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Forschung MPC | ERC Grant
ERC Advanced Grant: hybridFRET - deciphering biomolecular structure and dynamics (12/2015 - 05/2021)

To understand and modulate biological processes, we need their spatiotemporal molecular models. In this project we propose to build these models by a holistic approach. The recent methodological and technical advances in fluorescence spectroscopy and microscopy as well as in multi-scale modelling of complex biochemical systems set the stage to tackle cross-fertilizing challenges in biophysics, biochemistry and cell biology. The applicant proposes to develop a novel integrative platform for a Molecular Fluorescence Microscope (MFM) to achieve ultimate resolution in space (sub-nanometer) and time (picoseconds) for characterizing structure and dynamics of proteins. MFM will combine Multi-parameter Fluorescence Detection with Computational Microscopy (molecular dynamics and coarse grained simulations) in a hybrid approach, first, to derive a complete molecular description of all fluorescence properties of the tailored dyes in proteins (objectives 1 and 2) and, second, to utilize this information in simulations to report on the protein properties (objective 3). In this hybrid approach high precision FRET measurements are the core experimental technique (hybridFRET). The MFM will allow us to tackle the central biophysical question of how intra- and intermolecular domain interactions modulate proteins' overall structure, dynamics, and thus ultimately function (objective 4). In this proposal we will apply MFM to two prototypic proteins of significant medical relevance. The combination with Multi-parameter Fluorescence Image Spectroscopy will exploit the ultimate resolution of the MFM for molecular protein imaging in live cells. To follow and ultimately understand biological processes, we need their spatiotemporal models of the integrative fluorescence spectroscopy platform. Until now, no holistic use of fluorescence spectroscopy for structural modelling of proteins has been reported.

More information on the European Research Council (ERC)

List of publications together with research data:


Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.
Agam, G., Gebhardt, C., Popara, M., Mächtel, R., Folz, J., Ambrose, B., Chamachi, N., Chung, S. Y., Craggs, T. D., de Boer, M., Grohmann, D., Ha, T., Hartmann, A., Hendrix, J., Hirschfeld, V., Hübner, C. G., Hugel, T., Kammerer, D., Kang, H.-S., Kapanidis, A. N., Krainer, G., Kramm, K., Lemke, E., Lerner, E., Margeat, E., Martens, K., Michaelis, J., Mitra, J., Muñoz, G. G. M., Quast, R., Robb, N. B,, Sattler, M., Schlierf, M., Schneider, J., Schröder, T., Sefer, A., Tan, P. S., Thurn, J., Tinnefeld, P., van Noort, J., Weiss, S., Wendler, N., Zijlstra, N., Barth, A., Seidel, C. A. M., Lamb, D. C., Cordes, T.
Nat. Methods 20, 523-535 (2023)
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Fuzzy supertertiary interactions within PSD-95 enable ligand binding.
Hamilton, G. L., Sakia, N., Basak, S., Welcome, F. S., Wu, F., Kubiak, J., Hao, Y., Seidel, C. A. M., Ding, F., Sanabria, H., Bowen, M. E.
eLife 11, e77242 (2022)
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Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks.
Opanasyuk, O., Barth, A., Peulen, T.-O., Felekyan, S., Kalinin S., Sanabria H., Seidel, C. A. M.
J. Chem. Phys. 157, e031501 (2022)
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Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines.
Barth, A., Opanasyuk, O., Peulen, T.-O., Felekyan, S., Kalinin, S., Sanabria, H.,
J. Chem. Phys. 156, e141501 (2022)
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FRET nanoscopy enables seamless imaging of molecular assemblies with sub-nanometer resolution.
Budde, J.-H., van der Voort, N.T.M., Felekyan, S., Folz, J., Kühnemuth, R., Lauterjung, P., Köhler, M., Schönle, A., Sindram, J., Otten, M., Karg, M., Herrmann, C., Barth, A. , Seidel, C. A. M.
arXiv (2021)
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Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues.
Dziuba, D., Didier, P., Ciaco, S., Barth, A., Seidel, C. A. M., Mély, Y.
Chem. Soc. Rev. 50, 7062-7107 (2021)
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FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.
Lerner, E., Barth, A., Hendrix, J., Ambrose, B., Birkedal, V., Blanchard, S. C., Börner, R., Chung. H. S., Cordes, T., Craggs, T. D., Deniz, A. A., Diao J., Fei J., Gonzalez, R. L., Gopich, I. V., Ha, T., Hanke, C. A., Haran, G., Hatzakis, N. S., Hohng S., Hong, S.-C., Hugel, T., Ingargiola, A., Joo, C., Kapanidis, A. N., Kim, H. D., Laurence, T., Lee, N. K., Lee, T.-H., Lemke E.-A., Margeat, E., Michaelis, J., Michalet, X., Myong, S., Nettels, D., Peulen, T.-O., Ploetz, E., Razvag, Y., Robb, N. C., Schuler, B., Soleimaninejad, H., Tang, C., Vafabakhsh, R., Lamb, D. C., Seidel, C. A. M., Weiss, S.
eLife 10, e60416 (2021)
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Automated and optimally FRET-assisted structural modeling.
Dimura, M., Peulen, T.-O., Sanabria, H., Rodnin, D., Hemmen, K.,Hanke, C.A., Seidel, C. A. M., Gohlke, H.
Nat. Commun. 11, e5394 (2020)
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Resolving dynamics and function of transient states in single enzyme molecules
Sanabria, H., Rodnin, D., Hemmen, K., Peulen, T.-O., Felekyan, S., Fleissner, M. R., Dimura, M., Koberling, F., Kühnemuth, R., Hubbell, W., Gohlke, H., Seidel, C. A. M.
Nat Commun. 11, e1231 (2020)
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Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET
Lehmann, K., Felekyan, S., Kühnemuth, R., Dimura, M., Tóth, K+, Seidel, C. A. M.+, Langowski, J.
Nucleic Acids Res. 48, 1551-71 (2020)
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Specific conformational dynamics and expansion underpin a multi-step mechanism for specific binding of p27 with Cdk2/Cyclin A
Tsytlonok, M., Hemmen, K., Hamilton, G., Kolimi, N., Felekyan, S., Seidel, C. A. M., Tompa, P., Sanabria, H.
J. Mol. Biol. 432, 2998-3017 (2020)
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Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
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., Svergun, D.I., Tajkhorshid, E., Trewhella, J., Vallat, B., Velankar, S., Vuister, G.W., Webb, B., Westbrook, J.D., White, K.L., Sali, A.
Structure 27, 1745-1759 (2019)
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Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation
Tsytlonok, M., Sanabria, H., Wang, Y., Felekyan, S., Hemmen, K., Phillips, A.H., Yun, M.-K., Waddell, B., Park, C.-G., Vaithiyalingam, S., Iconaru, L., White, S.W., Tompa, P., Seidel, C.A.M., Kriwacki, R.
Nat. Commun. 10, e1676 (2019)
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High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minute
Gansen, A., Felekyan, S., Kühnemuth, R., Lehmann, K., Tóth, K., Seidel, C.A.M., Langowski, J.
Nat. Commun. 9, e4628 (2018)
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Precision and accuracy of single-molecule FRET measurements - a multi-laboratory benchmark study
Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, 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., Götz, 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., Hübner, 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., Ngo, T. Qiu, R., Robb, N. C., Röcker, C., Sanabria, H., Schlierf, M., Schröder, T., Schuler, B., Seidel, H, Streit, L., Thurn, J., Tinnefeld, P., Tyagi, S., Vandenberk, N., Vera, A. M., Weninger, K. R., Wünsch, B., Yanez-Orozco, I. S., Michaelis, J., Seidel, C. A. M., Craggs, T. D., Hugel, T.
Nat. Methods 15, 669–676 (2018)
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Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α
Kilic, S., Felekyan, S., Doroshenko, O., Boichenko, I., Dimura, M., Vardanyan, H., Bryan, L. C., Arya, G., Seidel, C. A. M., Fierz, B.
Nat. Commun. 9, e235 (2018)
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Combining graphical and analytical Methods with molecular simulations to analyze time-resolved FRET-measurements of labeled macromolecules accurately
Peulen, T.-O., Opanasyuk, O., Seidel, C. A. M.
J. Phys. Chem. B. 121, 8211-8241 (2017)
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Quantitatve FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems
Dimura, M., Peulen, T.-O., Hanke, C. A., Prakash, A., Gohlke, H., Seidel, C. A. M.
Curr. Opin. Struct. Biol. 40, 163-185 (2016)
Full text | Research Data |

In preparation

Sensing the local environment and higher-order structure of RNA by flexibly coupled fluorescent labels.
Prakash, A., Hanke, C.A., Doroshenko, O., Salama, N., Bulat, B. Opanasyuk, O., Kühnemuth, R., Barth, A., Seidel, C.A.M.
To be submitted.

FRET-assisted structural modeling of dynamic protein ensembles.
Hanke, C.A., Larbig, A., Reschke, B., Dimura, M., Mulnaes, D., Gohlke, G., Seidel, C.A.M.
To be submitted to Structure

Diffusion with traps: experiment, simulation, and theory to describe the dynamics of flexibly linked fluorophores in biomolecular FRET.
Kalinin, S., Fulle, S., Hanke, C.A., Peulen, T. O., Sindbert, S., Felekyan, S., Kühnemuth, R., Gohlke, H., Seidel, C.A.M.
To be submitted to J. Phys. Chem. B

Rapid channel insertion of Tc toxins and the modulation of its probability.
Roderer, D., Kucher, S., Folz, J., Kühnemuth, R., Assafa, T.E., Bordignon, E., Seidel, C.A.M., Raunser, S.
To be submitted.

Dynamic co-existing conformers of a RNA four-way junction resolved by FRET, SAXS, and integrative modeling.
Hanke, C.A.,Vardanyan, H., Sindbert, S., Kalinin, S., Dimura, M., Peulen, T.-O., Soltysinski, T., Lach, G., Springstubbe, D., Apel, B., Snell, E., Grant, T.D., Lipfert, J., Müller, S., Bujnicki, J., Gohlke, H., Seidel C.A.M.
To be submitted.

Activation and inhibition conformational dynamics of the Abl tyrosine kinase regulatory core followed by single-molecule FRET.
Schlotte, J., Felekyan, S., Habazettl, J.M., Hertel-Hering, I., Sonti, R., Kubiak, J., Hantschel, O., Seidel, C.A.M., Grzesiek, S.
To be submitted.

Functional FRET imaging: Revealing structural features and affinities of protein complexes in living cells with nanometer resolution.
Greife, A., Peulen, T.-O., Somssich, M., Kühnemuth, R., Stahl, Y., Simon, R., Weidtkamp-Peters, S., Seidel, C.A.M.
To be submitted.