HHU StartMNFChemistryMPCOur ResearchERC Advanced Grant: hybridFRET

ERC Advanced Grant: hybridFRET - deciphering biomolecular structure and dynamics (12/2015 - 11/2020)

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:


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)
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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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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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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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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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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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Automated and optimally FRET-assisted structural modeling
Dimura, M., Peulen, T.-O., Sanabria, H., Rodnin, D., Hemmen, K., Seidel, C.A.M., Gohlke, H.
arXiv:1909.02148 [q-bio.QM]

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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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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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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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), arXiv:1812.06937 [q-bio.BM]
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In preparation

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

Analyzing kinetic networks by FRET indicators in single-molecule experiments
Sanabria, H., Peulen, T.-O., Opanasyuk, O., Felekyan, S., Kalinin, S., Seidel, C.A.M.
Feature article for J. Chem. Phys.

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., Kühnemuth, R., Sindbert, S., Felekyan, S., Gohlke, H., Seidel, C.A.M.

An integrative approach maps motions and conformers necessary for oligomerization of the large GTPase hGBP1
Peulen, T.-O., Hengstenberg, C.S., Biehl, R., Dimura, M., Lorenz, C., Valeri, A., Ince, S., Vöpel, T., Faragó, B., Gohlke, H., Klare, J.P., Stadler, A., Seidel, C.A.M., Herrmann, C.

Responsible for the content: E-MailProf. Dr. Claus Seidel