ArticleProceedings of the National Academy of Sciences of the United States of America2008
Computing the stability diagram of the Trp-cage miniprotein.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water.Molecules (Basel, Switzerland) · 2023Article
- Folding-unfolding asymmetry and aRoyal Society open science · 2023Article
- Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.Journal of chemical information and modeling · 2023Article
- The Influence of Deuterium Isotope Effects on Structural Rearrangements, Ensemble Equilibria, and Hydrogen Bonding in Protic Ionic Liquids.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
- Topological bio-scaling analysis as a universal measure of protein folding.Royal Society open science · 2022Article
- Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.The journal of physical chemistry letters · 2020Article
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
- Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein.Biophysical journal · 2019Article
- Approximating dynamic proximity with a hybrid geometry energy-based kernel for diffusion maps.The Journal of chemical physics · 2019Article
- Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.Journal of biological physics · 2017Article
- Pressure effects on collective density fluctuations in water and protein solutions.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Putting the Piezolyte Hypothesis under Pressure.Biophysical journal · 2017Article
- Computational investigation of cold denaturation in the Trp-cage miniprotein.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Water Determines the Structure and Dynamics of Proteins.Chemical reviews · 2016Review
- Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function.The journal of physical chemistry. B · 2016Article
- A hydrodynamic view of the first-passage folding of Trp-cage miniprotein.European biophysics journal : EBJ · 2016Article
- Itinerary profiling to analyze a large number of protein-folding trajectories.Biophysics and physicobiology · 2016Article
- Intrinsic Localized Modes in Proteins.Scientific reports · 2015Article
- New Insights into Protein (Un)Folding Dynamics.The journal of physical chemistry letters · 2015Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We report molecular dynamics simulations of the equilibrium folding/unfolding thermodynamics of an all-atom model of the Trp-cage miniprotein in explicit solvent. Simulations are used to sample the folding/unfolding free energy difference and its derivatives along 2 isochores. We model the DeltaG(u)(P,T) landscape using the simulation data and propose a stability diagram model for Trp-cage. We find the proposed diagram to exhibit features similar to globular proteins with increasing hydrostatic pressure destabilizing the native fold. The observed energy differences DeltaE(u) are roughly linearly temperature-dependent and approach DeltaE(u) = 0 with decreasing temperature, suggesting that the system approached the region of cold denaturation. In the low-temperature denatured state, the native helical secondary structure elements are largely preserved, whereas the protein conformation changes to an "open-clamp" configuration. A tighter packing of water around nonpolar sites, accompanied by an increasing solvent-accessible surface area of the unfolded ensemble, seems to stabilize the unfolded state at elevated pressures.
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