CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging. Here, we present a novel integrated strategy to combine the highly complementary experimental data from cryoEM and NMR computationally by molecular dynamics simulations to derive an atomistic model, which is not attainable by either approach alone. We use the HIV-1 capsid protein (CA) C-terminal domain as well as the large capsid assembly to demonstrate the feasibility of this approach, termed NMR CS-biased cryoEM structure refinement.
Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
Juan R
0000-0003-1171-6816
JR
Perilla
Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.
Gongpu
G
Zhao
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States.
Manman
M
Lu
Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.
Jiying
J
Ning
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States.
Guangjin
G
Hou
Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.
In-Ja L
IL
Byeon
Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.
Angela M
0000-0001-9072-3525
AM
Gronenborn
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States.
Tatyana
0000-0002-0346-1131
T
Polenova
Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.|Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN, U.K.|Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus , Didcot OX11 0DE, U.K.
Peijun
0000-0003-1803-691X
P
Zhang
D036022:Capsid Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D015497:HIV-1 / Q000737:chemistry* / Q000648:ultrastructure*; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular
D036022:Capsid Proteins