Biological functions critically depend on the ability of macromolecules to change their conformation, to bind and to form complexes. Understanding (1) how structure and dynamics are coupled on the molecular level and (2) how these molecular interactions give rise to cellular processes are major goals in the molecular sciences. We develop methods based on both simulations and experiments to contribute to these goals.
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In this research project we develop a rigorous methodological framework to model the nanomechanics of large macromolecules and their complexes. In contrast to bottom-up coarse-graining models, we are using a data-based strategy to identify semirigid subunits and he equations of motion between them by computing models that optimally math simulation and experimental data. People involved: Stefan Bernhard
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Protein interactions play a key role in virtually every biological process. But, despite their fundamental importance, the underlying biophysical mechanisms of these processes are often just poorly understood. In this respect, this project aims at establishing a new methodology which allows the systematic study of the dynamical mechanism of protein:protein or protein:ligand binding. People involved: Martin Held
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Diffusion, i.e. motion due to thermal energy is an essential player in determining the functionality of cells, as it distributes, transports and mixes the interacting particles. Single Particle tracking experiments are now available to follow individual dye-labeled molecules in spacetime. As these experiments often only monitor some of the properties of interest (e.g. 2-dimensional projection, no information if the molecule is bound to other molecules or not), there is often some amount of hidden information that can potentially be reconstructed with modeling. We develop Langevin-dynamics based Hidden Markov Models for this. People involved: Arash Azhand
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Finally, we are working on a simulation suite for particle dynamics on a cellular level, Cellular Molecular Dynamics (CMD). Here, individual particles correspond to biomolecules (e.g. proteins), which can react with another (e.g. binding, catalysis), and diffuse around in an interparticle potential (e.g. electrostatics and van der Waals repulsion). In
collaboration with P. Knaus (FU Berlin), we have proposed, based on simulations, a mode for the interaction of type I and II BMP receptors with their ligands which is currently tested experimentally. In the SFB 740 (Collaboration with K.-P. Hofmann and M. Heck) we are currently preparing a project aimed at simulation the primary vision processes in the rod cell that is initiated by photoexcitation of rhodopsin and leads to a change of membrane potential at the axonal end. People involved: Johannes Seibert, Martin Fischbach, Martin Held
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