ArticleJournal of the American Chemical Society2011
Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 75 citations in OpenAlex.
- Factors controlling protein evolvability-at the molecular scale.European biophysics journal : EBJ · 2026Article
- Analysis of proteins in the light of mutations.European biophysics journal : EBJ · 2024Review
- Mapping HDX-MS Data to Protein Conformations through Training Ensemble-Based Models.Journal of the American Society for Mass Spectrometry · 2023Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Proteins' Evolution upon Point Mutations.ACS omega · 2022Article
- Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.Journal of chemical theory and computation · 2022Article
- Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook.Frontiers in immunology · 2022Review
- Achieving a realistic native protein ensemble by HDX-MS and computational modeling.Biophysical journal · 2021Article
- Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.Molecules (Basel, Switzerland) · 2021Review
- Dramatic Shape Changes Occur as CytochromeThe journal of physical chemistry. B · 2020Article
- Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.Biophysical journal · 2020Article
- Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias.The journal of physical chemistry. B · 2019Article
- A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.Structure (London, England : 1993) · 2019Article
- Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery.Biophysical journal · 2019Article
- POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens.Journal of the American Society for Mass Spectrometry · 2019Article
- Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS).Journal of the American Society for Mass Spectrometry · 2019Article
- Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins.The journal of physical chemistry. B · 2018Article
- Theory, simulations, and experiments show that proteins fold by multiple pathways.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics.The FEBS journal · 2017Article
- Fast Protein Translation Can Promote Co- and Posttranslational Folding of Misfolding-Prone Proteins.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.
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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.