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Kinetic Traps in the Folding of ßa-Repeat Proteins: CheY Initially Misfolds before Accessing the Native Conformation

journal contribution
posted on 2023-06-08, 05:31 authored by Sagar V Kathuria, Iain Day, Louise A Wallace, C Robert Matthews
The beta alpha-repeat class of proteins, represented by the (beta alpha)(8) barrel and the alpha/beta/alpha sandwich, are among the most common structural platforms in biology. Previous studies on the folding mechanisms of these motifs have revealed or suggested that the initial event involves the submillisecond formation of a kinetically trapped species that must at least partially unfold before productive folding to the respective native conformation can occur. To test the generality of these observations, CheY, a bacterial response regulator, was subjected to an extensive analysis of its folding reactions. Although earlier studies had proposed the formation of an off-pathway intermediate, the data available were not sufficient to rule out an alternative on-pathway mechanism. A global analysis of single- and double-jump kinetic data, combined with equilibrium unfolding data, was used to show that CheY folds and unfolds through two parallel channels defined by the state of isomerization of a prolyl peptide bond in the active site. Each channel involves a stable, highly structured folding intermediate whose kinetic properties are better described as the properties of an off-pathway species. Both intermediates subsequently flow through the unfolded state ensemble and adopt the native cis-prolyl isomer prior to forming the native state. Initial collapse to off-pathway folding intermediates is a common feature of the folding mechanisms of beta alpha-repeat proteins, perhaps reflecting the favored partitioning to locally determined substructures that cannot directly access the native conformation. Productive folding requires the dissipation of these prematurely folded substructures as a prelude to forming the larger-scale transition state that leads to the native conformation. Results from Go-modeling studies in the accompanying paper elaborate on the topological frustration in the folding free-energy landscape of CheY.

History

Publication status

  • Published

Journal

Journal of Molecular Biology

ISSN

0022-2836

Publisher

Elsevier

Issue

2

Volume

382

Page range

467-484

Department affiliated with

  • Chemistry Publications

Full text available

  • No

Peer reviewed?

  • Yes

Legacy Posted Date

2012-02-06

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