Different folding transition states may result in the same native structure

  title={Different folding transition states may result in the same native structure},
  author={Ana Rosa Viguera and Luis Serrano and Matthias Wilmanns},
  journal={Nature Structural Biology},
The crystal structures of two circular permutants of the α-spectrin SH3 domain with new termini within the RT loop (S19–P20s) and the distal loop (N47–D48s) have been determined at 2.02 and 1.77 Å resolution respectively. Both fold into the same three-dimensional structure as the wild-type SH3 domain except for the engineered loop that fuses the wild-type termini. The cleaved RT loop in S19–P20s loses nine conserved hydrogen bonds through local hydrogen bond unzipping; no hydrogen bond… 
The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
The protein engineering analysis of the α-spectrin SH3 domain at three different stability conditions reveals a folding transition state structured around the distal loop β-hairpin and the 310-helix, suggesting a transition state ensemble with little conformational variability.
Obligatory steps in protein folding and the conformational diversity of the transition state
Analysis of the existence of obligatory steps in the folding reaction of the α-spectrin SH3 domain by mutating Asp 48 (D48G), which is at position i+3 of an isolated two-residue type II' β-turn, indicates that transition state ensembles in β-sheet proteins could be quite defined and conformationally restricted.
Loop length, intramolecular diffusion and protein folding
The results suggest that transition state ensembles could be more homogenous then recently postulated and diffusion of different parts of the molecule relative to each other is taking place on going from the denatured ensemble to the transition state.
Role of native topology investigated by multiple unfolding simulations of four SH3 domains.
Results indicate that, at least for small beta-sheet proteins, the folding mechanism is primarily defined by the native state topology, whilst specific interactions determine the statistically predominant folding route.
Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states.
Correlation of folding rates with AGADIR predictions of non- native helical structure in the diverging turn region, along with previous NMR evidence for non-native structure in this region of the unfolded state of the drkN SH3 domain, suggests that the free energy of the unfolding state also plays a role in stability.
Similarities between the spectrin SH3 domain denatured state and its folding transition state.
It is proposed that the DSE of a protein will resemble the intermediate or transition state of its nearest rate-limiting step, as a consequence of simple energetic and kinetic principles.
Circularization changes the folding transition state of the src SH3 domain.
The robustness of the src SH3-domain folding transition state to changes in topology is tested by covalently constraining regions of the protein with disulfide crosslinks and then performing kinetic analysis on point mutations in the context of these modified proteins.
Rational redesign of the folding pathway of a modular protein
This work shows that this simple architecture makes it straightforward to direct the folding pathway of a repeat protein by design, and finds that folding of wild-type myotrophin is initiated at the C-terminal repeats.


The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding.
It is suggested that the mechanism of folding ofCI2 may be a common theme in protein folding whereby fundamental folding units of larger proteins, which are modelled by the folding of CI2, form by nucleation-condensation events and coalesce, perhaps in a hierarchical manner.
Conserved residues and the mechanism of protein folding
A method based on the alignment of many sequences designed to fold into the native conformation of a protein to identify the positions where amino acids are most conserved in designed sequences is applied to chymotrypsin inhibitor 2 (CI2).
Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.
The main transition state for the folding of barnase has some fully formed secondary and tertiary structural elements in the major transition state, and barnase appears to form by a framework process, however, the fully formed framework may be preceded by a global collapse, and a unified folding scheme is presented.
Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein.
The refolding from denaturing conditions of a small four-helix bundle, the acyl-coenzyme A binding protein, has been investigated by utilizing an array of fast-reaction techniques, indicating that the different elements of structure form effectively concomitantly.
Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: observation of Hammond behavior for the gross structure of the transition state and anti-Hammond behavior for structural elements for unfolding/folding of barnase.
The structure of alpha-helix 1, which appears to be an initiation point and forms early in the folding of wild-type protein, may be radically destabilized to the extent that it forms late in the folded of mutants.
Crystal structure of a Src-homology 3 (SH3) domain
The three-dimensional struc-ture at 1.8 Å resolution of the SH3 domain of the cytoskeletal protein spectrin expressed in Escherichia coli is reported and it is suggested that a protein ligand binds to this conserved surface of SH3.
Conformational Analysis of Peptides Corresponding to β-Hairpins and a β-Sheet that Represent the Entire Sequence of the α-Spectrin SH3 Domain
Abstract In an attempt to identify potential folding initiation sites for a small, all β-protein domain, we have examined the conformational preferences in aqueous solution of peptides that span the
Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.
  • A. Fersht
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1995
The nucleation-condensation mechanism of CI2 fulfills the criteria for fast folding, and stable intermediates do form in the folding of more complex proteins, and this may be an unavoidable consequence of increasing size and nucleation at more than one site.