ArticleBiophysical journal2016
The Exact NOE as an Alternative in Ensemble Structure Determination.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 45 citations in OpenAlex.
- Going high-throughput: Dynamic conformations and interactionsMagnetic resonance letters · 2027Review
- Pulse Programme Considerations for Quantitative NOE Analysis.Magnetic resonance in chemistry : MRC · 2026Article
- Goldilocks-Inspired Design of Mid-Size Macrocycles for Selective Targeting of Human Melanocortin Receptors.Journal of medicinal chemistry · 2026Article
- Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles.Nature biotechnology · 2026Article
- Restraining Interproton Angular and Distance Dynamics with KEnRef.The journal of physical chemistry. B · 2026Article
- Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and AmideInternational journal of molecular sciences · 2025Article
- Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.Structural dynamics (Melville, N.Y.) · 2023Article
- Ensemble determination by NMR data deconvolution.Nature reviews. Chemistry · 2023Review
- Water irradiation devoid pulses enhance the sensitivity ofJournal of biomolecular NMR · 2023Article
- Atomic resolution protein allostery from the multi-state structure of a PDZ domain.Nature communications · 2022Article
- Advances in the exact nuclear Overhauser effect 2018-2022.Methods (San Diego, Calif.) · 2022Review
- Optimization and validation of multi-state NMR protein structures using structural correlations.Journal of biomolecular NMR · 2022Article
- Article
- Solution NMR Spectroscopy as a Tool to Study DNAzyme Structure and Function.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- Transferred-Rotational-Echo Double Resonance.The journal of physical chemistry. A · 2021Article
- Recent Developments in Data-Assisted Modeling of Flexible Proteins.Frontiers in molecular biosciences · 2021Review
- Reducing the measurement time of exact NOEs by non-uniform sampling.Journal of biomolecular NMR · 2020Article
- Enhancing NMR derived ensembles with kinetics on multiple timescales.Journal of biomolecular NMR · 2020Article
- Minimal NMR distance information for rigidity of protein graphs.Discrete applied mathematics (Amsterdam, Netherlands : 1988) · 2019Article
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Authors and funding
4 authors at 1 institution in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure-function paradigm is increasingly replaced by the structure-dynamics-function paradigm. All protein activity is steered by the interplay between enthalpy and entropy. Conformational dynamics serves as a proxy of conformational entropy. Therefore, it is essential to study not only the average conformation but also the spatial sampling of a protein on all timescales. To this purpose, we have established a protocol for determining multiple-state ensembles of proteins based on exact nuclear Overhauser effects (eNOEs). We have recently extended our previously reported eNOE data set for the protein GB3 by a very large set of backbone and side-chain residual dipolar couplings and three-bond J couplings. Here, we demonstrate that at least four structural states are required to represent the complete data set by dissecting the contributions to the CYANA target function, which quantifies restraint violations in structure calculation. We present a four-state ensemble of GB3, which largely preserves the characteristics obtained from eNOEs only. Due to the abundance of the input data, the ensemble and χ(1) angles in particular are well suited for cross-validation of the input data and comparison to x-ray structures. Principal component analysis is used to automatically identify and validate relevant states of the ensembles. Overall, our findings suggest that eNOEs are a valuable alternative to traditional NMR probes in spatial elucidation of proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.