ArticleProtein science : a publication of the Protein Society2009
Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping: the phone cord effect in protein folding.
Article in Protein science : a publication of the Protein Society, 2009. 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, 22 citations in OpenAlex.
- Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies.PLoS computational biology · 2024Article
- The Structural Rule Distinguishing a Superfold: A Case Study of Ferredoxin Fold and the Reverse Ferredoxin Fold.Molecules (Basel, Switzerland) · 2022Article
- Modeling protein folding in vivo.Biology direct · 2018Article
- Mapping the Geometric Evolution of Protein Folding Motor.PloS one · 2016Article
- Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome.Acta crystallographica. Section F, Structural biology communications · 2015Article
- Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins.Journal of chemical theory and computation · 2014Article
- Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.PloS one · 2013Article
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Abstract
The remarkable predominance of right-handedness in beta-alpha-beta helical crossovers has been previously explained in terms of thermodynamic stability and kinetic accessibility, but a different kinetic trapping mechanism may also play a role. If the beta-sheet contacts are made before the crossover helix is fully formed, and if the backbone angles of the folding helix follows the energetic pathway of least resistance, then the helix would impart a torque on the ends of the two strands. Such a torque would tear apart a left-handed conformation but hold together a right-handed one. Right-handed helical crossovers predominate even in all-alpha proteins, where previous explanations based on the preferred twist of the beta sheet do not apply. Using simple molecular simulations, we can reproduce the right-handed preference in beta-alpha-beta units, without imposing specific beta-strand geometry. The new kinetic trapping mechanism is dubbed the "phone cord effect" because it is reminiscent of the way a helical phone cord forms superhelices to relieve torsional stress. Kinetic trapping explains the presence of a right-handed superhelical preference in alpha helical crossovers and provides a possible folding mechanism for knotted proteins.
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