ArticleBiophysical journal2007
On the characterization of protein native state ensembles.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- NumSimEX: A method using EXX hydrogen exchange mass spectrometry to map the energetics of protein folding landscapes.Protein science : a publication of the Protein Society · 2025Article
- Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome.Genome medicine · 2022Article
- Localizing Frustration in Proteins Using All-Atom Energy Functions.The journal of physical chemistry. B · 2019Article
- APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations.Molecules (Basel, Switzerland) · 2019Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.PLoS computational biology · 2015Article
- p38α MAPK and Type I Inhibitors: Binding Site Analysis and Use of Target Ensembles in Virtual Screening.Molecules (Basel, Switzerland) · 2015Article
- Integrative, dynamic structural biology at atomic resolution--it's about time.Nature methods · 2015Review
- Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface.Proteome science · 2012Article
- Sparse estimation for structural variability.Algorithms for molecular biology : AMB · 2011Article
- Ensemble-based methods for describing protein dynamics.Current opinion in pharmacology · 2010Review
- Tracing conformational changes in proteins.BMC structural biology · 2010Article
- Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex.Proteins · 2010Article
- Article
- Probing the flexibility of large conformational changes in protein structures through local perturbations.PLoS computational biology · 2009Article
- High resolution approach to the native state ensemble kinetics and thermodynamics.Biophysical journal · 2008Article
- Tryptophan fluorescence reveals the presence of long-range interactions in the denatured state of ribonuclease Sa.Biophysical journal · 2008Article
- Unfolding the fold of cyclic cysteine-rich peptides.Protein science : a publication of the Protein Society · 2008Article
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Authors and funding
3 authors.
Funding
Abstract
Describing and understanding the biological function of a protein requires a detailed structural and thermodynamic description of the protein's native state ensemble. Obtaining such a description often involves characterizing equilibrium fluctuations that occur beyond the nanosecond timescale. Capturing such fluctuations remains nontrivial even for very long molecular dynamics and Monte Carlo simulations. We propose a novel multiscale computational method to exhaustively characterize, in atomistic detail, the protein conformations constituting the native state with no inherent timescale limitations. Applications of this method to proteins of various folds and sizes show that thermodynamic observables measured as averages over the native state ensembles obtained by the method agree remarkably well with nuclear magnetic resonance data that span multiple timescales. By characterizing equilibrium fluctuations at atomistic detail over a broad range of timescales, from picoseconds to milliseconds, our method offers to complement current simulation techniques and wet-lab experiments and can impact our understanding and description of the relationship between protein flexibility and function.
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