ArticleJournal of chemical theory and computation2013
Local vs global motions in protein folding.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction.Biomolecules · 2021Review
- In Silico Evaluation of Cyclophilin Inhibitors as Potential Treatment for SARS-CoV-2.Open forum infectious diseases · 2021Article
- Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2021Article
- From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.ACS chemical neuroscience · 2018Article
- Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.ACS chemical neuroscience · 2017Article
- Intrinsic Localized Modes in Proteins.Scientific reports · 2015Article
- Preventing fibril formation of a protein by selective mutation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Accounting for a mirror-image conformation as a subtle effect in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Authors and funding
4 authors.
Funding
Abstract
It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respectively, were analyzed. The key residues involved in the folding of the FBP28 WW domain are elucidated by this analysis. The correlations between local and global motions are found. It is shown that most of the residues in the folding trajectories of the system studied here move in a concerted fashion, following the dynamics of the whole system. This demonstrates how the choice of a pathway has to involve concerted movements in order for this protein to fold. This finding also sheds light on the effectiveness of principal component analysis (PCA) for the description of the folding dynamics of the system studied. It is demonstrated that the FEL along the PCs, computed by considering only several critically-placed residues, can correctly describe the folding dynamics.
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