ArticleBiophysical journal2013
Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism.
Article in Biophysical journal, 2013. 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.
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.Biophysical journal · 2020Article
- Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.Journal of biological physics · 2017Article
- Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.Biophysical journal · 2017Article
- A hydrodynamic view of the first-passage folding of Trp-cage miniprotein.European biophysics journal : EBJ · 2016Article
- Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage.The journal of physical chemistry letters · 2015Article
- Redundancy of the genetic code enables translational pausing.Frontiers in genetics · 2014Review
- Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.PloS one · 2014Article
- Assessment of local friction in protein folding dynamics using a helix cross-linker.The journal of physical chemistry. B · 2013Article
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1 author.
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Abstract
In this work a new method for the automatic exploration and calculation of multidimensional free energy landscapes is proposed. Inspired by metadynamics, it uses several collective variables that are relevant for the investigated process and a bias potential that discourages the sampling of already visited configurations. The latter potential allows escaping a local free energy minimum following the direction of slow motions. This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables. The method is tested on the Ace-Ala3-Nme peptide, and then it is applied to investigate the Trp-cage folding mechanism. For this protein, within a few hundreds of nanoseconds, a broad range of conformations is explored, including nearly native ones, initiating the simulation from a completely unfolded conformation. Finally, several folding/unfolding trajectories give a systematic description of the Trp-cage folding pathways, leading to a unified view for the folding mechanisms of this protein. The proposed mechanism is consistent with NMR chemical shift data at increasing temperature and recent experimental observations pointing to a pivotal role of secondary structure elements in directing the folding process toward the native state.
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