ArticleBiophysical journal2010
The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins.Journal of chemical information and modeling · 2020Article
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex.Biophysical journal · 2018Article
- Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes.European biophysics journal : EBJ · 2018Article
- Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-likeInternational journal of molecular sciences · 2018Article
- Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape.Biophysical journal · 2016Article
- SMOG 2: A Versatile Software Package for Generating Structure-Based Models.PLoS computational biology · 2016Article
- Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.Journal of chemical theory and computation · 2014Article
- Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches.Biophysical journal · 2014Article
- Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.PloS one · 2014Article
- Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
- Diffusion models of protein folding.Physical chemistry chemical physics : PCCP · 2011Article
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6 authors.
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Abstract
We present a method for calculating the configurational-dependent diffusion coefficient of a globular protein as a function of the global folding process. Using a coarse-grained structure-based model, we determined the diffusion coefficient, in reaction coordinate space, as a function of the fraction of native contacts formed Q for the cold shock protein (TmCSP). We find nonmonotonic behavior for the diffusion coefficient, with high values for the folded and unfolded ensembles and a lower range of values in the transition state ensemble. We also characterized the folding landscape associated with an energetically frustrated variant of the model. We find that a low-level of frustration can actually stabilize the native ensemble and increase the associated diffusion coefficient. These findings can be understood from a mechanistic standpoint, in that the transition state ensemble has a more homogeneous structural content when frustration is present. Additionally, these findings are consistent with earlier calculations based on lattice models of protein folding and more recent single-molecule fluorescence measurements.
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