Berlin 2024 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 21: Poster IIIb

BP 21.20: Poster

Mittwoch, 20. März 2024, 11:00–14:30, Poster C

Modelling contrast-variation SAXS experiments by explicit-solvent molecular dynamics — •Noora Aho and Jochen Hub — Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany

Small angle X-ray scattering (SAXS) has established its role in structural biology during the last decades, providing information on the shape, interactions and large-scale conformational transitions of biomolecules in solution. In addition, so called contrast-variation SAXS, where the scattering data is recorder at multiple solvent electron densities, adds the possibility to measure electron densities of biomolecular assemblies enabling the visualisation of distinct biomolecules. The interpretation of experimental SAXS data requires the accurate calculation of SAXS curves from structural models. To achieve this, explicit-solvent molecular dynamics (MD) is a powerful method, taking into account both the atomistic accuracy and correct thermal fluctuations in the scattering curve calculations.

In this work, our aim is to expand the application of explicit-solvent MD simulations from conventional SAXS to contrast-variation SAXS experiments. We model the ferrichrome membrane transporter protein FhuA in the presence of lanthanide contrast agents in explicit solvent and calculate corresponding SAXS curves using MD simulations. In addition to supplementing experimental SAXS data for the specific protein, our simulations serve as an example of the possibilities of explicit-solvent MD in interpretation of advanced SAXS experiments.

Keywords: molecular dynamics; simulation; x-ray scattering; protein