ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2012
Parameterization of solvent-protein interaction and its use on NMR protein structure determination.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- NMR-guided rational exploration of co-factors in boosting theMagnetic resonance letters · 2025Article
- Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State.Frontiers in molecular biosciences · 2021Article
- NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins.Journal of biomolecular NMR · 2019Article
- Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics.Methods (San Diego, Calif.) · 2018Article
- Xplor-NIH for molecular structure determination from NMR and other data sources.Protein science : a publication of the Protein Society · 2018Article
- Solvent saturation transfer to proteins (SSTP) for structural and functional characterization of proteins.Journal of biomolecular NMR · 2018Article
- An Exhaustive Search Algorithm to Aid NMR-Based Structure Determination of Rotationally Symmetric Transmembrane Oligomers.Scientific reports · 2017Article
- Characterization of Protein-Protein Interfaces in Large Complexes by Solid-State NMR Solvent Paramagnetic Relaxation Enhancements.Journal of the American Chemical Society · 2017Article
- RNA structure refinement using NMR solvent accessibility data.Scientific reports · 2017Article
- High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.Journal of biomolecular NMR · 2017Article
- Prediction of Protein Structure Using Surface Accessibility Data.Angewandte Chemie (International ed. in English) · 2016Article
- A target-protection mechanism of antibiotic resistance at atomic resolution: insights into FusB-type fusidic acid resistance.Scientific reports · 2016Article
- A decadentate Gd(III)-coordinating paramagnetic cosolvent for protein relaxation enhancement measurement.Journal of biomolecular NMR · 2014Article
- Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes.Chemphyschem : a European journal of chemical physics and physical chemistry · 2013Review
- Structural analysis of protein-protein interactions in type I polyketide synthases.Critical reviews in biochemistry and molecular biologyReview
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3 authors.
Funding
Abstract
NMR structure determination is frequently hindered by an insufficient amount of distance information for determining the correct fold of the protein in its early stages. In response we introduce a simple and general structure-based metric that can be used to incorporate NMR-based restraints on protein surface accessibility. This metric is inversely proportional to the sum of the inverse square distances to neighboring heavy atoms. We demonstrate the use of this restraint using a dataset from the water to protein magnetization transfer experiment on the protein Bax and the solvent paramagnetic relaxation enhancement experiment on the protein ubiquitin and Qua1 homodimer. The calculated solvent accessibility values using the new empirical function are well correlated with the experimental data. By incorporating an associated energy term into Xplor-NIH, we show that structure calculation with a limited number of additional experimental restraints, improves both the precision and accuracy of the resulting structures. This new empirical energy term will have general applicability to other types of solvent accessibility data.
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