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Sequential Unfolding of Individual Helices of Bacterioopsin Observed in Molecular Dynamics Simulations of Extraction from the Purple Membrane

Michele Seeber ^*, Francesca Fanelli , Emanuele Paci ^*  and Amedeo Caflisch ^*

^* Department of Biochemistry, University of Zurich, Zurich, Switzerland; Dulbecco Telethon Institute, Department of Chemistry, University of Modena and Reggio Emilia, Italy; and Physics and Astronomy, University of Leeds, Leeds, United Kingdom

Correspondence: Address reprint requests to E. Paci, E-mail: e.paci{at}leeds.ac.uk; or to A. Caflisch, E-mail: caflisch{at}bioc.unizh.ch.

Multiple molecular dynamics simulations of bacterioopsin pulling from its C-terminus show that its -helices unfold individually. In the first metastable state observed in the simulations, helix G is unfolded at its C-terminal segment while the rest of helix G (residues 200–216) is folded and opposes resistance because of a salt-bridge network consisting of Asp-212 and Lys-216 on helix G and Arg-82 and Asp-85 on helix C. Helix G unfolds inside the bundle because the external force is applied to its C-terminal end in a direction perpendicular to the surface of the membrane. Inversely, helix F has to flip by 180° to exit from the membrane because the applied force and the helical N-C axis point in opposite directions. At the highest peak of the force, which cannot be interpreted in single-molecule force spectroscopy experiments, helix F has a pronounced kink at Pro-186. Mutation of Pro-186 and/or the charged side chains mentioned above, which are involved in very favorable electrostatic interactions in the low-dielectric region of the membrane, are expected to reduce the highest peak of the force. Helices E and D unfold in a similar way to helices G and F, respectively. Hence, the force-distance profile and sequence of events during forced unfolding of bacterioopsin are influenced by the up-and-down topology of the seven-helix bundle. The sequential extraction of individual helices from the membrane suggests that the spontaneous (un)folding of bacterioopsin proceeds through metastable bundles of fewer than seven helices. The metastable states observed in the simulations provide atomic level evidence that corroborates the interpretation of very recent force spectroscopy experiments of bacteriorhodopsin refolding.

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