Gupta, Rupal, Huilan Zhang, Manman Lu, Guangjin Hou, Marc Caporini, Melanie Rosay, Werner Maas, et al. “Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies.” The Journal of Physical Chemistry B 123, no. 24 (June 20, 2019): 5048–58.
https://doi.org/10.1021/acs.jpcb.9b02293.
We report dynamic nuclear polarization (DNP) enhanced magic angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their lifecycles and infectivity through modulation of their structures and dynamics. While static structures of capsids from several viruses are now accessible with near-atomic level resolution, atomic-level understanding of functionally important motions in assembled capsids is lacking. We observed up to 64-fold signal enhancements by DNP, which permitted in-depth analysis of these assemblies. For the HIV-1 CA assemblies, remarkably high spectral resolution in the 3D and 2D heteronuclear datasets permitted the assignments of a significant fraction of backbone and side chain resonances. Using an integrated DNP MAS NMR and molecular dynamics simulations approach, the conformational space sampled by the assembled CA at cryogenic temperatures was mapped. Qualitatively, remarkable agreement was observed for the experimental 13C/15N chemical shift distributions and those calculated from substructures along the MD trajectory. Residues that are mobile at physiological temperatures are frozen out in multiple conformers at cryogenic conditions, resulting in broad experimental and calculated chemical shift distributions. Overall, our results suggest that DNP MAS NMR measurements in combination with MD simulations facilitate a thorough understanding of the dynamic signatures of viral capsids.