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Author

Nielsen, Janni, Lauritsen, Johanne, Pedersen, Jannik N., Nowak, Jan S., Bendtsen, Malthe K., Kleijwegt, Giulia, Lusser, Kaija, Pitarch, Laia C., Moreno, Julián V., Schneider, Matthias M., Krainer, Georg, Goksøyr, Louise, Khalifé, Paul, Kaalund, Sanne Simone, Aznar, Susana, Kjærgaard, Magnus, Sereikaité, Vita, Strømgaard, Kristian, Knowles, Tuomas P.J., Nielsen, Morten Agertoug, Sander, Adam F., Romero-Ramos, Marina, Otzen, Daniel E., Nielsen, Janni, Lauritsen, Johanne, Pedersen, Jannik N., Nowak, Jan S., Bendtsen, Malthe K., Kleijwegt, Giulia, Lusser, Kaija, Pitarch, Laia C., Moreno, Julián V., Schneider, Matthias M., Krainer, Georg, Goksøyr, Louise, Khalifé, Paul, Kaalund, Sanne Simone, Aznar, Susana, Kjærgaard, Magnus, Sereikaité, Vita, Strømgaard, Kristian, Knowles, Tuomas P.J., Nielsen, Morten Agertoug, Sander, Adam F., Romero-Ramos, Marina, and Otzen, Daniel E.

Published
2024

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Author

Nielsen, Janni, Lauritsen, Johanne, Pedersen, Jannik N., Nowak, Jan S., Bendtsen, Malthe K., Kleijwegt, Giulia, Lusser, Kaija, Pitarch, Laia C., Moreno, Julián V., Schneider, Matthias M., Krainer, Georg, Goksøyr, Louise, Khalifé, Paul, Kaalund, Sanne Simone, Aznar, Susana, Kjærgaard, Magnus, Sereikaité, Vita, Strømgaard, Kristian, Knowles, Tuomas P.J., Nielsen, Morten Agertoug, Sander, Adam F., Romero-Ramos, Marina, Otzen, Daniel E., Nielsen, Janni, Lauritsen, Johanne, Pedersen, Jannik N., Nowak, Jan S., Bendtsen, Malthe K., Kleijwegt, Giulia, Lusser, Kaija, Pitarch, Laia C., Moreno, Julián V., Schneider, Matthias M., Krainer, Georg, Goksøyr, Louise, Khalifé, Paul, Kaalund, Sanne Simone, Aznar, Susana, Kjærgaard, Magnus, Sereikaité, Vita, Strømgaard, Kristian, Knowles, Tuomas P.J., Nielsen, Morten Agertoug, Sander, Adam F., Romero-Ramos, Marina, and Otzen, Daniel E.

Published
2024

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

Author

Agam, Ganesh, 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, Cordes, Thorben, Agam, Ganesh, 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

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

4. Impact of cholesterol and Lumacaftor on the folding of CFTR helical hairpins

Author

Schenkel, Mathias, Ravamehr-Lake, Dorna, Czerniak, Tomasz, Saenz, James P., Krainer, Georg, Schlierf, Michael, Deber, Charles M., Schenkel, Mathias, Ravamehr-Lake, Dorna, Czerniak, Tomasz, Saenz, James P., Krainer, Georg, Schlierf, Michael, and Deber, Charles M.

Abstract

Cystic fibrosis (CF) is caused by mutations in the gene that codes for the chloride channel cystic fibrosis transmembrane conductance regulator (CFTR). Recent advances in CF treatment have included use of small-molecule drugs known as modulators, such as Lumacaftor (VX-809), but their detailed mechanism of action and interplay with the surrounding lipid membranes, including cholesterol, remain largely unknown. To examine these phenomena and guide future modulator development, we prepared a set of wild type (WT) and mutant helical hairpin constructs consisting of CFTR transmembrane (TM) segments 3 and 4 and the intervening extracellular loop (termed TM3/4 hairpins) that represent minimal membrane protein tertiary folding units. These hairpin variants, including CF-phenotypic loop mutants E217G and Q220R, and membrane-buried mutant V232D, were reconstituted into large unilamellar phosphatidylcholine (POPC) vesicles, and into corresponding vesicles containing 70 mol% POPC +30 mol% cholesterol, and studied by single-molecule FRET and circular dichroism experiments. We found that the presence of 30 mol% cholesterol induced an increase in helicity of all TM3/4 hairpins, suggesting an increase in bilayer cross-section and hence an increase in the depth of membrane insertion compared to pure POPC vesicles. Importantly, when we added the corrector VX-809, regardless of the presence or absence of cholesterol, all mutants displayed folding and helicity largely indistinguishable from the WT hairpin. Fluorescence spectroscopy measurements suggest that the corrector alters lipid packing and water accessibility. We propose a model whereby VX-809 shields the protein from the lipid environment in a mutant-independent manner such that the WT scaffold prevails. Such ‘normalization’ to WT conformation is consistent with the action of VX-809 as a protein-folding chaperone.

Published
2022

5. Impact of cholesterol and Lumacaftor on the folding of CFTR helical hairpins

Author

Schenkel, Mathias, Ravamehr-Lake, Dorna, Czerniak, Tomasz, Saenz, James P., Krainer, Georg, Schlierf, Michael, Deber, Charles M., Schenkel, Mathias, Ravamehr-Lake, Dorna, Czerniak, Tomasz, Saenz, James P., Krainer, Georg, Schlierf, Michael, and Deber, Charles M.

Abstract

Cystic fibrosis (CF) is caused by mutations in the gene that codes for the chloride channel cystic fibrosis transmembrane conductance regulator (CFTR). Recent advances in CF treatment have included use of small-molecule drugs known as modulators, such as Lumacaftor (VX-809), but their detailed mechanism of action and interplay with the surrounding lipid membranes, including cholesterol, remain largely unknown. To examine these phenomena and guide future modulator development, we prepared a set of wild type (WT) and mutant helical hairpin constructs consisting of CFTR transmembrane (TM) segments 3 and 4 and the intervening extracellular loop (termed TM3/4 hairpins) that represent minimal membrane protein tertiary folding units. These hairpin variants, including CF-phenotypic loop mutants E217G and Q220R, and membrane-buried mutant V232D, were reconstituted into large unilamellar phosphatidylcholine (POPC) vesicles, and into corresponding vesicles containing 70 mol% POPC +30 mol% cholesterol, and studied by single-molecule FRET and circular dichroism experiments. We found that the presence of 30 mol% cholesterol induced an increase in helicity of all TM3/4 hairpins, suggesting an increase in bilayer cross-section and hence an increase in the depth of membrane insertion compared to pure POPC vesicles. Importantly, when we added the corrector VX-809, regardless of the presence or absence of cholesterol, all mutants displayed folding and helicity largely indistinguishable from the WT hairpin. Fluorescence spectroscopy measurements suggest that the corrector alters lipid packing and water accessibility. We propose a model whereby VX-809 shields the protein from the lipid environment in a mutant-independent manner such that the WT scaffold prevails. Such ‘normalization’ to WT conformation is consistent with the action of VX-809 as a protein-folding chaperone.

Published
2022

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

Author

Hellenkamp, Björn, 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, Hugel, Thorsten, Hellenkamp, Björn, 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

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

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

Author

Hellenkamp, Björn, 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, Hugel, Thorsten, Hellenkamp, Björn, 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

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

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

Author

Hellenkamp, Björn, 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, Hugel, Thorsten, Hellenkamp, Björn, 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

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

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

Author

Hellenkamp, Björn, 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, Hugel, Thorsten, Hellenkamp, Björn, 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

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

10. 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 A.M., Craggs, Timothy D., Hugel, Thorsten, 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 A.M., Craggs, Timothy D., and Hugel, Thorsten

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

11. Erratum to: 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, 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, and Seidel, Henning

Published
2018

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