Dissertation Christian Kappel

Bacteriorhodopsin is a model system for membrane proteins. This seven transmembrane helical protein isembedded within a membrane structure called purple membrane. Its structural stability against mechanical stress was recentlyinvestigated by atomic force microscopy experiments, in which single proteins were extracted from the purple membrane. Here,we study this process by all-atom molecular dynamics simulations, in which single bacteriorhodopsin molecules were extractedand unfolded from an atomistic purple membrane model. In our simulations, key features from the experiments like force profilesand location of key residues that resist mechanical unfolding were reproduced. These key residues were seen to be stabilized bya dynamic network of intramolecular interactions. Further, the unfolding pathway was found to be velocity-dependent. Simula-tions in which the mechanical stress was released during unfolding revealed relaxation motions that allowed characterization ofthe nonequilibrium processes during fast extraction.