ArticleBiophysical journal2012
Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Molecular dynamics as a tool for unveiling protein-like folding behavior in urethane-based macromolecules: the effect of chain length on the secondary structure of oligourethanes.Polymer chemistry · 2025Article
- Umbrella Refinement of Ensembles-An Alternative View of Ensemble Optimization.Molecules (Basel, Switzerland) · 2025Article
- Accelerating Molecular Dynamics through Informed Resetting.Journal of chemical theory and computation · 2025Article
- A Stochastic Landscape Approach for Protein Folding State Classification.Journal of chemical theory and computation · 2024Article
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.Protein science : a publication of the Protein Society · 2022Article
- Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature.Life (Basel, Switzerland) · 2022Article
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
- Effects of Externally Applied Electric Fields on the Manipulation of Solvated-Chignolin Folding: Static- versus Alternating-Field Dichotomy at Play.The journal of physical chemistry. B · 2022Article
- Deep learning the slow modes for rare events sampling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case.Frontiers in molecular biosciences · 2021Article
- Mutation-induced change in chignolin stability from π-turn to α-turn.RSC advances · 2020Article
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.Biophysical reviews · 2019Review
- Theoretical analysis on thermodynamic stability of chignolin.Scientific reports · 2019Article
- Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm.Molecules (Basel, Switzerland) · 2019Article
- Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.Journal of chemical theory and computation · 2019Article
- Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory.Biophysics and physicobiology · 2019Review
- Relaxation mode analysis for molecular dynamics simulations of proteins.Biophysical reviews · 2018Review
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4 authors.
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Abstract
We study the folding of the designed hairpin chignolin, using simulations with four different force fields. Interestingly, we find a misfolded, out-of-register, structure comprising 20-50% of the ordered structures with three force fields, but not with a fourth. A defining feature of the misfold is that Gly-7 adopts a β(PR) conformation rather than α(L). By reweighting, we show that differences between the force fields can mostly be attributed to differences in glycine properties. Benchmarking against NMR data suggests that the preference for β(PR) is not a force-field artifact. For chignolin, we show that including the misfold in the ensemble results in back-recalculated NMR observables in slightly better agreement with experiment than parameters calculated from a folded ensemble only. For comparison, we show by NMR and circular dichroism spectroscopy that the G7K mutant of chignolin, in which formation of this misfold is impossible, is well folded with stability similar to the wild-type and does not populate the misfolded state in simulation. Our results highlight the complexity of interpreting NMR data for small, weakly structured, peptides in solution, as well as the importance of accurate glycine parameters in force fields, for a correct description of turn structures.
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