eLife (Mar 2021)
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
- Eitan Lerner,
- Anders Barth,
- Jelle Hendrix,
- Benjamin Ambrose,
- Victoria Birkedal,
- Scott C Blanchard,
- Richard Börner,
- Hoi Sung Chung,
- Thorben Cordes,
- Timothy D Craggs,
- Ashok A Deniz,
- Jiajie Diao,
- Jingyi Fei,
- Ruben L Gonzalez,
- Irina V Gopich,
- Taekjip Ha,
- Christian A Hanke,
- Gilad Haran,
- Nikos S Hatzakis,
- Sungchul Hohng,
- Seok-Cheol Hong,
- Thorsten Hugel,
- Antonino Ingargiola,
- Chirlmin Joo,
- Achillefs N Kapanidis,
- Harold D Kim,
- Ted Laurence,
- Nam Ki Lee,
- Tae-Hee Lee,
- Edward A Lemke,
- Emmanuel Margeat,
- Jens Michaelis,
- Xavier Michalet,
- Sua Myong,
- Daniel Nettels,
- Thomas-Otavio Peulen,
- Evelyn Ploetz,
- Yair Razvag,
- Nicole C Robb,
- Benjamin Schuler,
- Hamid Soleimaninejad,
- Chun Tang,
- Reza Vafabakhsh,
- Don C Lamb,
- Claus AM Seidel,
- Shimon Weiss
Affiliations
- Eitan Lerner
- ORCiD
- 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 Jerusalem, Jerusalem, Israel
- Anders Barth
- ORCiD
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
- Jelle Hendrix
- ORCiD
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
- Benjamin Ambrose
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
- Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus University, Aarhus, Denmark
- Scott C Blanchard
- ORCiD
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States
- Richard Börner
- ORCiD
- Laserinstitut HS Mittweida, University of Applied Science Mittweida, Mittweida, Germany
- Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
- Thorben Cordes
- ORCiD
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Timothy D Craggs
- ORCiD
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
- Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of Medicine, Cincinnati, United States
- Jingyi Fei
- ORCiD
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
- Ruben L Gonzalez
- ORCiD
- Department of Chemistry, Columbia University, New York, United States
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
- Taekjip Ha
- ORCiD
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, United States
- Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
- Gilad Haran
- ORCiD
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
- Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark; Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
- Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea University, Seoul, Republic of Korea
- Thorsten Hugel
- ORCiD
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Antonino Ingargiola
- ORCiD
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los Angeles, Los Angeles, United States
- Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
- Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
- Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, United States
- Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, United States
- Nam Ki Lee
- ORCiD
- School of Chemistry, Seoul National University, Seoul, Republic of Korea
- Tae-Hee Lee
- Department of Chemistry, Pennsylvania State University, University Park, United States
- Edward A Lemke
- ORCiD
- Departments of Biology and Chemistry, Johannes Gutenberg University, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany
- Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de Montpellier, Montpellier, France
- Jens Michaelis
- Institüt of Biophysics, Ulm University, Ulm, Germany
- Xavier Michalet
- ORCiD
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los Angeles, Los Angeles, United States
- Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
- Daniel Nettels
- Department of Biochemistry and Department of Physics, University of Zurich, Zurich, Switzerland
- Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
- Evelyn Ploetz
- ORCiD
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München, Germany
- 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 Jerusalem, Jerusalem, Israel
- Nicole C Robb
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Benjamin Schuler
- ORCiD
- Department of Biochemistry and Department of Physics, University of Zurich, Zurich, Switzerland
- Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of Melbourne, Parkville, Australia
- Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
- Don C Lamb
- ORCiD
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München, Germany
- Claus AM Seidel
- ORCiD
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
- Shimon Weiss
- ORCiD
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los Angeles, Los Angeles, United States; Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los Angeles, Los Angeles, United States
- DOI
- https://doi.org/10.7554/eLife.60416
- Journal volume & issue
-
Vol. 10
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.
Keywords
