ArticleNature communications2016
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
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- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- A two-step mechanism for sugar translocation.Nature structural & molecular biology · 2026Article
- Improving Conformational Ensembles of Folded Proteins in Go̅Martini.Journal of chemical theory and computation · 2026Article
- Efficient sampling of large-scale transition pathways and intermediate conformations in sub-mesoscopic protein complexes.Nature communications · 2026Article
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- Extended Sampling of Macromolecular Conformations from Uniformly Distributed Points on Multidimensional Normal Mode Hyperspheres.Journal of chemical theory and computation · 2024Article
- MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization.Nucleic acids research · 2024Article
- 3D animation as a tool for integrative modeling of dynamic molecular mechanisms.Structure (London, England : 1993) · 2024Review
- Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction.Journal of chemical information and modeling · 2024Article
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- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Molecular effects of site-specific phosphate-methylated primer on the structure and motions of Taq DNA polymerase.Computational and structural biotechnology journal · 2023Article
- BioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamics.Journal of structural biology: X · 2023Review
- CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations.Communications biology · 2022Article
- Targeting protein conformations with small molecules to control protein complexes.Trends in biochemical sciences · 2022Review
- SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2.PLoS computational biology · 2022Article
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Authors and funding
5 authors.
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Abstract
Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.
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