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  4. Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies
 
research article

Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

Gupta, Rupal
•
Zhang, Huilan
•
Lu, Manman
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June 20, 2019
The Journal of Physical Chemistry B

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 life cycles 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, a remarkably high spectral resolution in the 3D and 2D heteronuclear data sets permitted the assignment of a significant fraction of backbone and side-chain resonances. Using an integrated DNP MAS NMR and molecular dynamics (MD) simulation approach, the conformational space sampled by the assembled capsid at cryogenic temperatures was mapped. Qualitatively, a remarkable agreement was observed for the experimental C-13/N-15 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.

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Type
research article
DOI
10.1021/acs.jpcb.9b02293
Web of Science ID

WOS:000472800700004

Author(s)
Gupta, Rupal
Zhang, Huilan
Lu, Manman
Hou, Guangjin
Caporini, Marc  
Rosay, Melanie
Maas, Werner
Struppe, Jochem
Ahn, Jinwoo
Byeon, In-Ja L.
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Date Issued

2019-06-20

Published in
The Journal of Physical Chemistry B
Volume

123

Issue

24

Start page

5048

End page

5058

Subjects

Chemistry, Physical

•

Chemistry

•

hiv-1 capsid protein

•

enhanced mas nmr

•

structural biology

•

coat protein

•

conformational distributions

•

virus nucleoprotein

•

chemical-shift

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intact virus

•

cryo-em

•

bacteriophage

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LRM  
Available on Infoscience
July 13, 2019
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/159104
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