Disentangling dynamics in biomolecules with experiment and simulation

• Applicant: Albert Smith-Penzel, Ph.D.
• Subject Area: Biophysics ; Biochemistry
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 450148812

In the first period of this project, it was shown that timescale-specific dynamics analysis - via detectors - could be applied to a combination of NMR and MD data. By also using novel techniques for separating motions and identifying cross-correlations in motion, it was possible to perform in-depth characterization of dynamics in several biological systems. Specifically, a comprehensive description of motion in a biological membrane was described as a function of position and timescale (the dynamic landscape), a comparative analysis of timescale specific amplitude and cross-correlation was performed for a G-protein-coupled receptor (GPCR) in its inactive (apo) and active (bound) states, and a detailed analysis of side-chain motion in a fibrillar protein was obtained.In the second period, the central focus will be on applying the developed techniques to answer specific biological questions, which are not easily resolved based on structural information alone, but rather depend on the dynamic characteristics of the system. Basal activity in the Growth Hormone Secratagogue Receptor (GHSR) will be investigated, where a single-point mutation in GHSR (A204E) occurring in the highly flexible extracellular loop 2 results in a significant decrease of basal activity. Dynamics of the GlpG protein and the surrounding membrane will be studied, where protein–membrane interactions result in a modified membrane thickness (and likely dynamics), which in turn increases GlpG activity. Cross-correlated analysis and the dynamic landscape approaches, developed in the first period, will be applied to understand how the protein and membrane interact to form a complex dynamic system. Allosteric effects will be studied in the κ-opioid GPCR (KOR), where different ligands lead to activation of different signaling pathways. By studying several different ligands bound to KOR, detector and cross-correlation analyses will be applied in order to understand how signals propagate from the ligand binding pocket to the G-protein binding pocket, and how different ligands may influence the signaling (biased signaling). Finally, a model system, the WALP-16 peptide, will be investigated in membranes using NMR, MD, and single molecule FRET to expand the detector analysis to fluorescence data. For this project, the detector analysis will be modified to be applicable to FRET-based correlation functions, thus providing a new, complimentary source of timescale-sensitive dynamics data that can be combined with MD and NMR for comprehensive dynamics characterization.

• DFG Programme: Research Grants