Combining NMR spectroscopy with MD simulations to determine the conformational landscape of multi-domain proteins at atomic resolution

Michael Kovermann

The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing large interdomain mobility. However, molecular recognition and signal transduction are associated with conformational substates that are populated in solution.

High-resolution NMR spectroscopy in combination with dual-scale MD simulations can be synergistically applied to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far.

This talk proposes a general application of the methodology developed by combining NMR spectroscopic approaches with MD simulations to demystify multi-domain proteins occurring in nature.