ArticleProceedings of the National Academy of Sciences of the United States of America2021
Non-Markovian modeling of protein folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 117 citations in OpenAlex.
- Gillespie-based simulation and inference for non-Markovian stochastic reaction networks.Briefings in bioinformatics · 2026Article
- Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Static and dynamic rough energy landscapes can lead to identical diffusivity.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Subdiffusion from competition between multi-exponential friction memory and energy barriers.The European physical journal. E, Soft matter · 2025Article
- Non-Markovian equilibrium and non-equilibrium barrier-crossing kinetics in asymmetric double-well potentials.The European physical journal. E, Soft matter · 2025Article
- Nonequilibrium relaxation exponentially delays the onset of quantum diffusion.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Markov-Type State Models to Describe Non-Markovian Dynamics.Journal of chemical theory and computation · 2025Article
- Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal.Journal of computational chemistry · 2025Article
- Long-term memory induced correction to Arrhenius law.Nature communications · 2024Article
- Memory Corrections to Markovian Langevin Dynamics.Entropy (Basel, Switzerland) · 2024Article
- The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media.Nature communications · 2024Article
- Accurate Memory Kernel Extraction from Discretized Time-Series Data.Journal of chemical theory and computation · 2024Article
- Mechanism of DNA origami folding elucidated by mesoscopic simulations.Nature communications · 2024Article
- Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.The Journal of chemical physics · 2024Article
- Chemically Specific Systematic Coarse-Grained Polymer Model with Both Consistently Structural and Dynamical Properties.JACS Au · 2024Article
- Accurate estimates of dynamical statistics using memory.The Journal of chemical physics · 2024Article
- MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.Briefings in bioinformatics · 2024Article
- Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.The Journal of chemical physics · 2023Article
- Fast protein folding is governed by memory-dependent friction.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We extract the folding free energy landscape and the time-dependent friction function, the two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular dynamics (MD) simulations of the α-helix forming polypeptide [Formula: see text] for a one-dimensional reaction coordinate based on the sum of the native H-bond distances. Folding and unfolding times from numerical integration of the GLE agree accurately with MD results, which demonstrate the robustness of our GLE-based non-Markovian model. In contrast, Markovian models do not accurately describe the peptide kinetics and in particular, cannot reproduce the folding and unfolding kinetics simultaneously, even if a spatially dependent friction profile is used. Analysis of the GLE demonstrates that memory effects in the friction significantly speed up peptide folding and unfolding kinetics, as predicted by the Grote-Hynes theory, and are the cause of anomalous diffusion in configuration space. Our methods are applicable to any reaction coordinate and in principle, also to experimental trajectories from single-molecule experiments. Our results demonstrate that a consistent description of protein-folding dynamics must account for memory friction effects.
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