A05 - Nanoscale dynamics of proteins and their interaction

The core experimental aim of the project is to develop a new single-molecule spectroscopic method, dynamic single-molecule Metal Induced Energy Transfer (or dynamic smMIET), which will be suited to study the conformational dynamics of intrinsically disordered peptides (sequences of FG-repeat proteins from the nuclear pore), and of small folding protein motifs, in particular helix-turn-helix (HTH) and WW-domain motifs. SmMIET is based on the distance-dependent quenching of the fluorescence emission of fluorescent molecules by metallic or semi-metallic thin films, and it requires labeling of the peptide/protein of interest by only one dye, in contrast to single-molecule Förster Resonance Energy Transfer, which requires labeling with a donor and an acceptor dye label. In parallel, we will develop and apply a new protocol for the 1:1 simulation of these smMIET experiments.

Members of this project:

Prof. Dr. Jörg Enderlein
Prof. Dr. Helmut Grubmüller
Dipl. Phys. Andreas Russek
Dipl. Steffen Mühle


Rico, F., Russek, A., González, L., Grubmüller, H. and Scheuring, S. (2019)
Heterogeneous and rate-dependent streptavidin–biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations
PNAS, 116(14): 6594-6601, DOI:10.1073/pnas.1816909116

Graen, T. M. D., Hoefling, M. and Grubmüller, H. (2014)
AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations
J. Chem. Theory Comput., DOI:10.1021/ct500869p

Groenhof, G. (2013)
Introduction to QM/MM Simulations
Monticelli, L. & Salonen, E.Biomolecular SimulationsChapter3Humana Press,, 924, DOI:10.1007/978-1-62703-017-5

Hoefling, M. and Grubmüller, H. (2013)
In silico FRET from simulated dye dynamics
Comput. Phys. Commun.Elsevier B.V.,, 184(3): 841-852, DOI:10.1016/j.cpc.2012.10.018

Inhester, L., Groenhof, G. and Grubmüller, H. (2013)
Core hole screening and decay rates of double core ionized first row hydrides.
J. Chem. Phys., 138(16): 164304, DOI:10.1063/1.4801660

Enderlein, J. (2012)
Modification of förster resonance energy transfer efficiency at interfaces.
Int. J. Mol. Sci., 13(11): 15227-40, DOI:10.3390/ijms131115227

Enderlein, J. (2012)
Polymer Dynamics, Fluorescence Correlation Spectroscopy, and the Limits of Optical Resolution
Phys. Rev. Lett., 108(10): 108101, DOI:10.1103/PhysRevLett.108.108101