The Structure of the Major Transition State for Folding of an FF Domain from Experiment and Simulation

Jemth, Per; Day, Ryan; Gianni, Stefano; Khan, Farhan R.; Allen, Mark D.; Daggett, Valerie; Fersht, Alan R.

doi:10.1016/j.jmb.2005.04.067

Cited by 73 publications

(130 citation statements)

References 67 publications

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“…Several classes of model proteins have been studied to date, including all-beta sheet proteins such as the SH3 domain [21,52], and all-α-helical proteins such as the FF domain [1,9,53,54].…”

Section: Model Proteins To Study Foldingmentioning

confidence: 99%

“…The folding intermediates of all of the aforementioned proteins form non-native tertiary interactions [1,[55][56][57], and in some cases, such as the engrailed homodomain and FF domain, have non-native helical boundaries. They fold via a framework or nucleation condensation mechanism [54,56,[58][59][60], which are probably two manifestations of a single mechanism [61].…”

Section: Model Proteins To Study Foldingmentioning

confidence: 99%

“…The rate-limiting transition state (between I and N) was later studied by Fersht and coworkers using φ-value analysis [54]. They found that native secondary and tertiary interactions are conserved in a single region of the transition state comprising the C-terminus of H1, the H1-H2 loop, and the N-terminus of H2, which strongly suggests a nucleation-condensation mechanism of folding.…”

Section: The Ff Domain From Hypa/fbp11 Folds Via An On-pathway Intermmentioning

confidence: 99%

“…Following the established protocol for FF domain purification [54], the overnight cultures were pelleted and resuspended in lysis buffer (50mM sodium phosphate, 20mM imidazole, 400mM …”

Section: Protein Purificationmentioning

confidence: 99%

“…The FF domain was postulated to fold by a nucleation-condensation mechanism based on φ-value analysis [54], as the region comprising the C-terminus of H1, the H1-H2 loop and the Nterminus of H2 forms native secondary and tertiary interactions in the major transition state while the remainder of the protein does not. The structure of the FF folding intermediate is indeed only completely native in the predicted region, but it also has fully native helices H1 and H2, which suggests a framework model.…”

Section: Mechanism Of Ff Foldingmentioning

confidence: 99%

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Cross-Validation of the Structure of a Transiently Formed and Low Populated FF Domain Folding Intermediate Determined by Relaxation Dispersion NMR and CS-Rosetta

et al. 2011

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We have recently reported the atomic resolution structure of a low populated and transiently formed on-pathway folding intermediate of the FF domain from human HYPA/FBP11 [Korzhnev, D. M.; Religa, T. L.; Banachewicz, W.; Fersht, A. R.; Kay, L.E. Science 2011, 329, 1312–1316]. The structure was determined on the basis of backbone chemical shift and bond vector orientation restraints of the invisible intermediate state measured using relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy that were subsequently input into the database structure determination program, CS-Rosetta. As a cross-validation of the structure so produced, we present here the solution structure of a mimic of the folding intermediate that is highly populated in solution, obtained from the wild-type domain by mutagenesis that destabilizes the native state. The relaxation dispersion/CS-Rosetta structures of the intermediate are within 2 Å of those of the mimic, with the nonnative interactions in the intermediate also observed in the mimic. This strongly confirms the structure of the FF domain folding intermediate, in particular, and validates the use of relaxation dispersion derived restraints in structural studies of invisible excited states, in general.

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Section: Model Proteins To Study Foldingmentioning

confidence: 99%

Section: Model Proteins To Study Foldingmentioning

confidence: 99%

Section: The Ff Domain From Hypa/fbp11 Folds Via An On-pathway Intermmentioning

confidence: 99%

“…Following the established protocol for FF domain purification [54], the overnight cultures were pelleted and resuspended in lysis buffer (50mM sodium phosphate, 20mM imidazole, 400mM …”

Section: Protein Purificationmentioning

confidence: 99%

Section: Mechanism Of Ff Foldingmentioning

confidence: 99%

See 3 more Smart Citations