Forschung im HLRN-Verbund 2011

27A. B.C.HWDPBDHWDPBDHWDHSDHSDHSDPBDNBD1NBD2NBD1MgNBD2NBD1NBD2ADPclosed open SecYEG-boundFigure 1: Large-scale conformational changes of the SecA motor during protein translocation. (A-C) SecA in theclosed (A), open (B), and SecYEG-bound states (C) from refs [3], [1], [4], respectively. The nucleotidebinds at the interface between NBD1 and NBD2. HSD and HWD denote, respectively, the Helical ScaffoldDomain and the Helical Wing Domain. In panel (B), the atoms of the ADP molecule are colored asfollows: carbon - cyan, nitrogen - blue, oxygen - red, and phosphorus - brown; the magnesium ion isdepicted in green. The crystal structures of SecA closed and open states are from B. subtilis, and that ofSecYEG-bound SecY is from T. maritima. Note the differences in the orientation of the PBD relative tothe remaining of the protein in the closed, open, and SecYEG-bound states of SecA.general concepts that govern the design of membranetransporters and receptors. We will performMD simulations to assess the dynamics andlipid interactions of ChR-2 homology models, andof bacteriorhodopsin mutants. Particularly importantis to derive information about the dynamicsof internal water molecules. The work on understandinghow specific amino-acid interactions affectthe structure and dynamics of the protein, andthe dynamics of the internal water molecules, willcontribute to deriving a molecular understanding ofhow ChR-2 works.More Information1. Osborne AR, Clemmons WM Jr, Rapoport TA(2004). A large conformational change of thetranslocation ATPase SecA. Proc Natl Acad SciUSA 101: 10937-10942.2. Robson A, Booth AEG, Gold VAM, Clarke AR,Collinson I (2007). A large conformationalchange couples the ATP binding site of SecAto the SecA protein channel. J Mol Biol 374:965-976.3. Hunt JF, Weinkauf S, Henry L, Fak JJ, McNicholasP, Olivier DB, Deisenhofer J (2002). Nucleotidecontrol of interdomain interactions inthe conformational reaction cycle of SecA. Science297: 2018-2026.4. Zimmer J, Nam Y, Rapoport TA (2008). Structureof a complex of the ATPase SecA and theprotein translocation channel. Nature 455: 936-943.FundingFreie Universität Berlin, Department of PhysicsChemie