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

Kathuria, Sagar V.; Day, Iain J.; Wallace, Louise; Matthews, C. Robert

doi:10.1016/j.jmb.2008.06.054

Cited by 46 publications

(107 citation statements)

References 66 publications

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“…4 C and F) because the new termini disrupt the frustrated region. These results are consistent with the ILV cluster model for folding, in that the WT connectivity is driven to fold to the off-pathway I BP species by the premature formation of cluster 1 spanning the interfacial contacts (14). The local connectivity of the larger cluster 2 in Cpβ4 enables it to outcompete the formation of cluster 1.…”

Section: Stability and Secondary Structure Of Submillisecond Intermedsupporting

confidence: 85%

“…Therefore we used Go-model simulations to resolve the underlying structural basis of the differences in the I BP stability and infer the kinetic model that is most consistent with the experimental observables. Previous experimental work has concluded that the I OFF is not a consequence of the proline isomerization reaction (14,21). Likewise, in computational work where the trans geometry was enforced via harmonic restraints, CheY still was able to access the folded state from the unfolded configurations.…”

Section: Stability and Secondary Structure Of Submillisecond Intermedmentioning

confidence: 94%

“…However, simulations have found that topological frustration, e.g., the premature formation of a substructure that impedes access to the productive TSE, can lead to the accumulation of intermediates (I) that must unfold to some extent to traverse the folding reaction coordinate successfully (8,10,11). Experimental and computational studies on the folding of the α-subunit of Trp synthase (12,13), the chemotaxis response regulator Y (CheY) (10,14), a pair of apo-flavodoxins (8,15,16), and tandem titan domains (17) revealed frustration in the form of off-pathway intermediates (I OFF ). Thus, as-yet unexplored aspects of sequence and structure can add complexity to folding reactions.…”

mentioning

confidence: 99%

“…The proposed kinetic folding mechanism (Fig. 1C) (14) involves two parallel folding channels defined by the cis and trans isomers of the prolyl peptide bond between K109/P110. The unfolded proteins (U) in both the major trans (U t ) (90%) and minor cis (U c ) (10%) channels sample an off-pathway submillisecond intermediate (I BP ), I BPt and I BPc , respectively, before the rate-limiting isomerization reaction in the I BPt →I BPc step.…”

mentioning

confidence: 99%

“…However, native-centric simulations identified contacts between the N-and C-terminal subdomains, centered around (βα)3-4, early in folding that are incompatible with access to the productive TSE and that lead to frustration in the folding mechanism (10). Another perspective is provided by the branched chain aliphatic side chains (BASiC) hypothesis, which supposes that large clusters of isoleucine, leucine, and valine (ILV) side chains serve as cores of stability in folding intermediates (11,14). Both these clusters have been shown to have a high contact density (22).…”

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confidence: 99%

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Modulation of frustration in folding by sequence permutation

Nobrega

Arora

Kathuria

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an offpathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N-and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.CF-SAXS | Go models | CheY permutants | protein-folding intermediates H ighly denatured states of globular proteins resemble statistical random coils when examined with low-resolution techniques such as X-ray scattering (1) and hydrodynamic analyses (2). However, a higher-resolution view provided by experimental models (3-6) and simulations (7) shows that the conformational ensemble is biased toward low-contact-order (CO) structures, e.g., α-helices, β-turns, and β-hairpins, which form and melt in less than a few microseconds. During folding, these nascent structures presumably coalesce into higher-order assemblies of ever-increasing free energy until reaching the transition-state ensemble (TSE) that leads to the native conformation. From another perspective, this assembly process mediates a global collapse of the chain in an unfavorable solvent (8). Landscape theory (9) posits that, in the simplest scenario, native-like substructures appear and lead without pause to the TSE and the native conformation in an apparent two-state fashion. However, simulations have found that topological frustration, e.g., the premature formation of a substructure that impedes access to the productive TSE, can lead to the accumulation of intermediates (I) that must unfold to some extent to traverse the folding reaction coordinate...

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Section: Stability and Secondary Structure Of Submillisecond Intermedsupporting

confidence: 85%

Section: Stability and Secondary Structure Of Submillisecond Intermedmentioning

confidence: 94%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Modulation of frustration in folding by sequence permutation

Nobrega

Arora

Kathuria

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Clusters of isoleucine, leucine, and valine side chains define cores of stability in high‐energy states of globular proteins: Sequence determinants of structure and stability

et al. 2015

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Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high-energy states that populate their folding free-energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high-energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high-energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account Abbreviations: NH, main chain amide hydrogen; BASiC, branched aliphatic side chain; ILV, isoleucine leucine valine; vdW, van der Waals; HX, hydrogen exchange; H-bond, hydrogen bond; FIRST, floppy inclusions and rigid substructure topography; GNM, Gaussian network model; BEST, biology using ensemble-based structural thermodynamics; aTS, alpha subunit of tryptophan synthase; sIGPS, indole-3-glycerolphosphate synthase from S.

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Environment‐dependent long‐range structural distortion in a temperature‐sensitive point mutant

et al. 2011

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Extensive environment-dependent rearrangement of the helix-turn-helix DNA recognition region and adjacent L-tryptophan binding pocket is reported in the crystal structure of dimeric E. coli trp aporepressor with point mutation Leu75Phe. In one of two subunits, the eight residues immediately C-terminal to the mutation are shifted forward in helical register by three positions, and the five following residues form an extrahelical loop accommodating the register shift. In contrast, the second subunit has wildtype-like conformation, as do both subunits in an isomorphous wildtype control structure. Treated together as an ensemble pair, the distorted and wildtype-like conformations of the mutant apoprotein agree more fully than either conformation alone with previously reported NOE measurements, and account more completely for its diverse biochemical and biophysical properties. The register-shifted segment Ile79-Ala80-Thr81-Ile82-Thr83 is helical in both conformations despite low helical propensity, suggesting an important structural role for the steric constraints imposed by b-branched residues in helical conformation.

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

Cited by 46 publications

References 66 publications

Modulation of frustration in folding by sequence permutation

Modulation of frustration in folding by sequence permutation

Clusters of isoleucine, leucine, and valine side chains define cores of stability in high‐energy states of globular proteins: Sequence determinants of structure and stability

Environment‐dependent long‐range structural distortion in a temperature‐sensitive point mutant

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