Modeling Supramolecular Assemblies using solid-state NMR and cryoEM Data

Nikolaos G. Sgourakis (National Institutes of Health)

We describe recent advances using the program Rosetta for Hybrid structure modeling of large, insoluble supramolecular assemblies with complex symmetries. Rather than starting from existing models of the individual subunits, the internal monomer conformations and the rigid body degrees of freedom are sampled simultaneously guided by both the experimental constraints and the Rosetta all atom energy. Different sources of experimental information are combined in an iterative, multi-step modeling procedure: Cryo-electron microscopy (cryoEM) data define the overall envelope of the assembly and relative orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. The calculated structures are cross-validated using independent data sets of ssNMR constraints, biochemical experiments and scanning transmission electron microscopy measurements. I will discuss recent applications of the approach ranging from modeling the Type-III secretion system needle from Shigella flexneri to an intact viral capsid and a distinct polymorphism of A. amyloid fibrils.

This work is funded by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH).

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