ArticleProceedings of the National Academy of Sciences of the United States of America2014
Benchmarking all-atom simulations using hydrogen exchange.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- DreamFold: A World Model to efficiently generate protein folding pathways in the latent space.Protein science : a publication of the Protein Society · 2026Article
- Probe capsid structure stability and dynamics of adeno-associated virus as an important viral vector for gene therapy by hydrogen-deuterium exchange-mass spectrometry.Protein science : a publication of the Protein Society · 2024Article
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- 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
- Protein folding - seeing is deceiving.Protein science : a publication of the Protein Society · 2021Article
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20.Journal of chemical theory and computation · 2021Article
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20.Journal of chemical theory and computation · 2021Article
- Dynamics of an LPS translocon induced by substrate and an antimicrobial peptide.Nature chemical biology · 2021Article
- Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.Journal of molecular biology · 2020Review
- Regulation of Co-transcriptional Pre-mRNA Splicing by mMolecular cell · 2019Article
- Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins.Frontiers in molecular biosciences · 2019Article
- Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.Computational and structural biotechnology journal · 2019Review
- Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.PLoS computational biology · 2018Article
- Article
- New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.Physical chemistry chemical physics : PCCP · 2018Review
- Molecular recognition and packing frustration in a helical protein.PLoS computational biology · 2017Article
- Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.Science (New York, N.Y.) · 2017Article
- Dielectric screening effect of electronic polarization and intramolecular hydrogen bonding.Protein science : a publication of the Protein Society · 2017Article
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Authors and funding
7 authors.
Funding
Abstract
Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.
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