ArticlePLoS computational biology2015
Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- How the Extent of Protein Folding and Oligomerization Modulate Condensate Formation and Properties.The journal of physical chemistry letters · 2025Article
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures.The journal of physical chemistry. B · 2021Article
- Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly.Accounts of chemical research · 2021Review
- Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations.Biophysical journal · 2020Article
- Successes and challenges in simulating the folding of large proteins.The Journal of biological chemistry · 2020Review
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-likeInternational journal of molecular sciences · 2018Article
- On the folding of a structurally complex protein to its metastable active state.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Molecular recognition and packing frustration in a helical protein.PLoS computational biology · 2017Article
- Understanding protein domain-swapping using structure-based models of protein folding.Progress in biophysics and molecular biology · 2017Review
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- Constructing sequence-dependent protein models using coevolutionary information.Protein science : a publication of the Protein Society · 2016Article
- Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?Journal of the Royal Society, Interface · 2015Article
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2 authors.
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Abstract
The bacterial colicin-immunity proteins Im7 and Im9 fold by different mechanisms. Experimentally, at pH 7.0 and 10°C, Im7 folds in a three-state manner via an intermediate but Im9 folding is two-state-like. Accordingly, Im7 exhibits a chevron rollover, whereas the chevron arm for Im9 folding is linear. Here we address the biophysical basis of their different behaviors by using native-centric models with and without additional transferrable, sequence-dependent energies. The Im7 chevron rollover is not captured by either a pure native-centric model or a model augmented by nonnative hydrophobic interactions with a uniform strength irrespective of residue type. By contrast, a more realistic nonnative interaction scheme that accounts for the difference in hydrophobicity among residues leads simultaneously to a chevron rollover for Im7 and an essentially linear folding chevron arm for Im9. Hydrophobic residues identified by published experiments to be involved in nonnative interactions during Im7 folding are found to participate in the strongest nonnative contacts in this model. Thus our observations support the experimental perspective that the Im7 folding intermediate is largely underpinned by nonnative interactions involving large hydrophobics. Our simulation suggests further that nonnative effects in Im7 are facilitated by a lower local native contact density relative to that of Im9. In a one-dimensional diffusion picture of Im7 folding with a coordinate- and stability-dependent diffusion coefficient, a significant chevron rollover is consistent with a diffusion coefficient that depends strongly on native stability at the conformational position of the folding intermediate.
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