfer (smFRET). Unique cysteinyl pairs on PBD and apposed domains were labeled with donor/acceptor dyes. Derivatives were analyzed using pulsed interleaved excitation and multi-parameter fluorescence detection. The PBD undergoes significant rotational motions, occupying at least three distinct states in dimeric and four in monomeric soluble SecA. Nucleotides do not affect smFRET-detectable PBD dynamics. These findings lay the foundations for single-molecule dissection of translocase mechanics and suggest models for possible PBD involvement during catalysis.
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Affiliation(s)
- Niels Vandenberk
- KU Leuven, Department of Chemistry, Division for Molecular Imaging and Photonics, Laboratory for Photochemistry and Spectroscopy, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Athina G Portaliou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Valentina Zorzini
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, Division for Molecular Imaging and Photonics, Laboratory for Photochemistry and Spectroscopy, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Jelle Hendrix
- KU Leuven, Department of Chemistry, Division for Molecular Imaging and Photonics, Laboratory for Photochemistry and Spectroscopy, Celestijnenlaan 200F, B-3001 Leuven, Belgium; Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, B-3590 Diepenbeek, Belgium.
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium.
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39
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Otosu T, Yamaguchi S. Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Concepts and Applications. Molecules 2018; 23:E2972. [PMID: 30441830 PMCID: PMC6278346 DOI: 10.3390/molecules23112972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/07/2018] [Accepted: 11/13/2018] [Indexed: 01/03/2023] Open
Abstract
We review the basic concepts and recent applications of two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), which is the extension of fluorescence correlation spectroscopy (FCS) to analyze the correlation of fluorescence lifetime in addition to fluorescence intensity. Fluorescence lifetime is sensitive to the microenvironment and can be a "molecular ruler" when combined with FRET. Utilization of fluorescence lifetime in 2D FLCS thus enables us to quantify the inhomogeneity of the system and the interconversion dynamics among different species with a higher time resolution than other single-molecule techniques. Recent applications of 2D FLCS to various biological systems demonstrate that 2D FLCS is a unique and promising tool to quantitatively analyze the microsecond conformational dynamics of macromolecules at the single-molecule level.
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Affiliation(s)
- Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan.
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan.
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40
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Gansen A, Felekyan S, Kühnemuth R, Lehmann K, Tóth K, Seidel CAM, Langowski J. High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes. Nat Commun 2018; 9:4628. [PMID: 30401903 DOI: 10.1038/s41467-018-06758-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/17/2018] [Indexed: 11/08/2022] Open
Abstract
Nucleosomes play a dual role in compacting the genome and regulating the access to DNA. To unravel the underlying mechanism, we study fluorescently labeled mononucleosomes by multi-parameter FRET measurements and characterize their structural and dynamic heterogeneity upon NaCl-induced destabilization. Species-selective fluorescence lifetime analysis and dynamic photon distribution analysis reveal intermediates during nucleosome opening and lead to a coherent structural and kinetic model. In dynamic octasomes and hexasomes the interface between the H2A-H2B dimers and the (H3-H4)2 tetramer opens asymmetrically by an angle of ≈20° on a 50 and 15 µs time scale, respectively. This is followed by a slower stepwise release of the dimers coupled with DNA unwrapping. A mutation (H2A-R81A) at the interface between H2A and H3 facilitates initial opening, confirming the central role of the dimer:tetramer interface for nucleosome stability. Partially opened states such as those described here might serve as convenient nucleation sites for DNA-recognizing proteins.
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41
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Affiliation(s)
- Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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42
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Schrimpf W, Lemmens V, Smisdom N, Ameloot M, Lamb DC, Hendrix J. Crosstalk-free multicolor RICS using spectral weighting. Methods 2018; 140-141:97-111. [DOI: 10.1016/j.ymeth.2018.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 11/16/2022] Open
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43
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Vishwakarma RK, Cao AM, Morichaud Z, Perumal AS, Margeat E, Brodolin K. Single-molecule analysis reveals the mechanism of transcription activation in M. tuberculosis. Sci Adv 2018; 4:eaao5498. [PMID: 29806016 PMCID: PMC5966222 DOI: 10.1126/sciadv.aao5498] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 04/10/2018] [Indexed: 06/01/2023]
Abstract
The σ subunit of bacterial RNA polymerase (RNAP) controls recognition of the -10 and -35 promoter elements during transcription initiation. Free σ adopts a "closed," or inactive, conformation incompatible with promoter binding. The conventional two-state model of σ activation proposes that binding to core RNAP induces formation of an "open," active, σ conformation, which is optimal for promoter recognition. Using single-molecule Förster resonance energy transfer, we demonstrate that vegetative-type σ subunits exist in open and closed states even after binding to the RNAP core. As an extreme case, RNAP from Mycobacterium tuberculosis preferentially retains σ in the closed conformation, which is converted to the open conformation only upon binding by the activator protein RbpA and interaction with promoter DNA. These findings reveal that the conformational dynamics of the σ subunit in the RNAP holoenzyme is a target for regulation by transcription factors and plays a critical role in promoter recognition.
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Affiliation(s)
- Rishi Kishore Vishwakarma
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
| | - Anne-Marinette Cao
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
| | | | - Emmanuel Margeat
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
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44
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Ghosh A, Karedla N, Thiele JC, Gregor I, Enderlein J. Fluorescence lifetime correlation spectroscopy: Basics and applications. Methods 2018; 140-141:32-39. [DOI: 10.1016/j.ymeth.2018.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022] Open
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45
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Schrimpf W, Barth A, Hendrix J, Lamb DC. PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data. Biophys J 2018; 114:1518-1528. [PMID: 29642023 PMCID: PMC5954487 DOI: 10.1016/j.bpj.2018.02.035] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/15/2018] [Accepted: 02/12/2018] [Indexed: 11/24/2022] Open
Abstract
Fluorescence microscopy and spectroscopy data hold a wealth of information on the investigated molecules, structures, or organisms. Nowadays, the same fluorescence data set can be analyzed in many ways to extract different properties of the measured sample. Yet, doing so remains slow and cumbersome, often requiring incompatible software packages. Here, we present PAM (pulsed interleaved excitation analysis with MATLAB), an open-source software package written in MATLAB that offers a simple and efficient workflow through its graphical user interface. PAM is a framework for integrated and robust analysis of fluorescence ensemble, single-molecule, and imaging data. Although it was originally developed for the analysis of pulsed interleaved excitation experiments, PAM has since been extended to support most types of data collection modalities. It combines a multitude of powerful analysis algorithms, ranging from time- and space-correlation analysis, over single-molecule burst analysis, to lifetime imaging microscopy, while offering intrinsic support for multicolor experiments. We illustrate the key concepts and workflow of the software by discussing data handling and sorting and provide step-by-step descriptions for the individual usage cases.
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Affiliation(s)
- Waldemar Schrimpf
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Anders Barth
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Biomedical Research Institute (BIOMED), Advanced Optical Microscopy Centre, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, KU Leuven, Heverlee, Belgium
| | - Don C Lamb
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
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46
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Voith von Voithenberg L, Lamb DC. Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics. Bioessays 2018; 40. [DOI: 10.1002/bies.201700078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 12/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lena Voith von Voithenberg
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
- BIOSS Centre for Signalling Studies; Schänzlestr. 18 79104 Freiburg Germany
| | - Don C. Lamb
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
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47
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Luitz MP, Barth A, Crevenna AH, Bomblies R, Lamb DC, Zacharias M. Covalent dye attachment influences the dynamics and conformational properties of flexible peptides. PLoS One 2017; 12:e0177139. [PMID: 28542243 PMCID: PMC5441599 DOI: 10.1371/journal.pone.0177139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/21/2017] [Indexed: 11/23/2022] Open
Abstract
Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET) or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET). The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP). Using the intrinsically disordered S-peptide as a model system, we investigate the impact of terminal fluorescence labeling on the molecular properties. We perform extensive molecular dynamics simulations on the labeled and unlabeled peptide and compare the results with in vitro PET-FCS measurements. Experimental and simulated timescales of end-to-end fluctuations were found in excellent agreement. Comparison between simulations with and without labels reveal that the π-stacking interaction between the fluorophore labels traps the conformation of S-peptide in a single dominant state, while the unlabeled peptide undergoes continuous conformational rearrangements. Furthermore, we find that the open to closed transition rate of S-peptide is decreased by at least one order of magnitude by the fluorophore attachment. Our approach combining experimental and in silico methods provides a benchmark for the simulations and reveals the significant effect that fluorescence labeling can have on the conformational dynamics of small biomolecules, at least for inherently flexible short peptides. The presented protocol is not only useful for comparing PET-FCS experiments with simulation results but provides a strategy to minimize the influence on molecular properties when chosing labeling positions for fluorescence experiments.
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Affiliation(s)
- Manuel P. Luitz
- Department Physik, T38, Technische Universität München, 85748 Garching, Germany
| | - Anders Barth
- Department Chemie, Physikalische Chemie, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Alvaro H. Crevenna
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Rainer Bomblies
- Department Physik, T38, Technische Universität München, 85748 Garching, Germany
| | - Don C. Lamb
- Department Chemie, Physikalische Chemie, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Martin Zacharias
- Department Physik, T38, Technische Universität München, 85748 Garching, Germany
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48
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Kilpatrick LE, Hill SJ. The use of fluorescence correlation spectroscopy to characterize the molecular mobility of fluorescently labelled G protein-coupled receptors. Biochem Soc Trans 2016; 44:624-9. [PMID: 27068980 DOI: 10.1042/BST20150285] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/10/2023]
Abstract
The membranes of living cells have been shown to be highly organized into distinct microdomains, which has spatial and temporal consequences for the interaction of membrane bound receptors and their signalling partners as complexes. Fluorescence correlation spectroscopy (FCS) is a technique with single cell sensitivity that sheds light on the molecular dynamics of fluorescently labelled receptors, ligands or signalling complexes within small plasma membrane regions of living cells. This review provides an overview of the use of FCS to probe the real time quantification of the diffusion and concentration of G protein-coupled receptors (GPCRs), primarily to gain insights into ligand–receptor interactions and the molecular composition of signalling complexes. In addition we document the use of photon counting histogram (PCH) analysis to investigate how changes in molecular brightness (ε) can be a sensitive indicator of changes in molecular mass of fluorescently labelled moieties.
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49
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Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr Opin Struct Biol 2016; 40:163-185. [PMID: 27939973 DOI: 10.1016/j.sbi.2016.11.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023]
Abstract
Förster Resonance Energy Transfer (FRET) combined with single-molecule spectroscopy probes macromolecular structure and dynamics and identifies coexisting conformational states. We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET). We discuss procedures to incorporate prior structural knowledge and to obtain optimal distance networks. Finally, a workflow for hybrid-FRET is presented that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails. To test this workflow, we simulate realistic single-molecule experiments and resolve three protein conformers, exchanging at 30μs and 10ms, with accuracies of 1-3Å RMSD versus the target structure. Incorporation of data from other spectroscopies and imaging is also discussed.
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Affiliation(s)
- Mykola Dimura
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas O Peulen
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christian A Hanke
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Aiswaria Prakash
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Claus Am Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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50
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Ishii K, Tahara T. Correction of the afterpulsing effect in fluorescence correlation spectroscopy using time symmetry analysis. Opt Express 2015; 23:32387-32400. [PMID: 26699028 DOI: 10.1364/oe.23.032387] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Afterpulsing of a photon-counting detector is a common problem in fluorescence correlation spectroscopy. We have developed a numerical procedure which eliminates the afterpulsing effect by analyzing the time reversal asymmetry of photon data that are recorded with a time-correlated single photon counting device. This method was applied to experimental data and was compared with a previous method [Rev. Sci. Instrum. 76, 033102 (2005).]. It is demonstrated that the present method can completely eliminate the afterpulsing effect even in the case of a sample solution that contains multiple fluorophores having different fluorescence lifetimes, for which the previous method underestimates the correlation amplitude. We also show a modification of the previous method incorporating the time symmetry analysis.
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