Atomistic structures and dynamics of biomolecules from low-resolution scattering data

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The interplay between experiment and simulation has developed to an important driving force for biomolecular research, yet with recent developments new challenges arise. For instance, the interest in structures of large biomolecular assemblies or membrane proteins has augmented the requirement to interpret low-resolution scattering data, because crystals of such structures frequently diffract poorly. Likewise, the emerging technique of time-resolved wide-angle X-ray scattering (TR-WAXS) can in principle measure conformational transitions of proteins in solution at near-atomic resolution, yet the reduced TR-WAXS spectra are difficult to interpret at a molecular level. Within the Emmy-Noether group, we will apply molecular dynamics (MD) simulations and related computational methods to interpret such X-ray scattering data that alone provide only reduced information. In particular, we will develop new refinement algorithms, that aim to overcome the limitations of current refinement protocols at low resolution. The key essence of these algorithms will be to reduce the dimensionality of the search space using a correlation analysis, in order to concentrate the sampling within a low-dimensional configurational space, where a successful refinement is more promising. Complementary to these efforts to refine static structures, we will apply measured TR-WAXS spectra as additional driving forces into MD simulations, to yield an unbiased interpretation of the WAXS data at atomic detail. We will focus that analysis on proton pumps such as rhodopsin, and we thus aim to derive the structural cycle of these important membrane proteins based on only a single experiment. Apart from the focus on the interpretation of X-ray data, I aim to build upon my previous studies on the selectivity of membrane channels within this Emmy-Noether grant. Using extensive MD simulations, we first aim to identify the selectivity filters and mechanisms of a set of membrane channels, including a urea transporter, the formate channel FocA, and a beta-barrel pore. In a second step we will use the understanding of molecular filters, in order to rationally design a molecular filter from scratch with preselected selectivity characteristics.