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arXiv · 2006.03091

The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices

Eitan Lerner·Benjamin Ambrose·Anders Barth·Victoria Birkedal·Scott C. Blanchard·Richard Borner·Thorben Cordes·Timothy D. Craggs·Taekjip Ha·Gilad Haran·Thorsten Hugel·Antonino Ingargiola·Achillefs Kapanidis·Don C. Lamb·Ted Laurence·Nam ki Lee·Edward A. Lemke·Emmanuel Margeat·Jens Michaelis·Xavier Michalet·Daniel Nettels·Thomas-Otavio Peulen·Benjamin Schuler·Claus A. M. Seidel·Hamid So-leimaninejad·Shimon Weiss
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Abstract

Single-molecule F\"{o}rster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the technique by an ever-increasing number of groups has generated many improvements and variations in the technique itself, in methods for sample preparation and characterization, in analysis of the data from such experiments, and in analysis codes and algorithms. Recently, several labs that employ smFRET have joined forces to try to bring the smFRET community together in adopting a consensus on how to perform experiments and analyze results for achieving quantitative structural information. These recent efforts include multi-lab blind-tests to assess the accuracy and precision of smFRET between different labs using different procedures, the formal assembly of the FRET community and development of smFRET procedures to be considered for entries in the wwPDB. Here we delve into the different approaches and viewpoints in the field. This position paper describes the current "state-of-the field", points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and a list of resources that are openly available. To make further progress, we strongly encourage 'open science' practices. We hope that this position paper will provide a roadmap for newcomers to the field, as well as a reference for seasoned practitioners.

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Eitan Lerner, Benjamin Ambrose, Anders Barth, Victoria Birkedal, Scott C. Blanchard, Richard Borner, Thorben Cordes, Timothy D. Craggs, Taekjip Ha, Gilad Haran, Thorsten Hugel, Antonino Ingargiola, Achillefs Kapanidis, Don C. Lamb, Ted Laurence, Nam ki Lee, Edward A. Lemke, Emmanuel Margeat, Jens Michaelis, Xavier Michalet, Daniel Nettels, Thomas-Otavio Peulen, Benjamin Schuler, Claus A. M. Seidel, Hamid So-leimaninejad, Shimon Weiss. 2020-06-04. The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices. https://doi.org/10.7554/elife.60416

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