Literature DB >> 29348210

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer.

Eitan Lerner1, Thorben Cordes2,3, Antonino Ingargiola1, Yazan Alhadid1, SangYoon Chung1, Xavier Michalet1, Shimon Weiss1,4,5.   

Abstract

Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2018        PMID: 29348210      PMCID: PMC6200918          DOI: 10.1126/science.aan1133

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  147 in total

Review 1.  Beyond kinetic traps in RNA folding.

Authors:  D K Treiber; J R Williamson
Journal:  Curr Opin Struct Biol       Date:  2001-06       Impact factor: 6.809

Review 2.  Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.

Authors:  Eva Meirovitch; Yury E Shapiro; Antonino Polimeno; Jack H Freed
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-05       Impact factor: 9.795

3.  Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments.

Authors:  Eyal Nir; Xavier Michalet; Kambiz M Hamadani; Ted A Laurence; Daniel Neuhauser; Yevgeniy Kovchegov; Shimon Weiss
Journal:  J Phys Chem B       Date:  2006-11-09       Impact factor: 2.991

Review 4.  RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

Authors:  Shi-Jie Chen
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

Review 5.  Using sm-FRET and denaturants to reveal folding landscapes.

Authors:  Euan Shaw; Patrick St-Pierre; Kaley McCluskey; Daniel A Lafontaine; J Carlos Penedo
Journal:  Methods Enzymol       Date:  2014       Impact factor: 1.600

6.  Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.

Authors:  Jan-Willem van de Meent; Jonathan E Bronson; Chris H Wiggins; Ruben L Gonzalez
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

Review 7.  Combining single-molecule manipulation and single-molecule detection.

Authors:  Juan Carlos Cordova; Dibyendu Kumar Das; Harris W Manning; Matthew J Lang
Journal:  Curr Opin Struct Biol       Date:  2014-10-17       Impact factor: 6.809

Review 8.  Single-Particle Cryo-EM at Crystallographic Resolution.

Authors:  Yifan Cheng
Journal:  Cell       Date:  2015-04-23       Impact factor: 41.582

9.  Dynamic profiling of double-stranded RNA binding proteins.

Authors:  Xinlei Wang; Lela Vukovic; Hye Ran Koh; Klaus Schulten; Sua Myong
Journal:  Nucleic Acids Res       Date:  2015-07-16       Impact factor: 16.971

10.  FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.

Authors:  Antonino Ingargiola; Eitan Lerner; SangYoon Chung; Shimon Weiss; Xavier Michalet
Journal:  PLoS One       Date:  2016-08-17       Impact factor: 3.240

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  105 in total

Review 1.  Approaches for measuring the dynamics of RNA-protein interactions.

Authors:  Donny D Licatalosi; Xuan Ye; Eckhard Jankowsky
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-08-20       Impact factor: 9.957

2.  Single-molecule FRET methods to study the dynamics of proteins at work.

Authors:  Hisham Mazal; Gilad Haran
Journal:  Curr Opin Biomed Eng       Date:  2019-08-23

3.  Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy.

Authors:  Jaba Mitra; Monika A Makurath; Thuy T M Ngo; Alice Troitskaia; Yann R Chemla; Taekjip Ha
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-03       Impact factor: 11.205

4.  Three-Color Single-Molecule FRET and Fluorescence Lifetime Analysis of Fast Protein Folding.

Authors:  Janghyun Yoo; John M Louis; Irina V Gopich; Hoi Sung Chung
Journal:  J Phys Chem B       Date:  2018-10-10       Impact factor: 2.991

5.  ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling.

Authors:  Hugh Wilson; Quan Wang
Journal:  Nat Methods       Date:  2021-06-14       Impact factor: 28.547

6.  Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis.

Authors:  Jochem N A Vink; Stan J J Brouns; Johannes Hohlbein
Journal:  Biophys J       Date:  2020-10-04       Impact factor: 4.033

7.  Application of millisecond time-resolved solid state NMR to the kinetics and mechanism of melittin self-assembly.

Authors:  Jaekyun Jeon; Kent R Thurber; Rodolfo Ghirlando; Wai-Ming Yau; Robert Tycko
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-06       Impact factor: 11.205

8.  Stacking-induced fluorescence increase reveals allosteric interactions through DNA.

Authors:  Michael J Morten; Sergio G Lopez; I Emilie Steinmark; Aidan Rafferty; Steven W Magennis
Journal:  Nucleic Acids Res       Date:  2018-11-30       Impact factor: 16.971

9.  Lanthanide-Based Nanosensors: Refining Nanoparticle Responsiveness for Single Particle Imaging of Stimuli.

Authors:  Jason R Casar; Claire A McLellan; Chris Siefe; Jennifer A Dionne
Journal:  ACS Photonics       Date:  2020-10-16       Impact factor: 7.529

Review 10.  Structural Dynamics of Glutamate Signaling Systems by smFRET.

Authors:  Ryan J Durham; Danielle R Latham; Hugo Sanabria; Vasanthi Jayaraman
Journal:  Biophys J       Date:  2020-10-20       Impact factor: 4.033

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