We are developing methods to predict protein-protein interactions and how proteins bind to surfaces. These methods rely on Brownian dynamics simulation with SDA and molecular dynamics simulation. In SDA can be used to simulate the association of two solutes, e.g. two proteins, in implicit solvent. SDA can also be applied to simulate the diffusion of many solutes, e.g. a concentrated protein solution, to investigate oligomerization and diffusion in macromolecularly crowded environments, see Mereghetti et al, J. Phys. Chem. B, 2012.
We apply these approaches to biological problems with experimentalists. An example is the docking of an enzyme that contributes in the N-terminal processing of nascent polypeptide chains to the ribosome, see Sandikci et al, Nat. Struct. Mol. Biol. 2013.
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