Department of Theoretical Biophysics

Department of Theoretical Biophysics

Prof. Dr. Gerhard Hummer, Director

Our goal is to develop detailed and quantitative descriptions of key biomolecular processes, including energy conversion, molecular transport, signal transduction, and enzymatic catalysis.

Life relies on the intricate interactions of proteins, nucleic acids, lipids and other biomolecules. Our goal is to develop detailed and quantitative descriptions of key biomolecular processes, including energy conversion, molecular transport, signal transduction, and enzymatic catalysis. The growing understanding of the function of living organisms at the molecular level increasingly drives advances in modern medicine. Moreover, revealing the physical and chemical mechanisms exploited in biological systems guides the development of new technologies.

In our research we develop, implement, and use a broad range of computational and theoretical methods that allow us to explore the structure, stability, dynamics, and molecular functions of biomolecules and their complexes. We use high-performance computers and work in close collaboration with experimental groups that employ a wide variety of tools, from x-ray crystallography and electron microscopy to single-molecule fluorescence and force spectroscopy. Our computational and theoretical studies aid in the interpretation of increasingly complex measurements, and guide the design of future experiments.

Bridging between fundamental physics, chemistry and biology, we study biomolecular processes over a broad resolution range, from quantum mechanics to chemical kinetics, from atomistic descriptions of physical processes and chemical reactions in molecular dynamics simulations to highly coarse-grained models of the non-equilibrium operation of molecular machines and network descriptions of protein interactions. Focus areas of our research include the structure, motion, and function of dynamic supra-molecular assemblies; the function of proteins involved in bioenergetics; studies of proton transfer and pumping; the theory of single-molecule experiments, with particular emphasis on force spectroscopy; membrane channel and transporter function; peptide and protein folding; complex formation and ligand binding; reaction kinetics; hydrophobic effect and electrostatics; and the development of new methods for the characterisation of biomolecules and their assemblies using statistical mechanics and molecular simulation. In addition, we are also exploring the interface between biology and technology, concentrating on nanofluidics and energy conversion.

Selected Publications

Zimmerli, C. E.; Allegretti, M.; Rantos, V.; Goetz, S. K.; Obarska-Kosinska, A.; Zagoriy, I.; Halavatyi, A.; Hummer, G.; Mahamid, J.; Kosinski, J. et al.
Nuclear pores dilate and constrict in cellulo.
Science 374 (6573), eabd9776 (2021)
Ho, N. T.;  Siggel, M.; Camacho, K. V.; Bhaskara, R. M. ;  Hicks, J. M.; Yao, Y.-C.; Zhang, Y.; Köfinger, J.; Hummer, G. ;  Noy, A.
Membrane fusion and drug delivery with carbon nanotube porins.
Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2016974118 (2021)
Mehdipour, A. R.; Hummer, G.
Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike.
Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2100425118 (2021)
Benayad, Z. ; von Bülow, S.; Stelzl, L. S.; Hummer, G.
Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model.
Journal of Chemical Theory and Computation 17 (1), pp. 525 - 537 (2021)
Turoňová, B.; Sikora, M.; Schürmann, C.; Hagen, W. J. H.; Welsch, S.; Blanc, F. E. C.; von Bülow, S.; Gecht, M.; Bagola, K.; Hörner, C. et al.
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Science 370 (6513), pp. 203 - 208 (2020)
Shin, D.; Mukherjee, R.; Grewe, D.; Bojkov, D.; Baek, K.; Bhattacharya, A. ; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G. et. al.
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.
Nature 587 (7835), pp. 657 - 662 (2020)
Pietrek, L. M.; Stelzl, L. S.; Hummer, G.
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations.
Journal of Chemical Theory and Computation 16 (1), pp. 725 - 737 (2020)
Vögele, M.; Bhaskara, R.; Mulvihill, E.; van Pee, K.; Yildiz, Ö.; Kühlbrandt, W.; Müller, D. J.; Hummer, G.
Membrane perforation by the pore-forming toxin pneumolysin.
Proceedings of the National Academy of Sciences of the United States of America 116 (27), pp. 13352 - 13357 (2019)
Bhaskara, R.; Grumati, P.; Garcia-Pardo, J.; Kalayil, S.; Covarrubias-Pinto, A.; Chen, W.; Kudryashev, M.; Đikić, I.; Hummer, G.
Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy.
Nature Communications 10, 2370 (2019)
von Bülow, S.; Siggel, M.; Linke, M.; Hummer, G.
Dynamic cluster formation determines viscosity and diffusion in dense protein solutions.
Proceedings of the National Academy of Sciences of the United States of America 116 (20), pp. 9843 - 9852 (2019)
Okazaki, K.-i.; Wöhlert, D.; Warnau, J.; Jung, H.; Yildiz, Ö.; Kühlbrandt, W.; Hummer, G.
Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting.
Nature Communications 10, 1742 (2019)
Go to Editor View