ArticleBiopolymers2012
Computer modeling of nitroxide spin labels on proteins.
Article in Biopolymers, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 69 citations in OpenAlex.
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Review
- A guideline for the distance measurement plans of site-directed spin labels for structural prediction of nucleic acids.Journal of molecular modeling · 2023Article
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling.PLoS computational biology · 2023Article
- Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches.Biomolecules · 2022Review
- Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET.Nature communications · 2022Article
- Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.PLoS computational biology · 2021Article
- DEER Analysis of GPCR Conformational Heterogeneity.Biomolecules · 2021Review
- Structural Model of the Proline-Rich Domain of Huntingtin Exon-1 Fibrils.Biophysical journal · 2020Article
- Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction.Biophysical journal · 2020Article
- PELDOR/DEER: An Electron Paramagnetic Resonance Method to Study Membrane Proteins in Lipid Bilayers.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.The journal of physical chemistry. A · 2019Article
- Disruption of the E. coli LptC dimerization interface and characterization of lipopolysaccharide and LptA binding to monomeric LptC.Protein science : a publication of the Protein Society · 2018Article
- Electron spin-labelling of the EutC subunit in BFree radical research · 2018Article
- Characterization of and lipopolysaccharide binding to the E. coli LptC protein dimer.Protein science : a publication of the Protein Society · 2018Article
- Article
- Characterization of the Domain Orientations of E. coli 5'-Nucleotidase by Fitting an Ensemble of Conformers to DEER Distance Distributions.Structure (London, England : 1993) · 2016Article
- The double-histidine Cu²⁺-binding motif: a highly rigid, site-specific spin probe for electron spin resonance distance measurements.Angewandte Chemie (International ed. in English) · 2015Article
- Simulating the distance distribution between spin-labels attached to proteins.The journal of physical chemistry. B · 2015Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Electron paramagnetic resonance using site-directed spin labeling can be used as an approach for determination of protein structures that are difficult to solve by other methods. One important aspect of this approach is the measurement of interlabel distances using the double electron-electron resonance (DEER) method. Interpretation of experimental data could be facilitated by a computational approach to calculation of interlabel distances. We describe an algorithm, PRONOX, for rapid computation of interlabel distances based on calculation of spin label conformer distributions at any site of a protein. The program incorporates features of the label distribution established experimentally, including weighting of favorable conformers of the label. Distances calculated by PRONOX were compared with new DEER distances for amphiphysin and annexin B12 and with published data for FCHo2 (F-BAR), endophilin, and α-synuclein, a total of 44 interlabel distances. The program reproduced these distances accurately (r(2) = 0.94, slope = 0.98). For 9 of the 11 distances for amphiphysin, PRONOX reproduced the experimental data to within 2.5 Å. The speed and accuracy of PRONOX suggest that the algorithm can be used for fitting to DEER data for determination of protein tertiary structure.
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Registered trials
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.