ArticlePLoS computational biology2012
The dominant folding route minimizes backbone distortion in SH3.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- On Markov blankets and hierarchical self-organisation.Journal of theoretical biology · 2020Article
- Structure of the human monomeric NEET protein MiNT and its role in regulating iron and reactive oxygen species in cancer cells.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The Active Inference Approach to Ecological Perception: General Information Dynamics for Natural and Artificial Embodied Cognition.Frontiers in robotics and AI · 2018Article
- Constructing sequence-dependent protein models using coevolutionary information.Protein science : a publication of the Protein Society · 2016Article
- Knowing one's place: a free-energy approach to pattern regulation.Journal of the Royal Society, Interface · 2015Article
- Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble.PloS one · 2015Article
- Pierced Lasso Bundles are a new class of knot-like motifs.PLoS computational biology · 2014Article
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3 authors.
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Abstract
Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding.
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