ArticleProceedings of the National Academy of Sciences of the United States of America2011
Making connections between ultrafast protein folding kinetics and molecular dynamics simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Modeling dual-range atomic interactions with physicochemical principles for molecular force fields.Bioinformatics (Oxford, England) · 2026Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- Modern Kinetics and Mechanism of Protein Folding: A Retrospective.The journal of physical chemistry. B · 2021Article
- Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure.The journal of physical chemistry. B · 2021Article
- A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy.Chemical science · 2018Article
- Complex Folding Landscape of Apomyoglobin at Acidic pH Revealed by Ultrafast Kinetic Analysis of Core Mutants.The journal of physical chemistry. B · 2018Article
- Heterogeneity in the Folding of Villin Headpiece Subdomain HP36.The journal of physical chemistry. B · 2018Article
- Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.Chemical reviews · 2017Review
- When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.The Biochemical journal · 2016Review
- Selenomethionine, p-cyanophenylalanine pairs provide a convenient, sensitive, non-perturbing fluorescent probe of local helical structure.Chemical communications (Cambridge, England) · 2016Article
- Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories.Chemical physics · 2013Article
- Protein folding kinetics and thermodynamics from atomistic simulation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Simple few-state models reveal hidden complexity in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Native state conformational heterogeneity of HP35 revealed by time-resolved FRET.The journal of physical chemistry. B · 2012Article
- Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation.Biophysical journal · 2012Article
- Minimalist probes for studying protein dynamics: thioamide quenching of selectively excitable fluorescent amino acids.Journal of the American Chemical Society · 2012Article
- Spectroscopic studies of protein folding: linear and nonlinear methods.Protein science : a publication of the Protein Society · 2012Review
- MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.Journal of chemical theory and computation · 2011Article
- Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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5 authors.
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Abstract
Determining the rate of forming the truly folded conformation of ultrafast folding proteins is an important issue for both experiments and simulations. The double-norleucine mutant of the 35-residue villin subdomain is the focus of recent computer simulations with atomistic molecular dynamics because it is currently the fastest folding protein. The folding kinetics of this protein have been measured in laser temperature-jump experiments using tryptophan fluorescence as a probe of overall folding. The conclusion from the simulations, however, is that the rate determined by fluorescence is significantly larger than the rate of overall folding. We have therefore employed an independent experimental method to determine the folding rate. The decay of the tryptophan triplet-state in photoselection experiments was used to monitor the change in the unfolded population for a sequence of the villin subdomain with one amino acid difference from that of the laser temperature-jump experiments, but with almost identical equilibrium properties. Folding times obtained in a two-state analysis of the results from the two methods at denaturant concentrations varying from 1.5-6.0 M guanidinium chloride are in excellent agreement, with an average difference of only 20%. Polynomial extrapolation of all the data to zero denaturant yields a folding time of 220 (+100,-70) ns at 283 K, suggesting that under these conditions the barrier between folded and unfolded states has effectively disappeared--the so-called "downhill scenario."
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