ArticleJournal of chemical theory and computation2014
Thermodynamics of Deca-alanine Folding in Water.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Calculating Free-Energy Differences Using an Average Force: A Tutorial for Adaptive Biasing Force Simulations.The journal of physical chemistry. B · 2025Article
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- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces.The journal of physical chemistry letters · 2023Article
- Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
- Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Confronting pitfalls of AI-augmented molecular dynamics using statistical physics.The Journal of chemical physics · 2020Article
- Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.The Journal of chemical physics · 2020Article
- Thermodynamics of helix formation in small peptides of varying length in vacuo, in implicit solvent, and in explicit solvent.Journal of molecular modeling · 2018Article
- Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association.Biochimica et biophysica acta. Biomembranes · 2017Article
- Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.Journal of the American Chemical Society · 2016Article
- Article
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Authors and funding
3 authors.
Funding
Abstract
The determination of the folding dynamics of polypeptides and proteins is critical in characterizing their functions in biological systems. Numerous computational models and methods have been developed for studying structure formation at the atomic level. Due to its small size and simple structure, deca-alanine is used as a model system in molecular dynamics (MD) simulations. The free energy of unfolding in vacuum has been studied extensively using the end-to-end distance of the peptide as the reaction coordinate. However, few studies have been conducted in the presence of explicit solvent. Previous results show a significant decrease in the free energy of extended conformations in water, but the α-helical state is still notably favored over the extended state. Although sufficient in vacuum, we show that end-to-end distance is incapable of capturing the full complexity of deca-alanine folding in water. Using α-helical content as a second reaction coordinate, we deduce a more descriptive free-energy landscape, one which reveals a second energy minimum in the extended conformations that is of comparable free energy to the α-helical state. Equilibrium simulations demonstrate the relative stability of the extended and α-helical states in water as well as the transition between the two states. This work reveals both the necessity and challenge of determining a proper reaction coordinate to fully characterize a given process.
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Registered trials
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.