ArticleProceedings of the National Academy of Sciences of the United States of America2006
Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed.
- Theoretical Study of the Influence of K20N Glycosylation on the Dynamic Behavior of Im7 Protein.Molecules (Basel, Switzerland) · 2025Article
- The mechanism of amyloid fibril growth from Φ-value analysis.Nature chemistry · 2025Article
- Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery.Biophysical journal · 2019Article
- Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data.International journal of molecular sciences · 2018Article
- Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.International journal of computational biology and drug design · 2018Article
- Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.Frontiers in molecular biosciences · 2017Article
- Forces Driving Chaperone Action.Cell · 2016Article
- The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view.Scientific reports · 2016Article
- Substrate protein folds while it is bound to the ATP-independent chaperone Spy.Nature structural & molecular biology · 2016Article
- Using hydroxyl radical footprinting to explore the free energy landscape of protein folding.Methods (San Diego, Calif.) · 2015Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- Notable Stabilization of α-Chymotrypsin by the Protic Ionic Additive, [ch][dhp]: Calorimetric Evidence for a Fine Enthalpy/Entropy Balance.International scholarly research notices · 2014Article
- Conformational dynamics is more important than helical propensity for the folding of the all α-helical protein Im7.Protein science : a publication of the Protein Society · 2013Article
- Folding of a large protein at high structural resolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Role of the iron axial ligands of heme carrier HasA in heme uptake and release.The Journal of biological chemistry · 2012Article
- Protein hydrogen exchange: testing current models.Protein science : a publication of the Protein Society · 2012Article
- Conformational properties of the unfolded state of Im7 in nondenaturing conditions.Journal of molecular biology · 2012Article
- Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes.Journal of the American Chemical Society · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
We present a detailed structural characterization of the intermediate state populated during the folding and unfolding of the bacterial immunity protein Im7. We achieve this result by incorporating a variety of experimental data available for this species in molecular dynamics simulations. First, we define the structure of the exchange-competent intermediate state of Im7 by using equilibrium hydrogen-exchange protection factors. Second, we use this ensemble to predict Phi-values and compare the results with the experimentally determined Phi-values of the kinetic refolding intermediate. Third, we predict chemical-shift measurements and compare them with the measured chemical shifts of a mutational variant of Im7 for which the kinetic folding intermediate is the most stable state populated at equilibrium. Remarkably, we found that the properties of the latter two species are predicted with high accuracy from the exchange-competent intermediate that we determined, suggesting that these three states are characterized by a similar architecture in which helices I, II, and IV are aligned in a native-like, but reorganized, manner. Furthermore, the structural ensemble that we obtained enabled us to rationalize the results of tryptophan fluorescence experiments in the WT protein and a series of mutational variants. The results show that the integration of diverse sets of experimental data at relatively low structural resolution is a powerful approach that can provide insights into the structural organization of this conformationally heterogeneous three-helix intermediate with unprecedented detail and highlight the importance of both native and non-native interactions in stabilizing its structure.
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.