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hybridFRET - deciphering biomolecular structure and dynamics

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Publications

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

Author(s): 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 Ka
Published in: eLife, 10, 2021, Page(s) e60416, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.60416

Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues

Author(s): Dmytro Dziuba, Pascal Didier, Stefano Ciaco, Anders Barth, Claus A. M. Seidel, Yves Mély
Published in: Chemical Society Reviews, 50/12, 2021, Page(s) 7062-7107, ISSN 0306-0012
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1cs00194a

Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α

Author(s): Sinan Kilic, Suren Felekyan, Olga Doroshenko, Iuliia Boichenko, Mykola Dimura, Hayk Vardanyan, Louise C. Bryan, Gaurav Arya, Claus A. M. Seidel, Beat Fierz
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-02619-5

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

Author(s): Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Benjamin Ambrose, Mikayel Aznauryan, Anders Barth, Victoria Birkedal, Mark E. Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Christian Gebhardt, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip Ha, Pengyu Hao, Christian A. Hanke, Andreas Hartmann, Jelle Hendrix, Lass
Published in: Nature Methods, 15/9, 2018, Page(s) 669-676, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0085-0

High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes

Author(s): Alexander Gansen, Suren Felekyan, Ralf Kühnemuth, Kathrin Lehmann, Katalin Tóth, Claus A. M. Seidel, Jörg Langowski
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-06758-1

Combining Graphical and Analytical Methods with Molecular Simulations to Analyze Time-resolved FRET-measurements of Labeled Macromolecules Accurately

Author(s): Thomas-Otavio Peulen, Oleg Opanasyuk, Claus A.M. Seidel
Published in: The Journal of Physical Chemistry B, 121, 2017, Page(s) 8211-8241, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.7b03441

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems

Author(s): Mykola Dimura, Thomas O Peulen, Christian A Hanke, Aiswaria Prakash, Holger Gohlke, Claus AM Seidel
Published in: Current Opinion in Structural Biology, 40, 2016, Page(s) 163-185, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2016.11.012

Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET

Author(s): Kathrin Lehmann, Suren Felekyan, Ralf Kühnemuth, Mykola Dimura, Katalin Tóth, Claus A M Seidel, Jörg Langowski
Published in: Nucleic Acids Research, 48/3, 2020, Page(s) 1551-1571, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1186

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Author(s): Berman, H.M., Adams, P.D., Bonvin, A.A., Burley, S.K., Carragher, B., Chiu, W., DiMaio, F., Ferrin, T.E., Gabanyi, M.J., Goddard, T.D., Griffin, P.R., Haas, J., Hanke, C.A., Hoch, J.C., Hummer, G., Kurisu, G., Lawson, C.L., Leitner, A., Markley, J.L., Meiler, J., Montelione, G.T., Phillips, G.N., Prisner, T., Rappsilber, J., Schriemer, D.C., Schwede, T., Seidel, C. A. M., Strutzenberg, T.S., Sverg
Published in: Structure, 27, 2019, Page(s) 1745-1759, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2019.11.002

Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A

Author(s): Maksym Tsytlonok, Katherina Hemmen, George Hamilton, Narendar Kolimi, Suren Felekyan, Claus A.M. Seidel, Peter Tompa, Hugo Sanabria
Published in: Journal of Molecular Biology, 432/9, 2020, Page(s) 2998-3017, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2020.02.010

Integrative dynamic structural biology unveils conformers essential for the oligomerization of a large GTPase

Author(s): Thomas-Otavio Peulen, Carola S. Hengstenberg, Ralf Biehl, Mykola Dimura, Charlotte Lorenz, Alessandro Valeri, Semra Ince, Tobias Vöpel, Bela Farago, Holger Gohlke, Johann Klare, Andreas M. Stadler, Claus A.M. Seidel, Christian Hermann
Published in: arXiv, 2020
Publisher: arXiv.org

Unraveling multi-state molecular dynamics in single-molecule FRET experiments - Part I: Theory of FRET-lines

Author(s): Anders Barth, Oleg Opanasyuk, Thomas-Otavio Peulen, Suren Felekyan, Stanislav Kalinin, Hugo Sanabria, Claus A.M. Seidel
Published in: arXiv, 2021
Publisher: arXiv.org

FRET nanoscopy enables seamless imaging of molecular assemblies with sub-nanometer resolution

Author(s): Jan-Hendrik Budde, Nicolaas van der Voort, Suren Felekyan, Julian Folz, Ralf Kühnemuth, Paul Lauterjung, Markus Köhler, Andreas Schönle, Julian Sindram, Marius Otten, Matthias Karg, Christian Herrmann, Anders Barth, Claus A. M. Seidel
Published in: arXiv, 2021
Publisher: arXiv.org

Resolving dynamics and function of transient states in single enzyme molecules

Author(s): Hugo Sanabria, Dmitro Rodnin, Katherina Hemmen, Thomas Peulen, Suren Felekyan, Mark R. Fleissner, Mykola Dimura, Felix Koberling, Ralf Kühnemuth, Wayne Hubbell, Holger Gohlke, Claus A.M. Seidel
Published in: 2018
Publisher: arXiv.org

Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation

Author(s): Maksym Tsytlonok, Hugo Sanabria, Yuefeng Wang, Suren Felekyan, Katherina Hemmen, Aaron Phillips, Mi-Kyung Yun, Brett Waddell, Cheon-Gil Park, Sivaraja Vaithiyalingam, Luigi Iconaru, Stephen W. White, Peter Tompa, Claus A. M. Seidel, Richard Kriwacki
Published in: 2018
Publisher: arXiv.org

Unraveling multi-state molecular dynamics in single-molecule FRET experiments - Part II: Quantitative analysis of multi-state kinetic networks

Author(s): Oleg Opanasyuk, Anders Barth, Thomas-Otavio Peulen, Suren Felekyan, Stanislav Kalinin, Hugo Sanabria, Claus A.M. Seidel
Published in: arXiv, 2021
Publisher: arXiv.org

Efficient FRET-assisted computational structural modelling

Author(s): Mykola Dimura
Published in: 2020
Publisher: Heinrich Heine University Duesseldorf

Accurate structural determination of biomolecules via single-molecule high-precision FRET measurements

Author(s): Olga Doroshenko
Published in: 2019
Publisher: Heinrich Heine University Duesseldorf

Mapping protein structure and dynamics by Förster Resonance Energy Transfer in vitro and in live cells

Author(s): Thomas-Otavio Peulen
Published in: 2017
Publisher: Heinrich Heine University Duesseldorf

Automated and optimally FRET-assisted structural modeling

Author(s): Mykola Dimura, Thomas-Otavio Peulen, Hugo Sanabria, Dmitro Rodnin, Katherina Hemmen, Christian A. Hanke, Claus A. M. Seidel, Holger Gohlke
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19023-1