Investigation of Molecular Dynamics of Substrate Transmembrane alpha-Helices by Solution and Solid-State NMR Spectroscopy

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Intramembrane proteolysis is an important mechanism of membrane protein processing with immediate relevance for the development of diseases. How this process takes place in the lipophilic environment and which details of the sequence or dynamic features of the substrates are essential for proteolysis are questions that are currently under debate. In this project we investigate the structural and dynamical requirements of selected substrate TM helices by liquid and solid-state NMR spectroscopy, currently the only experimental techniques to study dynamics of biomolecules at atomic detail. We will begin with two model TM helices: APP, a well-studied gamma-secretase substrate, and PINK1, substrate of the rhomboid protease PARL. In Goal 1 we will concentrate on the conformational plasticity of the TM domains in solution and membrane-mimicking environments focusing in particular on deviations from the canonical helical structure and searching for lowly populated states (hidden states) in exchange with the main conformation as well as the related dynamical parameters. We will directly measure dynamical parameters characterizing the TM domains such as local exchange rates and motional amplitudes for individual interatomic vectors in a range of membrane models. In Goal 2 we will investigate the impact of mutations of the two TM domains. Some of these mutations are already known to impair proteolysis. We will clarify how they alter TM helix flexibility. In Goal 3 we will study how the membrane influences TM helix structural and dynamic properties. The expected results will be compared with molecular dynamics simulations conducted in P7 and show if the TM domain dynamics is a relevant factor for the protease recognition and/or processing. Depending on progress in goals 1-3, protocols and experiments will be applied on selected novel substrates identified in P1/P2/P3 to judge the general validity of these studies.