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BP: Fachverband Biologische Physik

BP 5: Proteins

BP 5.6: Talk

Monday, March 23, 2009, 16:00–16:15, ZEU 260

Investigating The Protein Conducting Channel SecYEb from Methanococcus jannaschii Using Molecular Dynamics Simulation — •Andrew Aird and Jörg Wrachtrup — 3rd Physics Institute, Stuttgart University, D-70569 Stuttgart, Germany

Protein translocation, the transport of a protein through a pore is of great importance for all living organisms. It is essential for cells to have membrane channels which are able to transport proteins to different compartments inside the cell where they are needed. An example for such a channel is the protein conducting channel SecYEb from Methanococcus jannaschii. Molecular dynamics simulations are performed to understand the overall mechanism of protein transport across the membrane and address questions concerning the opening mechanism and sealing of the pore region against water and ions. Translocation processes usually take place on timescales (~ms) not accessible to standard molecular dynamics simulation. By using steered molecular dynamics simulation to accelerate the opening process together with statistical analysis using fluctuation theorems the potential of mean force for removal of the plug is obtained.