FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

eLife

Sungchul Hohng¹  Jens Michaelis²  Reza Vafabakhsh³  Harold D Kim⁴  Thorsten Hugel⁵  Xavier Michalet⁶  Don C Lamb⁷  Achillefs N Kapanidis⁸  Chun Tang⁹  Evelyn Ploetz⁹  Jingyi Fei^1,10  Yair Razvag^1,11  Eitan Lerner^1,12  Benjamin Schuler^1,12  Taekjip Ha^1,13  Thomas-Otavio Peulen^1,14  Jiajie Diao^1,15  Gilad Haran^1,16  Nikos S Hatzakis^1,17  Chirlmin Joo^1,18  Daniel Nettels^1,18  Victoria Birkedal^1,19  Ruben L Gonzalez^2,20  Edward A Lemke^2,21  Timothy D Craggs^2,22  Benjamin Ambrose^2,22  Ashok A Deniz^2,23  Claus AM Seidel^2,24  Seok-Cheol Hong^2,25  Scott C Blanchard^2,26  Emmanuel Margeat^2,27  Jelle Hendrix^2,28  Antonino Ingargiola^2,29  Sua Myong^3,30  Hoi Sung Chung^3,31  Irina V Gopich^3,31  Richard Börner^3,32  Anders Barth^3,33  Christian A Hanke^3,33  Nicole C Robb^3,34  Shimon Weiss^3,34  Nam Ki Lee^3,35  Thorben Cordes^3,36  Tae-Hee Lee^3,37  Ted Laurence^3,38  Hamid Soleimaninejad^3,39 

[1] Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;Institute of Molecular Biology (IMB), Mainz, Germany;Biological Optical Microscopy Platform (BOMP), University of Melbourne, Parkville, Australia;Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom;Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea University, Seoul, Republic of Korea;Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de Montpellier, Montpellier, France;College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China;Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands;Department of Biochemistry and Department of Physics, University of Zurich, Zurich, Switzerland;Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of Chicago, Chicago, United States;Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States;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;Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, United States;Department of Biophysics, Johns Hopkins University, Baltimore, United States;Department of Cancer Biology, University of Cincinnati School of Medicine, Cincinnati, United States;Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark;Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los Angeles, Los Angeles, United States;Department of Chemistry and iNANO center, Aarhus University, Aarhus, Denmark;Department of Chemistry, Columbia University, New York, United States;Department of Chemistry, Pennsylvania State University, University Park, United States;Department of Chemistry, University of Sheffield, Sheffield, United Kingdom;Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States;Department of Molecular Biosciences, Northwestern University, Evanston, United States;Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea;Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States;Departments of Biology and Chemistry, Johannes Gutenberg University, Mainz, Germany;Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium;Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany;Institüt of Biophysics, Ulm University, Ulm, Germany;Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States;Laserinstitut HS Mittweida, University of Applied Science Mittweida, Mittweida, Germany;Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany;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;Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, United States;Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany;School of Chemistry, Seoul National University, Seoul, Republic of Korea;School of Physics, Georgia Institute of Technology, Atlanta, United States;Warwick Medical School, University of Warwick, Coventry, United Kingdom;

关键词: FRET;    single-molecule;    conformation;    dynamics;    biomolecules;    community;   

DOI  :  10.7554/eLife.60416

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown