ArticleJournal of the American Chemical Society2014
Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 24 citations in OpenAlex.
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Chemical interactions modulate λProtein science : a publication of the Protein Society · 2023Article
- Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet.Nature communications · 2021Article
- Volume and compressibility differences between protein conformations revealed by high-pressure NMR.Biophysical journal · 2021Article
- A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure.The journal of physical chemistry. B · 2020Article
- Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Monitoring Hydrogen Exchange During Protein Folding by Fast Pressure Jump NMR Spectroscopy.Journal of the American Chemical Society · 2017Article
- Mapping fast protein folding with multiple-site fluorescent probes.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations.Journal of the American Chemical Society · 2015Article
- A hypothesis to reconcile the physical and chemical unfolding of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Role of solvation in pressure-induced helix stabilization.The Journal of chemical physics · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Density is an easily adjusted variable in molecular dynamics (MD) simulations. Thus, pressure-jump (P-jump)-induced protein refolding, if it could be made fast enough, would be ideally suited for comparison with MD. Although pressure denaturation perturbs secondary structure less than temperature denaturation, protein refolding after a fast P-jump is not necessarily faster than that after a temperature jump. Recent P-jump refolding experiments on the helix bundle λ-repressor have shown evidence of a <3 μs burst phase, but also of a ~1.5 ms "slow" phase of refolding, attributed to non-native helical structure frustrating microsecond refolding. Here we show that a λ-repressor mutant is nonetheless capable of refolding in a single explicit solvent MD trajectory in about 19 μs, indicating that the burst phase observed in experiments on the same mutant could produce native protein. The simulation reveals that after about 18.5 μs of conformational sampling, the productive structural rearrangement to the native state does not occur in a single swift step but is spread out over a brief series of helix and loop rearrangements that take about 0.9 μs. Our results support the molecular time scale inferred for λ-repressor from near-downhill folding experiments, where transition-state population can be seen experimentally, and also agrees with the transition-state transit time observed in slower folding proteins by single-molecule spectroscopy.
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