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.

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Recent Publications

Recent Journal Covers

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) in press doi:10.1038/nmeth.4638

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

Press Releases

  • 20.03.2018 Forscher beobachten Details der Schaltung des Ras-Proteins
  • 01.02.2018 Verleihung des Ruth Massenberg Preises an Dr. Daniel Mann
  • 16.01.2017 Der Computer als Mikroskop
  • 07.12.2016 Molekulare Schalter im Detail erforscht
  • 07.01.2015 Arbeitsweise des Proteins Channelrhodopsin-2 entschlüsselt Forscher verfolgen das Öffnen des Ionenkanals mit biophysikalischen Methoden „Angewandte Chemie“: Ergebnisse erlauben Maßanfertigung optogenetischer Werkzeuge
  • 15.10.2012 Stehen statt Liegen Zellwachstumsprotein bildet Doppelpack auf der Zellmembran Bochumer und Dortmunder Forscher messen Orientierung des Ras-Proteins
  • 10.09.2012 Wie eine Feder im Spielzeugauto RUB-Forscher klären Katalyse-Mechanismus des Zellwachstumsproteins Ras auf PNAS: Proteine bringen Spannung in Phosphatkette