ArticlePLoS computational biology2009
Analysis of the free-energy surface of proteins from reversible folding simulations.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- In silico ligand self-assembly drives binding recognition of natural products intoIn silico pharmacology · 2025Article
- Chemical interactions modulate λProtein science : a publication of the Protein Society · 2023Article
- Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Engineering folding dynamics from two-state to downhill: application to λ-repressor.The journal of physical chemistry. B · 2013Article
- Characterization of folding mechanisms of Trp-cage and WW-domain by network analysis of simulations with a hybrid-resolution model.The journal of physical chemistry. B · 2013Article
- Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations.The journal of physical chemistry letters · 2012Article
- Atomistic folding simulations of the five-helix bundle protein λ(6−85).Journal of the American Chemical Society · 2011Article
- Is protein folding sub-diffusive?PLoS computational biology · 2010Article
- Protein dynamics investigated by inherent structure analysis.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.
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