Changes of Protein Folding Pathways by Circular Permutation

Haglund, Ellinor; Lindberg, Magnus; Oliveberg, Mikael

doi:10.1074/jbc.m801776200

Cited by 61 publications

(101 citation statements)

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“…S6 wt is mainly biased towards the r1 pathway, whereas the permutant P 54-55 favors the r2 pathway. [9][10][11] In this study, we use NMR spectroscopy to characterize the structure and dynamics of S6 wt and P [54][55] in solution. The results presented here shed new light on how circular permutations affect protein structure, dynamics, and stability.…”

Section: Introductionmentioning

confidence: 99%

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P^54‐55

2009

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The ribosomal protein S6 from Thermus thermophilus has served as a model system for the study of protein folding, especially for understanding the effects of circular permutations of secondary structure elements. This study presents the structure of a permutant protein, the 96-residue P [54][55] , and the structure of its 101-residue parent protein S6 wt in solution. The data also characterizes the effects of circular permutation on the backbone dynamics of S6. Consistent with crystallographic data on S6 wt , the overall solution structures of both P 54-55 and S6 wt show a b-sheet of four antiparallel b-strands with two a-helices packed on one side of the sheet. In clear contrast to the crystal data, however, the solution structure of S6 wt reveals a disordered loop in the region between b-strands 2 and 3 (Leu43-Phe60) instead of a well-ordered stretch and associated hydrophobic mini-core observed in the crystal structure. Moreover, the data for P [54][55] show that the joined wild-type N-and C-terminals form a dynamically robust stretch with a hairpin structure that complies with the in silico design. Taken together, the results explain why the loop region of the S6 wt structure is relatively insensitive to mutational perturbations, and why P 54-55 is more stable than S6 wt : the permutant incision at Lys54-Asp55 is energetically neutral by being located in an already disordered loop whereas the new hairpin between the wild-type N-and C-termini is stabilizing.

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Section: Introductionmentioning

confidence: 99%

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P^54‐55

2009

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“…Folding of large proteins would, in principle, simplify folding of smaller proteins that are structurally overlapping to parallel. However, from studies of S6 where the bias between the 1 and 2 pathways has systematically been shifted by circular permutation, it is apparent that the edge strand ␤2 never participates in the nucleation process (6,8,10). Despite being an integral part of the native sheet, ␤2 appears to be outside the cooperative unit of S6 (Fig.…”

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“…Even so, the nucleation events of 1 and 2 are not entirely independent, but are coupled by a structural overlap in the form of the shared strand ␤1 (10). Such overlap between competing nuclei stands out as an efficient way of linking small cooperative subunits into larger structures without compromising global cooperativity or folding kinetics (10). Folding of large proteins would, in principle, simplify folding of smaller proteins that are structurally overlapping to parallel.…”

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Trimming Down a Protein Structure to Its Bare Foldons

Haglund

Danielsson

Saraboji

et al. 2012

Journal of Biological Chemistry

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Background: Structural cooperativity safeguards native proteins but is yet poorly understood. Results: Guided by the folding nucleus, we reduced the size of a protein without compromising its structural integrity. Conclusion: Folding nuclei are used in a modular fashion to extend or reduce the cooperative units of proteins. Significance: Understanding cooperativity is crucial for understanding protein function and for rational design of structural properties.

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“…In light of these previous data, the folding of the SAP97 PDZ2 domain may be viewed as a missing link between these two extreme folding pathways and reconciles apparently contrasting results. Because energy landscapes are funneled, folding may occur via alternative folding nuclei (45,46). When and if the forces stabilizing such nuclei are balanced, as in the case of pwPDZ2, small perturbations of reaction conditions may result in rerouting through an alternative folding pathway.…”

Section: Discussionmentioning

confidence: 99%

The Plastic Energy Landscape of Protein Folding

Haq

Jürgens

Celestine

et al. 2010

Journal of Biological Chemistry

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Protein domains usually fold without or with only transiently populated intermediates, possibly to avoid misfolding, which could result in amyloidogenic disease. Whether observed intermediates are productive and obligatory species on the folding reaction pathway or dispensable by-products is a matter of debate. Here, we solved the crystal structure of a small protein domain, SAP97 PDZ2 I342W C378A, and determined its folding pathway. The presence of a folding intermediate was demonstrated both by single and double-mixing kinetic experiments using urea-induced (un)folding as well as ligand-induced folding. This protein domain was found to fold via a triangular scheme, where the folding intermediate could be either on-or off-pathway, depending on the experimental conditions. Furthermore, we found that the intermediate was present at equilibrium, which is rarely seen in folding reactions of small protein domains. The folding mechanism observed here illustrates the roughness and plasticity of the protein folding energy landscape, where several routes may be employed to reach the native state. The results also reconcile the folding mechanisms of topological variants within the PDZ domain family.The role and even the presence of intermediates in the folding reactions of protein domains are under constant debate (1, 2). Domains that fold without populated intermediates appear to have been selected for during evolution, possibly to avoid misfolding (3). Yet the polymeric nature of proteins implies their folding energy landscape to be rough (4), and clearly, intermediates do occur, sometimes as high energy species, which can only be indirectly monitored (5-7) but sometimes as low energy species, which can be observed directly (8 -14). One problem with studying these intermediates is that they are only transiently populated and thus difficult to isolate and characterize. A successful strategy to isolate folding intermediates has been to destabilize the native state by mutation, which works if the intermediate state is less destabilized by the modification (9,11,15,16). Further, general mechanisms of folding may be deduced if several members of a protein family are compared, for example regarding the influence of sequence and topology on the folding reaction (17-20). We have used this strategy on the PDZ domain family of proteins (21-24) and demonstrated that the folding reaction of all members investigated so far involves an intermediate, which at least in one case is on-pathway (6), often high energy, but off-pathway and low energy compared with the denatured state for a circularly permutated bacterial PDZ domain (25). Here we describe the folding reaction of SAP97 PDZ2 I342W C378A, referred to as pseudo-wild type PDZ2 (pwPDZ2). A triangular scheme explains the folding of this pwPDZ2. The intermediate in the scheme is of low energy and either on-or off-pathway depending on experimental conditions. The folding reaction of pwPDZ2 thus reflects the plasticity of the energy landscape for protein folding. We also discuss how ...

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Changes of Protein Folding Pathways by Circular Permutation

Cited by 61 publications

References 44 publications

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P^54‐55

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P^54‐55

Trimming Down a Protein Structure to Its Bare Foldons

The Plastic Energy Landscape of Protein Folding

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Changes of Protein Folding Pathways by Circular Permutation

Cited by 61 publications

References 44 publications

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P54‐55

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P54‐55

Trimming Down a Protein Structure to Its Bare Foldons

The Plastic Energy Landscape of Protein Folding

Contact Info

Product

Resources

About

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P^54‐55

Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P^54‐55