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4 results on '"Craggs P"'

1. Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Author

Agam, Ganesh, Gebhardt, Christian, Popara, Milana, Mächtel, Rebecca, Folz, Julian, Ambrose, Benjamin, Chamachi, Neharika, Chung, Sang Yoon, Craggs, Timothy D, de Boer, Marijn, Grohmann, Dina, Ha, Taekjip, Hartmann, Andreas, Hendrix, Jelle, Hirschfeld, Verena, Hübner, Christian G, Hugel, Thorsten, Kammerer, Dominik, Kang, Hyun-Seo, Kapanidis, Achillefs N, Krainer, Georg, Kramm, Kevin, Lemke, Edward A, Lerner, Eitan, Margeat, Emmanuel, Martens, Kirsten, Michaelis, Jens, Mitra, Jaba, Moya Muñoz, Gabriel G, Quast, Robert B, Robb, Nicole C, Sattler, Michael, Schlierf, Michael, Schneider, Jonathan, Schröder, Tim, Sefer, Anna, Tan, Piau Siong, Thurn, Johann, Tinnefeld, Philip, van Noort, John, Weiss, Shimon, Wendler, Nicolas, Zijlstra, Niels, Barth, Anders, Seidel, Claus AM, Lamb, Don C, and Cordes, Thorben

Subjects
Biochemistry and Cell Biology, Biological Sciences, Affordable and Clean Energy, Fluorescence Resonance Energy Transfer, Reproducibility of Results, Proteins, Molecular Conformation, Laboratories, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.

Published
2023

2. Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Author

Hellenkamp, Björn, Schmid, Sonja, Doroshenko, Olga, Opanasyuk, Oleg, Kühnemuth, Ralf, Adariani, Soheila Rezaei, Ambrose, Benjamin, Aznauryan, Mikayel, Barth, Anders, Birkedal, Victoria, Bowen, Mark E, Chen, Hongtao, Cordes, Thorben, Eilert, Tobias, Fijen, Carel, Gebhardt, Christian, Götz, Markus, Gouridis, Giorgos, Gratton, Enrico, Ha, Taekjip, Hao, Pengyu, Hanke, Christian A, Hartmann, Andreas, Hendrix, Jelle, Hildebrandt, Lasse L, Hirschfeld, Verena, Hohlbein, Johannes, Hua, Boyang, Hübner, Christian G, Kallis, Eleni, Kapanidis, Achillefs N, Kim, Jae-Yeol, Krainer, Georg, Lamb, Don C, Lee, Nam Ki, Lemke, Edward A, Levesque, Brié, Levitus, Marcia, McCann, James J, Naredi-Rainer, Nikolaus, Nettels, Daniel, Ngo, Thuy, Qiu, Ruoyi, Robb, Nicole C, Röcker, Carlheinz, Sanabria, Hugo, Schlierf, Michael, Schröder, Tim, Schuler, Benjamin, Seidel, Henning, Streit, Lisa, Thurn, Johann, Tinnefeld, Philip, Tyagi, Swati, Vandenberk, Niels, Vera, Andrés Manuel, Weninger, Keith R, Wünsch, Bettina, Yanez-Orozco, Inna S, Michaelis, Jens, Seidel, Claus AM, Craggs, Timothy D, and Hugel, Thorsten

Subjects
Biological Sciences, Good Health and Well Being, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.

Published
2018

3. Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Author

Hellenkamp, Björn, Schmid, Sonja, Doroshenko, Olga, Opanasyuk, Oleg, Kühnemuth, Ralf, Rezaei Adariani, Soheila, Ambrose, Benjamin, Aznauryan, Mikayel, Barth, Anders, Birkedal, Victoria, Bowen, Mark E, Chen, Hongtao, Cordes, Thorben, Eilert, Tobias, Fijen, Carel, Gebhardt, Christian, Götz, Markus, Gouridis, Giorgos, Gratton, Enrico, Ha, Taekjip, Hao, Pengyu, Hanke, Christian A, Hartmann, Andreas, Hendrix, Jelle, Hildebrandt, Lasse L, Hirschfeld, Verena, Hohlbein, Johannes, Hua, Boyang, Hübner, Christian G, Kallis, Eleni, Kapanidis, Achillefs N, Kim, Jae-Yeol, Krainer, Georg, Lamb, Don C, Lee, Nam Ki, Lemke, Edward A, Levesque, Brié, Levitus, Marcia, McCann, James J, Naredi-Rainer, Nikolaus, Nettels, Daniel, Ngo, Thuy, Qiu, Ruoyi, Robb, Nicole C, Röcker, Carlheinz, Sanabria, Hugo, Schlierf, Michael, Schröder, Tim, Schuler, Benjamin, Seidel, Henning, Streit, Lisa, Thurn, Johann, Tinnefeld, Philip, Tyagi, Swati, Vandenberk, Niels, Vera, Andrés Manuel, Weninger, Keith R, Wünsch, Bettina, Yanez-Orozco, Inna S, Michaelis, Jens, Seidel, Claus AM, Craggs, Timothy D, and Hugel, Thorsten

Subjects
Bioengineering, Affordable and Clean Energy, Fluorescence Resonance Energy Transfer, Laboratories, Reproducibility of Results, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Published
2018

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