ArticleProceedings of the National Academy of Sciences of the United States of America2009
Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Unfolding cytochromes c-bJournal of inorganic biochemistry · 2020Article
- Dramatic Shape Changes Occur as CytochromeThe journal of physical chemistry. B · 2020Article
- Funneled angle landscapes for helical proteins.Journal of inorganic biochemistry · 2020Article
- Molecular Dynamics Ensemble Refinement of Intrinsically Disordered Peptides According to Deconvoluted Spectra from Circular Dichroism.Biophysical journal · 2020Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Opposing Intermolecular Tuning of CaBiophysical journal · 2017Article
- Genomic Energy Landscapes.Biophysical journal · 2017Review
- Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling.Frontiers in neuroscience · 2017Article
- How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome.Nature communications · 2016Article
- Cytochrome unfolding pathways from computational analysis of crystal structures.Journal of inorganic biochemistry · 2016Article
- Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.Protein science : a publication of the Protein Society · 2016Article
- Topology, structures, and energy landscapes of human chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Regulation and aggregation of intrinsically disordered peptides.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Learning To Fold Proteins Using Energy Landscape Theory.Israel journal of chemistry · 2014Article
- Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches.Biophysical journal · 2014Article
- Mechanisms of cellular proteostasis: insights from single-molecule approaches.Annual review of biophysics · 2014Review
- Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Snapshots of a protein folding intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Origin of the conformational heterogeneity of cardiolipin-bound cytochrome C.Journal of the American Chemical Society · 2012Article
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5 authors.
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Abstract
The denatured state of proteins is heterogeneous and susceptible to general hydrophobic and electrostatic forces, but to what extent does the funneled nature of protein energy landscapes play a role in the unfolded ensemble? We simulate the denatured ensemble of cytochrome c using a series of models. The models pinpoint the efficacy of incorporating energetic funnels toward the native state in contrast with models having no native structure-seeking tendency. These models also contain varying strengths of electrostatic effects and hydrophobic collapse. The simulations based on these models are compared with experimental distributions for the distances between a fluorescent donor and the heme acceptor that were extracted from time-resolved fluorescence energy transfer experiments on cytochrome c. Comparing simulations to detailed experimental data on several labeling sites allows us to quantify the dominant forces in denatured protein ensembles.
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