ArticleJournal of the American Chemical Society2015
Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 48 citations in OpenAlex.
- Structure of a transient protein-folding intermediate by pressure-jump NMR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- A Fluorescence-Based Temperature-Jump Apparatus for Illustrating Protein Dynamics on the Millisecond Time Scale.Analytical chemistry · 2025Article
- Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein.Chemical science · 2024Article
- Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways.The journal of physical chemistry letters · 2022Article
- Tandem surface-induced dissociation of protein complexes on an ultrahigh resolution platform.International journal of mass spectrometry · 2021Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in γ-Glu-(Pro)The journal of physical chemistry. B · 2020Article
- A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure.The journal of physical chemistry. B · 2020Article
- Studying biomolecular folding and binding using temperature-jump mass spectrometry.Nature communications · 2020Article
- Competition of individual domain folding with inter-domain interaction in WW domain engineered repeat proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Proteins: "Boil 'Em, Mash 'Em, Stick 'Em in a Stew".The journal of physical chemistry. B · 2019Review
- 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
- A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy.Chemical science · 2018Article
- Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology.Methods (San Diego, Calif.) · 2018Article
- Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Automated method to differentiate between native and mirror protein models obtained from contact maps.PloS one · 2018Article
- Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation.FEBS letters · 2017Article
- Protein unfolding mechanisms and their effects on folding experiments.F1000Research · 2017Review
- A chimeric protein-based malaria vaccine candidate induces robust T cell responses against Plasmodium vivax MSP1Scientific reports · 2016Article
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Authors and funding
5 authors at 1 institution in 1 country.
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Abstract
The unimolecular folding reaction of small proteins is now amenable to a very direct mechanistic comparison between experiment and simulation. We present such a comparison of microsecond pressure and temperature jump refolding kinetics of the engineered WW domain FiP35, a model system for β-sheet folding. Both perturbations produce experimentally a faster and a slower kinetic phase, and the "slow" microsecond phase is activated. The fast phase shows differences between perturbation methods and is closer to the downhill limit by temperature jump, but closer to the transiently populated intermediate limit by pressure jump. These observations make more demands on simulations of the folding process than just a rough comparison of time scales. To complement experiments, we carried out several pressure jump and temperature jump all-atom molecular dynamics trajectories in explicit solvent, where FiP35 folded in five of the six simulations. We analyzed our pressure jump simulations by kinetic modeling and found that the pressure jump experiments and MD simulations are most consistent with a 4-state kinetic mechanism. Together, our experimental and computational data highlight FiP35's position at the boundary where activated intermediates and downhill folding meet, and we show that this model protein is an excellent candidate for further pressure jump molecular dynamics studies to compare experiment and modeling at the folding mechanism level.
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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.