ArticleJournal of biomolecular NMR2012
Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.
Article in Journal of biomolecular NMR, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 51 citations in OpenAlex.
- Integrating NMR Restraints into Coarse-Grained Simulations: Toward Accurate Conformational Ensembles of Complex Protein Systems.Journal of the American Chemical Society · 2026Article
- Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data.Journal of chemical theory and computation · 2022Article
- The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes.Frontiers in molecular biosciences · 2022Article
- REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution.PLoS computational biology · 2021Article
- Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package.BMC bioinformatics · 2020Article
- Enhancing NMR derived ensembles with kinetics on multiple timescales.Journal of biomolecular NMR · 2020Article
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- Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1.Journal of molecular biology · 2018Article
- Data driven flexible backbone protein design.PLoS computational biology · 2017Article
- Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases.Scientific reports · 2017Article
- Finding Our Way in the Dark Proteome.Journal of the American Chemical Society · 2016Article
- Structure of a low-population binding intermediate in protein-RNA recognition.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.Chemical reviews · 2016Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach.Proteins · 2015Article
- ENCORE: Software for Quantitative Ensemble Comparison.PLoS computational biology · 2015Article
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- Characterization of the conformational fluctuations in the Josephin domain of ataxin-3.Biophysical journal · 2014Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.
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