Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

Autor: Anna Sefer, Eleni Kallis, Tobias Eilert, Carlheinz Röcker, Olga Kolesnikova, David Neuhaus, Sebastian Eustermann, Jens Michaelis

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-17 (2022)

Sm FRET studies of PARP-1 recognition of DNA lesion show that binding of F1F2 fragment results in a kinked DNA, while binding of F2 fragment alone yields an intermediate state. This dynamic equilibrium of states is influenced by inhibitors.

Externí odkaz: https://doaj.org/article/642a60ff46824c648ef3c679a670721e

Fast-NPS—A Markov Chain Monte Carlo-based analysis tool to obtain structural information from single-molecule FRET measurements

Autor: Jens Michaelis, Tobias Eilert, Florian Drechsler, Maximilian Beckers

Publikováno v: Computer Physics Communications. 219:377-389

The analysis tool and software package Fast-NPS can be used to analyse smFRET data to obtain quantitative structural information about macromolecules in their natural environment. In the algorithm a Bayesian model gives rise to a multivariate probabi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::cf9a15d1eabad10f962f0b3b57f66472
https://doi.org/10.1016/j.cpc.2017.05.027

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

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

Publikováno v: Nature Methods, 15(9), 669-676. Nature Publishing Group
Nature methods
Nature Methods 15 (2018) 9
Hellenkamp, Björn; Schmid, Sonja; Doroshenko, Olga; Opanasyuk, Oleg; Kühnemuth, Ralf; Rezaei Adariani, Soheila; et al.(2018). Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.. Nature methods, 15(9), 669-676. doi: 10.1038/s41592-018-0085-0. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/82n6186z
Nature Methods
Hellenkamp, B, Schmid, S, Doroshenko, O, Opanasyuk, O, Kuehnemuth, R, Adariani, S R, Ambrose, B, Aznauryan, M, Barth, A, Birkedal, V, Bowen, M E, Chen, H, Cordes, T, Eilert, T, Fijen, C, Gebhardt, C, Goetz, M, Gouridis, G, Gratton, E, Ha, T, Hao, P, Hanke, C A, Hartmann, A, Hendrix, J, Hildebrandt, L L, Hirschfeld, V, Hohlbein, J, Hua, B, Huebner, C G, Kallis, E, Kapanidis, A N, Kim, J-Y, Krainer, G, Lamb, D C, Lee, N K, Lemke, E A, Levesque, B, Levitus, M, McCann, J J, Naredi-Rainer, N, Nettels, D, Thuy Ngo, T, Qiu, R, Robb, N C, Roecker, C, Sanabria, H, Schlierf, M, Schroeder, T, Schuler, B, Seidel, H, Streit, L, Thurn, J, Tinnefeld, P, Tyagi, S, Vandenberk, N, Vera, A M, Weninger, K R, Wunsch, B, Yanez-Orozco, I S, Michaelis, J, Seidel, C A M, Craggs, T D & Hugel, T 2018, ' Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study ', Nature Methods, vol. 15, no. 9, pp. 669-676 . https://doi.org/10.1038/s41592-018-0085-0
Nature Methods, 15(9), 669-676
Nature Methods (online), 15(9)

Single-molecule Forster 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 reproducibili

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::72edbb856467f1a0f8cea053565b29e1
https://research.rug.nl/en/publications/6b30271d-1e88-40c6-a10a-544c2685cb93

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System

Autor: Carlheinz Röcker, Jens Michaelis, Julia Nagy, Tobias Eilert, Thilo Dörfler

Publikováno v: Journal of Visualized Experiments : JoVE

Single-molecule Forster Resonance Energy Transfer (smFRET) can be used to obtain structural information on biomolecular complexes in real-time. Thereby, multiple smFRET measurements are used to localize an unknown dye position inside a protein comple

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::158b6ca2a954e4a832b555cfc1aa7ca5
https://doi.org/10.3791/54782-v

Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

Autor: Tobias Eilert, Julia Nagy, Jens Michaelis

Publikováno v: The Journal of Chemical Physics. 148:123308

Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Baye

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fa0a2564c1471fcbc6be8cfb75e46a78
https://doi.org/10.1063/1.5006477