Welcome to the Computational Biophysics Group at Saarland University.
We develop methods related to molecular dynamics simulations, with the aim to understand the relationship between structure, dynamics, and function of biological macromolecules.
We are hiring: a PhD position is available in computational membrane biophysics. Find out more.
We have several interesting Bachelor and Master projects available. Find out more.
The function of biological membranes goes far beyond the formation of a mere barrier. Membranes are subject to ongoing structural remodeling, which is controlled by interactions with proteins and by the lipid composition. We develop free energy calculation techniques to understand how membrane composition and interactions with proteins (such as viral fusion proteins) enable functionally important events at membranes including membrane fusion, pore formation, or drug permeation.
Collecting experimental data is often difficult – but the interpretation of the data may be even more challenging, for instance because the information content of the experimental signals is low. We develop methods for combining MD simulations with experimental data to get the best of two worlds, with some focus on small-angle X-ray and neutron scattering data (SAXS/SANS). Our developments involve accurate SAXS/SANS predictions, protein structure and ensemble refinement, studies on the protein hydration shell, and modeling of experiments at X-ray free electron lasers. We share our methods via the web server WAXSiS and GROMACS-SWAXS.
Proteins are not static building blocks but instead carry out their function –and malfunction– by structural transitions (Structure-function-dynamics relationship). We combine MD simulations with experiential data and enhanced-sampling techniques, to observe proteins while they function in atomic detail. Our portfolio comprises studies of molecular motors, protein-RNA/DNA complexes, membrane channels, and enzymes related to cancer progression.
Microtubules are cytoskeletal filaments that exhibit dynamic tip instability and, as recent discoveries reveal, possess a dynamic lattice undergoing continuous tubulin loss and incorporation. In this study, we investigate the role of tau, a neuronal microtubule-associated protein (MAP) known for its stabilizing effects on microtubules, in modulating lattice dynamics. Using in vitro reconstitution, kinetic Monte Carlo modeling, and molecular dynamics simulations, we reveal that tau, despite lacking enzymatic activity, accelerates tubulin exchange within the lattice, particularly at topological defect sites. Tau appears to stabilize longitudinal tubulin–tubulin interactions while destabilizing lateral ones, thereby enhancing the mobility and repair of lattice defects. These results challenge the traditional view of tau as merely a stabilizer, uncovering its active role in dynamically modulating microtubule lattice structure.
The hydration shell is an integral part of proteins since it plays key roles for conformational transitions, molecular recognition, and enzymatic activity. While the dynamics of the hydration shell have been described by spectroscopic techniques, the structure of the hydration shell remain less understood due to the lack of hydration shell-sensitive structural probes with high spatial resolution. We combined temperature-ramp small-angle X-ray scattering (T-ramp SAXS) from 255–335 K with molecular simulations to show that the hydration shells of the GB3 domain and villin headpiece are remarkably temperature-sensitive. For proteins in the folded state, T-ramp SAXS data and explicit-solvent SAXS predictions consistently demonstrate decays of protein contrasts and radii of gyration with increasing temperature, which are shown to reflect predominantly temperature-sensitive depleting hydration shells. The depletion is not merely caused by enhanced disorder within the hydration shells but also by partial displacements of surface-coordinated water molecules. Together, T-ramp SAXS and explicit-solvent SAXS calculations provide a novel structural view on the protein hydration shell, which underlies temperature-dependent processes such as cold denaturation, thermophoresis, or biomolecular phase separation.
Present and former