ArticleBiophysical journal2014
A molecular interpretation of 2D IR protein folding experiments with Markov state models.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Uncertainties in Markov State Models of Small Proteins.Journal of chemical theory and computation · 2023Article
- Deep learning to decompose macromolecules into independent Markovian domains.Nature communications · 2022Article
- Origin of thiocyanate spectral shifts in water and organic solvents.The Journal of chemical physics · 2022Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity.The journal of physical chemistry. B · 2021Article
- Structure Changes of a Membrane Polypeptide under an Applied Voltage Observed with Surface-Enhanced 2D IR Spectroscopy.The journal of physical chemistry letters · 2021Article
- Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding.The journal of physical chemistry. B · 2020Article
- Revealing the Dynamical Role of Co-solvents in the Coupled Folding and Dimerization of Insulin.The journal of physical chemistry letters · 2020Article
- Adaptive Markov state model estimation using short reseeding trajectories.The Journal of chemical physics · 2020Article
- Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala.Biophysical journal · 2018Article
- Hydrophobic Collapse in N-Methylacetamide-Water Mixtures.The journal of physical chemistry. A · 2018Article
- Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.Chemical reviews · 2017Review
- Probing the Effects of Gating on the Ion Occupancy of the KJournal of the American Chemical Society · 2017Article
- Optimized parameter selection reveals trends in Markov state models for protein folding.The Journal of chemical physics · 2016Article
- Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy.Science (New York, N.Y.) · 2016Article
- Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.The journal of physical chemistry. B · 2016Article
- Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.Biophysical journal · 2016Article
- Fast-folding proteins under stress.Cellular and molecular life sciences : CMLS · 2015Review
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7 authors.
Funding
Abstract
The folding mechanism of the N-terminal domain of ribosomal protein L9 (NTL91-39) is studied using temperature-jump (T-jump) amide I' two-dimensional infrared (2D IR) spectroscopy in combination with spectral simulations based on a Markov state model (MSM) built from millisecond-long molecular dynamics trajectories. The results provide evidence for a compact well-structured folded state and a heterogeneous fast-exchanging denatured state ensemble exhibiting residual secondary structure. The folding rate of 26.4 μs(-1) (at 80°C), extracted from the T-jump response of NTL91-39, compares favorably with the 18 μs(-1) obtained from the MSM. Structural decomposition of the MSM and analysis along the folding coordinate indicates that helix-formation nucleates the global folding. Simulated difference spectra, corresponding to the global folding transition of the MSM, are in qualitative agreement with measured T-jump 2D IR spectra. The experiments demonstrate the use of T-jump 2D IR spectroscopy as a valuable tool for studying protein folding, with direct connections to simulations. The results suggest that in addition to predicting the correct native structure and folding time constant, molecular dynamics simulations carried out with modern force fields provide an accurate description of folding mechanisms in small proteins.
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