ArticleThe journal of physical chemistry. B2017
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts.The journal of physical chemistry. B · 2026Article
- Transient Occupancy and Pore Dynamics: IP6 Behavior in HIV-1The journal of physical chemistry. B · 2026Article
- High-resolution analysis of the human T-cell leukemia virus capsid protein reveals insights into immature particle morphology.Nature communications · 2025Article
- In-cell structure and variability of pyrenoid Rubisco.Nature communications · 2025Article
- In-cell Structure and Variability of Pyrenoid Rubisco.bioRxiv : the preprint server for biology · 2025Article
- IntegratingJournal of the American Chemical Society · 2024Article
- Structural Basis for Alternative Self-Assembly Pathways Leading to Different Human Immunodeficiency Virus Capsid-Like Nanoparticles.ACS nano · 2024Article
- Cryo-EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils.Protein science : a publication of the Protein Society · 2024Article
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.PLoS computational biology · 2022Article
- Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability.Protein science : a publication of the Protein Society · 2021Article
- Anomalous amide proton chemical shifts as signatures of hydrogen bonding to aromatic sidechains.Magnetic resonance (Gottingen, Germany) · 2021Article
- Article
- Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.Nature structural & molecular biology · 2020Article
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 2020Article
- High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.Journal of chemical information and modeling · 2019Article
- Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins.Current opinion in structural biology · 2019Review
- Integrated BioNMR - "getting by with a little help from my friends".Journal of magnetic resonance (San Diego, Calif. : 1997) · 2019Review
- Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques.Biomolecules · 2019Review
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9 authors.
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Abstract
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.
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