ArticleProtein science : a publication of the Protein Society2010
Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping.
Article in Protein science : a publication of the Protein Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 19 citations in OpenAlex.
- Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2023Article
- Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data.bioRxiv : the preprint server for biology · 2023Article
- Antiparallel Coiled-Coil Interactions Mediate the Homodimerization of the DNA Damage-Repair Protein PALB2.Biochemistry · 2018Article
- Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1).The Journal of biological chemistry · 2016Article
- A community resource of experimental data for NMR / X-ray crystal structure pairs.Protein science : a publication of the Protein Society · 2016Review
- The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.Journal of biomolecular NMR · 2015Article
- Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.Journal of biomolecular NMR · 2015Article
- Chemokine oligomerization in cell signaling and migration.Progress in molecular biology and translational science · 2013Review
- The use of residual dipolar coupling in studying proteins by NMR.Topics in current chemistry · 2012Review
- Characterizing weak protein-protein complexes by NMR residual dipolar couplings.European biophysics journal : EBJ · 2011Review
- Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.Journal of the American Chemical Society · 2011Article
- Structural NMR of protein oligomers using hybrid methods.Journal of structural biology · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 1 country.
Funding
Abstract
The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra- and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra- or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (K(d) 3.4 ± 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape-based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed.
Indexed as
Identifiers
What OpenQuestion holds
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.