1
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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. Reply to: On the statistical foundation of a recent single molecule FRET benchmark. Nat Commun 2024; 15:3626. [PMID: 38688911 PMCID: PMC11061175 DOI: 10.1038/s41467-024-47734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Markus Götz
- PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany.
| | - Anders Barth
- 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, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 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, USA
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 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 B Sletfjerding
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 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.
- Department of Chemistry, University of Basel, Basel, Switzerland.
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2
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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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3
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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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4
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Li J, Xie J, Godec A, Weninger KR, Liu C, Smith JC, Hong L. Non-ergodicity of a globular protein extending beyond its functional timescale. Chem Sci 2022; 13:9668-9677. [PMID: 36091909 PMCID: PMC9400594 DOI: 10.1039/d2sc03069a] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble. Here, by performing single-molecule fluorescence resonance energy transfer (smFRET) experiments and molecular dynamics (MD) simulations of a multi-domain globular protein, cytoplasmic protein-tyrosine phosphatase (SHP2), we demonstrate that the functional inter-domain motion is observationally non-ergodic over the time spans 10−12 to 10−7 s and 10−1 to 102 s. The difference between observational non-ergodicity and simple non-convergence is discussed. In comparison, a single-strand DNA of similar size behaves ergodically with an energy landscape resembling a one-dimensional linear chain. The observed non-ergodicity results from the hierarchical connectivity of the high-dimensional energy landscape of the protein molecule. As the characteristic time for the protein to conduct its dephosphorylation function is ∼10 s, our findings suggest that, due to the non-ergodicity, individual, seemingly identical protein molecules can be dynamically and functionally different. Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble.![]()
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Affiliation(s)
- Jun Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - JingFei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Aljaž Godec
- Mathematical BioPhysics Group, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Saikia N, Yanez-Orozco IS, Qiu R, Hao P, Milikisiyants S, Ou E, Hamilton GL, Weninger KR, Smirnova TI, Sanabria H, Ding F. Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. Cell Rep Phys Sci 2021; 2:100616. [PMID: 34888535 PMCID: PMC8654206 DOI: 10.1016/j.xcrp.2021.100616] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Department of Chemistry, Navajo Technical University, Chinle, AZ 86503, USA
| | | | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Erkang Ou
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - George L. Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Tatyana I. Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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6
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Larsen J, Rosholm KR, Kennard C, Pedersen SL, Munch HK, Tkach V, Sakon JJ, Bjørnholm T, Weninger KR, Bendix PM, Jensen KJ, Hatzakis NS, Uline MJ, Stamou D. How Membrane Geometry Regulates Protein Sorting Independently of Mean Curvature. ACS Cent Sci 2020; 6:1159-1168. [PMID: 32724850 PMCID: PMC7379390 DOI: 10.1021/acscentsci.0c00419] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Indexed: 05/06/2023]
Abstract
Biological membranes have distinct geometries that confer specific functions. However, the molecular mechanisms underlying the phenomenological geometry/function correlations remain elusive. We studied the effect of membrane geometry on the localization of membrane-bound proteins. Quantitative comparative experiments between the two most abundant cellular membrane geometries, spherical and cylindrical, revealed that geometry regulates the spatial segregation of proteins. The measured geometry-driven segregation reached 50-fold for membranes of the same mean curvature, demonstrating a crucial and hitherto unaccounted contribution by Gaussian curvature. Molecular-field theory calculations elucidated the underlying physical and molecular mechanisms. Our results reveal that distinct membrane geometries have specific physicochemical properties and thus establish a ubiquitous mechanistic foundation for unravelling the conserved correlations between biological function and membrane polymorphism.
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Affiliation(s)
- Jannik
B. Larsen
- Bionanotecnology
and Nanomedicine Laboratory, University
of Copenhagen, Copenhagen, Denmark
- Nano-Science
Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Kadla R. Rosholm
- Bionanotecnology
and Nanomedicine Laboratory, University
of Copenhagen, Copenhagen, Denmark
- Nano-Science
Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Celeste Kennard
- Department
of Chemical Engineering, University of South
Carolina, Columbia, South Carolina, United States
| | - Søren L. Pedersen
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Henrik K. Munch
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Vadym Tkach
- Bionanotecnology
and Nanomedicine Laboratory, University
of Copenhagen, Copenhagen, Denmark
- Nano-Science
Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - John J. Sakon
- Department
of Physics, North Carolina State University, Raleigh, North Carolina, United States
| | - Thomas Bjørnholm
- Bionanotecnology
and Nanomedicine Laboratory, University
of Copenhagen, Copenhagen, Denmark
- Nano-Science
Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Keith R. Weninger
- Department
of Physics, North Carolina State University, Raleigh, North Carolina, United States
| | | | - Knud J. Jensen
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Nikos S Hatzakis
- Bionanotecnology
and Nanomedicine Laboratory, University
of Copenhagen, Copenhagen, Denmark
- Nano-Science
Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Mark J. Uline
- Center
for Geometrically Engineered Cellular Systems, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemical Engineering, Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina, United States
- (M.J.U.) E-mail:
| | - Dimitrios Stamou
- Bionanotecnology
and Nanomedicine Laboratory, University
of Copenhagen, Copenhagen, Denmark
- Nano-Science
Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
- Department
of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center
for Geometrically Engineered Cellular Systems, University of Copenhagen, Copenhagen, Denmark
- (D.S.)
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7
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LeBlanc SJ, Gauer JW, Hao P, Case BC, Hingorani MM, Weninger KR, Erie DA. Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS. Nucleic Acids Res 2019; 46:10782-10795. [PMID: 30272207 PMCID: PMC6237781 DOI: 10.1093/nar/gky865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 03/14/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein–DNA and DNA–DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Jacob W Gauer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Brandon C Case
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Choi UB, Sanabria H, Smirnova T, Bowen ME, Weninger KR. Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins. Biomolecules 2019; 9:biom9030114. [PMID: 30909517 PMCID: PMC6468417 DOI: 10.3390/biom9030114] [Citation(s) in RCA: 30] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 01/08/2023] Open
Abstract
The common conception of intrinsically disordered proteins (IDPs) is that they stochastically sample all possible configurations driven by thermal fluctuations. This is certainly true for many IDPs, which behave as swollen random coils that can be described using polymer models developed for homopolymers. However, the variability in interaction energy between different amino acid sequences provides the possibility that some configurations may be strongly preferred while others are forbidden. In compact globular IDPs, core hydration and packing density can vary between segments of the polypeptide chain leading to complex conformational dynamics. Here, we describe a growing number of proteins that appear intrinsically disordered by biochemical and bioinformatic characterization but switch between restricted regions of conformational space. In some cases, spontaneous switching between conformational ensembles was directly observed, but few methods can identify when an IDP is acting as a restricted chain. Such switching between disparate corners of conformational space could bias ligand binding and regulate the volume of IDPs acting as structural or entropic elements. Thus, mapping the accessible energy landscape and capturing dynamics across a wide range of timescales are essential to recognize when an IDP is acting as such a switch.
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Affiliation(s)
- Ucheor B Choi
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
| | - Tatyana Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA.
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9
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Qiu R, DeRocco VC, Harris C, Sharma A, Hingorani MM, Erie DA, Weninger KR. Large conformational changes in MutS during
DNA
scanning, mismatch recognition and repair signaling. EMBO J 2019; 38:38/4/e101518. [DOI: 10.15252/embj.2019101518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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10
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Xu P, Hensley A, Chan E, Weninger KR. Toward Single Molecule FRET Studies of DNA Mismatch Repair in Live Bacteria. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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11
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LeBlanc SJ, Hao P, Hinds MA, Morgan AN, Gbozah K, Weninger KR, Erie DA. Investigating the Function of Mutl Conformational Changes in Mismatch Repair using smFRET. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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12
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LeBlanc SJ, Kulkarni P, Weninger KR. Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins. Biomolecules 2018; 8:biom8040140. [PMID: 30413085 PMCID: PMC6315554 DOI: 10.3390/biom8040140] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
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13
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Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, Hugel T. Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat Methods 2018; 15:984. [PMID: 30327572 PMCID: PMC7608346 DOI: 10.1038/s41592-018-0193-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Björn Hellenkamp
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.,Engineering and Applied Sciences, Columbia University, New York, NY, USA
| | - Sonja Schmid
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Olga Doroshenko
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Oleg Opanasyuk
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ralf Kühnemuth
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | | | | | - Mikayel Aznauryan
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Mark E Bowen
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Hongtao Chen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Eilert
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Carel Fijen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Markus Götz
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Giorgos Gouridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Taekjip Ha
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Christian A Hanke
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Andreas Hartmann
- B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Leuven, Belgium.,Dynamic Bioimaging Lab, Advanced Optical Microscopy Center and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - Lasse L Hildebrandt
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.,Microspectroscopy Research Facility Wageningen, Wageningen University & Research, Wageningen, The Netherlands
| | - Boyang Hua
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA
| | | | - Eleni Kallis
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Jae-Yeol Kim
- School of Chemistry, Seoul National University, Seoul, South Korea
| | - Georg Krainer
- B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany.,Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nam Ki Lee
- School of Chemistry, Seoul National University, Seoul, South Korea
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Mainz, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brié Levesque
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Marcia Levitus
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - James J McCann
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Nikolaus Naredi-Rainer
- Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Thuy Ngo
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA
| | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Nicole C Robb
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | | | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA
| | - Michael Schlierf
- B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Tim Schröder
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Henning Seidel
- Institute of Physics, University of Lübeck, Lübeck, Germany
| | - Lisa Streit
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Johann Thurn
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Philip Tinnefeld
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany.,Institute of Physical & Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology, Braunschweig, Germany
| | - Swati Tyagi
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Niels Vandenberk
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Leuven, Belgium
| | - Andrés Manuel Vera
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Bettina Wünsch
- Institute of Physical & Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology, Braunschweig, Germany
| | | | | | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
| | - Timothy D Craggs
- Department of Chemistry, University of Sheffield, Sheffield, UK. .,Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany.
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14
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Roushan M, Azad Z, Movahed S, Ray PD, Livshits GI, Lim SF, Weninger KR, Riehn R. Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement. Sci Rep 2018; 8:10036. [PMID: 29968756 PMCID: PMC6030079 DOI: 10.1038/s41598-018-28278-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/20/2018] [Indexed: 01/23/2023] Open
Abstract
We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD+).
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Zubair Azad
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Saeid Movahed
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Paul D Ray
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Gideon I Livshits
- Department of Physics, North Carolina State University, Raleigh, NC, USA.,Department of Chemistry, Osaka University, Osaka, 560-0043, Japan
| | - Shuang Fang Lim
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, NC, USA.
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15
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Abstract
DNA mismatch repair, which involves is a widely conserved set of proteins, is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch repair remain hidden due in part to the complexity and transient nature of the interactions between the mismatch repair proteins and DNA substrates. Single molecule methods offer the capability to uncover these transient but complex interactions and allow novel insights into mechanisms that underlie DNA mismatch repair. In this review, we discuss applications of single molecule methodology including electron microscopy, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair. These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair.
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Affiliation(s)
- Dorothy A Erie
- Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, United States
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16
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Abstract
![]()
MutS
recognizes base–base mismatches and base insertions/deletions
(IDLs) in newly replicated DNA. Specific interactions between MutS
and these errors trigger a cascade of protein–protein interactions
that ultimately lead to their repair. The inability to explain why
different DNA errors are repaired with widely varying efficiencies in vivo remains an outstanding example of our limited knowledge
of this process. Here, we present single-molecule Förster resonance
energy transfer measurements of the DNA bending dynamics induced by Thermus aquaticus MutS and the E41A mutant of MutS, which
is known to have error specific deficiencies in signaling repair.
We compared three DNA mismatches/IDLs (T-bulge, GT, and CC) with repair
efficiencies ranging from high to low. We identify three dominant
DNA bending states [slightly bent/unbent (U), intermediately
bent (I), and significantly bent (B)] and
find that the kinetics of interconverting among states varies widely
for different complexes. The increased stability of MutS–mismatch/IDL
complexes is associated with stabilization of U and lowering
of the B to U transition barrier. Destabilization
of U is always accompanied by a destabilization of B, supporting the suggestion that B is a “required”
precursor to U. Comparison of MutS and MutS-E41A dynamics
on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates
the changes in base–base hydrogen bonding that are required
to achieve the U state, which has been implicated in
repair signaling. Taken together with repair propensities, our data
suggest that the bending kinetics of MutS–mismatched DNA complexes
may control the entry into functional pathways for downstream signaling
of repair.
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Affiliation(s)
- Vanessa C DeRocco
- Department of Chemistry and ‡Curriculum in Applied Sciences and Engineering, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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17
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Mooney SM, Qiu R, Kim JJ, Sacho EJ, Rajagopalan K, Johng D, Shiraishi T, Kulkarni P, Weninger KR. Cancer/testis antigen PAGE4, a regulator of c-Jun transactivation, is phosphorylated by homeodomain-interacting protein kinase 1, a component of the stress-response pathway. Biochemistry 2014; 53:1670-9. [PMID: 24559171 PMCID: PMC4198062 DOI: 10.1021/bi500013w] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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] [Indexed: 01/02/2023]
Abstract
![]()
Prostate-associated gene 4 (PAGE4)
is a cancer/testis antigen that
is typically restricted to the testicular germ cells but is aberrantly
expressed in cancer. Furthermore, PAGE4 is developmentally regulated
with dynamic expression patterns in the developing prostate and is
also a stress-response protein that is upregulated in response to
cellular stress. PAGE4 interacts with c-Jun, which is activated by
the stress-response kinase JNK1, and plays an important role in the
development and pathology of the prostate gland. Here, we have identified
homeodomain-interacting protein kinase 1 (HIPK1), also a component
of the stress-response pathway, as a kinase that phosphorylates PAGE4
at T51. We show that phosphorylation of PAGE4 is critical for its
transcriptional activity since mutating this T residue abolishes its
ability to potentiate c-Jun transactivation. In vitro single molecule FRET indicates phosphorylation results in compaction
of (still) intrinsically disordered PAGE4. Interestingly, however,
while our previous observations indicated that the wild-type nonphosphorylated
PAGE4 protein interacted with c-Jun [RajagopalanK. et al. (2014) 1842, 154−16324263171], here we show that phosphorylation of PAGE4
weakens its interaction with c-Jun in vitro. These
data suggest that phosphorylation induces conformational changes in
natively disordered PAGE4 resulting in its decreased affinity for
c-Jun to promote interaction of c-Jun with another, unidentified,
partner. Alternatively, phosphorylated PAGE4 may induce transcription
of a novel partner, which then potentiates c-Jun transactivation.
Regardless, the present results clearly implicate PAGE4 as a component
of the stress-response pathway and uncover a novel link between components
of this pathway and prostatic development and disease.
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Affiliation(s)
- Steven M Mooney
- The James Buchanan Brady Urological Institute and Department of Urology, ‡Oncology, §Cellular and Molecular Medicine, and ∥Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University School of Medicine , 733 North Broadway, Baltimore, Maryland 21205, United States
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18
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Rajagopalan K, Qiu R, Mooney SM, Rao S, Shiraishi T, Sacho E, Huang H, Shapiro E, Weninger KR, Kulkarni P. The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation. Biochim Biophys Acta Mol Basis Dis 2013; 1842:154-63. [PMID: 24263171 DOI: 10.1016/j.bbadis.2013.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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: 07/15/2013] [Revised: 10/26/2013] [Accepted: 11/13/2013] [Indexed: 01/18/2023]
Abstract
The Cancer/Testis Antigen (CTA), Prostate-associated Gene 4 (PAGE4), is a stress-response protein that is upregulated in prostate cancer (PCa) especially in precursor lesions that result from inflammatory stress. In cells under stress, translocation of PAGE4 to mitochondria increases while production of reactive oxygen species decreases. Furthermore, PAGE4 is also upregulated in human fetal prostate, underscoring its potential role in development. However, the proteins that interact with PAGE4 and the mechanisms underlying its pleiotropic functions in prostatic development and disease remain unknown. Here, we identified c-Jun as a PAGE4 interacting partner. We show that both PAGE4 and c-Jun are overexpressed in the human fetal prostate; and in cell-based assays, PAGE4 robustly potentiates c-Jun transactivation. Single-molecule Förster resonance energy transfer experiments indicate that upon binding to c-Jun, PAGE4 undergoes conformational changes. However, no interaction is observed in presence of BSA or unilamellar vesicles containing the mitochondrial inner membrane diphosphatidylglycerol lipid marker cardiolipin. Together, our data indicate that PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions. To our knowledge, this is the first report demonstrating crosstalk between a CTA and a proto-oncogene. Disrupting PAGE4/c-Jun interactions using small molecules may represent a novel therapeutic strategy for PCa.
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Affiliation(s)
- Krithika Rajagopalan
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Steven M Mooney
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shweta Rao
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Takumi Shiraishi
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth Sacho
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Hongying Huang
- Department of Urology, New York University School of Medicine, New York, NY 10016, USA
| | - Ellen Shapiro
- Department of Urology, New York University School of Medicine, New York, NY 10016, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
| | - Prakash Kulkarni
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Stamou D, Christensen SM, Ehrlich N, Tkach V, Sakon JJ, Choi UB, Weninger KR. Cooperative All-Or-None Recruitment of Synaptotagmin C2AB on Single Vesicles Explains Why Ca2+ Regulates the Amplitude of SNARE Mediated Vesicle Fusion. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Sacho EJ, Weninger KR. Single Molecule FRET Studies of the DNA Mismatch Repair Protein MutSα using Specific Labeling with Unnatural Amino Acids. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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21
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Choi UB, McCann JJ, Weninger KR, Bowen ME. Beyond the random coil: stochastic conformational switching in intrinsically disordered proteins. Structure 2011; 19:566-76. [PMID: 21481779 DOI: 10.1016/j.str.2011.01.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 01/21/2011] [Accepted: 01/26/2011] [Indexed: 01/24/2023]
Abstract
Intrinsically disordered proteins (IDPs) participate in critical cellular functions that exploit the flexibility and rapid conformational fluctuations of their native state. Limited information about the native state of IDPs can be gained by the averaging over many heterogeneous molecules that is unavoidable in ensemble approaches. We used single molecule fluorescence to characterize native state conformational dynamics in five synaptic proteins confirmed to be disordered by other techniques. For three of the proteins, SNAP-25, synaptobrevin and complexin, their conformational dynamics could be described with a simple semiflexible polymer model. Surprisingly, two proteins, neuroligin and the NMDAR-2B glutamate receptor, were observed to stochastically switch among distinct conformational states despite the fact that they appeared intrinsically disordered by other measures. The hop-like intramolecular diffusion found in these proteins is suggested to define a class of functionality previously unrecognized for IDPs.
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Affiliation(s)
- Ucheor B Choi
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
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Brunger AT, Strop P, Vrljic M, Chu S, Weninger KR. Three-dimensional molecular modeling with single molecule FRET. J Struct Biol 2010; 173:497-505. [PMID: 20837146 DOI: 10.1016/j.jsb.2010.09.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/08/2010] [Indexed: 01/09/2023]
Abstract
Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes.
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Affiliation(s)
- Axel T Brunger
- The Howard Hughes Medical Institute, Stanford University, CA 94305, USA.
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Choi UB, Strop P, Vrljic M, Chu S, Brunger AT, Weninger KR. Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex. Nat Struct Mol Biol 2010; 17:318-24. [PMID: 20173763 PMCID: PMC2922927 DOI: 10.1038/nsmb.1763] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [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: 07/12/2009] [Accepted: 12/11/2009] [Indexed: 12/11/2022]
Abstract
Synchronous neurotransmission is triggered when Ca(2+) binds to synaptotagmin 1 (Syt1), a synaptic-vesicle protein that interacts with SNAREs and membranes. We used single-molecule fluorescence resonance energy transfer (FRET) between synaptotagmin's two C2 domains to determine that their conformation consists of multiple states with occasional transitions, consistent with domains in random relative motion. SNARE binding results in narrower intrasynaptotagmin FRET distributions and less frequent transitions between states. We obtained an experimentally determined model of the elusive Syt1-SNARE complex using a multibody docking approach with 34 FRET-derived distances as restraints. The Ca(2+)-binding loops point away from the SNARE complex, so they may interact with the same membrane. The loop arrangement is similar to that of the crystal structure of SNARE-induced Ca(2+)-bound Syt3, suggesting a common mechanism by which the interaction between synaptotagmins and SNAREs aids in Ca(2+)-triggered fusion.
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Affiliation(s)
- Ucheor B Choi
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
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Abstract
We combined single molecule fluorescence resonance energy transfer (smFRET) with single particle tracking in live cells to detect the in vivo conformation of individual proteins. We site-specifically labeled recombinant SNARE proteins with a FRET donor and acceptor before microinjecting them into cultured cells. We observed that individual proteins rapidly incorporated into folded complexes at the cell membrane, demonstrating the potential of this method to reveal dynamic interactions within cells.
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Affiliation(s)
- John J Sakon
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
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Weninger KR, Evans PG, Putterman SJ. Comment on "Mie scattering from a sonoluminescing bubble with high spatial and temporal resolution". Phys Rev E Stat Nonlin Soft Matter Phys 2001; 64:038301. [PMID: 11580487 DOI: 10.1103/physreve.64.038301] [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] [Subscribe] [Scholar Register] [Received: 08/09/2000] [Revised: 06/11/2001] [Indexed: 05/23/2023]
Abstract
A key parameter underlying the existence of sonoluminescence (or SL) is the time dependence of the radius R(t) of the collapsing bubble from which SL originates. With regard to the use of light scattering to measure this quantity, we wish to note that we disagree with the statement of Gompf and Pecha-highly compressed water causes the minimum in scattered light to occur 700 ps before SL-and that this effect leads to an overestimate of the bubble wall velocity. We discuss potential artifacts in their experimental arrangement and reply to their criticisms of our experiments on Mie scattering.
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Affiliation(s)
- K R Weninger
- Physics Department, University of California, Los Angeles, California 90095, USA
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Weninger KR, Camara CG, Putterman SJ. Observation of bubble dynamics within luminescent cavitation clouds: Sonoluminescence at the nano-scale. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 63:016310. [PMID: 11304356 DOI: 10.1103/physreve.63.016310] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2000] [Indexed: 11/07/2022]
Abstract
Measurements of acoustically driven cavitation luminescence indicate that this phenomenon is robust over a huge parameter space ranging from 10 kHz to >10 MHz. The minimum bubble radius achieved is an upper bound for the size of the light-emitting region and ranges from about 1 microm at 15 kHz to tens of nm at 11 MHz. Although lines can be discerned in the spectra of some cavitation clouds, they sit on top of a broadband continuum which can have greater spectral density in the ultraviolet than is observed for resonantly driven sonoluminescence from a single bubble.
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Affiliation(s)
- K R Weninger
- Physics Department, University of California, Los Angeles, CA 90095, USA
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Weninger KR, Evans PG, Putterman SJ. Time correlated single photon mie scattering from a sonoluminescing bubble. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 61:R1020-R1023. [PMID: 11046528 DOI: 10.1103/physreve.61.r1020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/1999] [Indexed: 05/23/2023]
Abstract
Application of time correlated single photon counting to pulsed Mie scattering enables one to resolve changes in light scattering to better than 50 ps. This technique is applied to the highly nonlinear motion of a sonoluminescing bubble. Physical processes, such as outgoing shock wave emission, that limit the interpretation of the data are measured with a streak camera and microscopy. Shock speeds about 6 km/s have been observed.
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Affiliation(s)
- KR Weninger
- Department of Physics, University of California, Los Angeles, California 90095, USA
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