Berlin 2005 – wissenschaftliches Programm

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AKB: Biologische Physik

AKB 200: Poster Session II

AKB 200.47: Poster

Dienstag, 8. März 2005, 17:00–19:00, Poster TU C

Osmotically induced water permeation through gramicidin and derivatives studied by computer simulations. — •Guillem Portella and Bert L. de Groot — Max Plank Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group Am Faßberg 11, 37077 Göttingen, Germany

Full atomistic molecular dynamics simulations provides deeper understanding of the microscopic energetic and structural determinants underlying permeation through molecular membrane channels. Gramicidin A has been used as a model channel extensively both experimentally and computationally. Here, we focus particularly on the efficient simulation of an osmotically induced water flux. So far, different methods have been developed to derive permeation rates from simulations: continuous-time random model aproximation from equilibrium simulations or external forces acting on molecules as a result of the osmotic gradient. We chose to explore a method that attempts to mimick the true situation in vitro or in vivo as closely as possible, namely by introducing a true osmotic gradient. This is achieved by a solute concentration gradient across the membrane. As membrane simulations are usually carried out using periodic boundary conditions, this creates a challenge to the simulation of osmotic gradients, as they would normally be balanced by diffusion across the periodic boundaries. In order to alleviate this problem, we created two different water compartments (with different solute concentrations) by simulating two bilayers, which allows to efficiently study osmotically induced permeation, as has recently been demonstrated for carbon nanotubes.