Welcome to the Biomolecular Simulations Project Group at the Department of Biophysics in Bochum
The three-dimensional structures of proteins evolved to support their dynamical function. Overcoming the large gap between the detailed functional understanding of protein structures, dynamics, and mechanisms in structural biology, and the descriptive understanding of protein interactions in systems biology poses a major challenge in modern life sciences. In the Department of Biophysics, we work on filling in this gap by a close multidisciplinary orchestrating of molecular biology, X-ray structure analysis, time-resolved vibrational (FTIR) spectroscopy, and biomolecular simulations, which provides spatio-temporal resolution of protein interactions at different scales. This approach provides the key to bridge the existing gap and to target at a detailed understanding of protein interactions close to physiological conditions. In this multidisciplinary framework, the biomolecular simulations are crucial to understand the complex experimental data sets, and draw conclusions on the dynamic protein mechanisms. Biomolecular simulations are perfectly suited to bridge the different scales and disciplines by connecting function and dynamics to structural data from diverse experimental sources. In particular, we decode functional processes occurring on the sub-Å level up to the macromolecular level from IR Spectra by visualizing molecular function with atomic detail through an ochestra of different biomolecular simulation techniques.
Recent Publications
Massarczyk M, Schlitter J, Kötting C, Rudack T, Gerwert K Monitoring transient events in IR-spectra using Local Mode Analysis. Proteins: Structure, Function, and Bioinformatics (2018) 86(10):1013-1019
Melo*, M. C. R., Bernardi*, R. C., Rudack T., Scheurer, M., Riplinger, C., Phillips, J. C., Maia, J. D. C., Rocha, G. D., Ribeiro, J. V., Stone, J. E., Neese, F., Schulten, K., Luthey-Schulten, Z. NAMD goes quantum: an integrative suite for hybrid simulations. Nature Methods (2018) 15(5):351-354
Schlitter, J. The Second Law of Thermodynamics as a Force Law. Entropy (2018) 20(4):234.
Guo Q., Lehmer C.*, Martínez-Sánchez A.*, Rudack T*, Beck F., Hartmann H., Pérez Berlanga M., Frottin F., Hipp M., Hart F. U., Edbauer D., Baumeister W., Fernández-Busnadiego R. In Situ Structural Studies of Neuronal C9ORF72 Poly-GA Aggregates Reveal Proteasome Accumulation and Impairment. Cell (2018) 172(4), 696-705.
Scheurer, M., Rodenkirch, P., Siggel, M., Bernardi, R. C., Schulten, K., Tajkhorshid E., Rudack T. "PyContact: Rapid, Customizable and Visual Analysis of Non-Covalent Interactions in MD Simulations." Biophysical Journal (2018) 293(11), 3871–3879.
Mann, D., Güldenhaupt, J., Schartner, J., Gerwert, K., Kötting, C. "The Protonation States of GTP and GppNHp in Ras Proteins" Journal of Biological Chemistry (2018) 114(3), 577–583.
Wehmer M.*, Rudack T.*, Beck F.*, Aufderheide A, Pfeifer G., Plitzko J.,Foerster F., Schulten K., Baumeister W., Sakkata E "Structural insights into the functional cycle of the ATPase module of the 26S proteasome." PNAS (2017) 114(4), 1305-1310.
Gerwert K., Mann D., Kötting C. "Common mechanisms of catalysis in small and heterotrimeric GTPases and their respective GAPs" Biol.Chem. (2017) ISSN (Online) 1437-4315, ISSN (Print) 1431-6730 DOI: https://doi.org/10.1515/hsz-2016-0314
Massarczyk,M.,Rudack,T.,Schlitter, J.,Kuhne,J., Kötting,C., Gerwert,K. "Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details" J. Phys. Chem. B (2017), 121(15), 3483–3492
Mann, D., Höweler, U., Kötting, C., Gerwert, K. "Elucidation of Single Hydrogen Bonds in GTPases via Experimental and Theoretical Infrared Spectroscopy" Biophysical J., (2017) 1 (112), 66-77
Mann, D., Teuber, C., Tennigkeit, S.A., Schröter, G., Gerwert, K., Kötting, C. "Mechanism of the intrinsic arginine finger in heterotrimeric G proteins" PNAS, (2016) 50 (113), E8041-E8050
Rudack, T., Jenrich, S., Brucker, S., Vetter, I.R., Gerwert, K, Kötting, C. "Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental and theoretical IR spectroscopy" J. Biol. Chem. (2015) 40 (290) 24079-24090