Change search
ReferencesLink to record
Permanent link

Direct link
The HD-exchange motions of S6 are insensitive to reversal of the protein-folding pathway
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. (Mikael Oliveberg)
(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

An increasing number of protein structures are found to encompass multiple folding nuclei, allowing their structures to be formed by several competing pathways. A typical example is the ribosomal protein S6 that comprises two folding nuclei (σ1 and σ2) defining two competing pathways in the folding energy landscape: s1→s2 and s2 →s1. The balance between the two pathways, and thus the order of folding events, is easily controlled by circular permutation. In this study we make use of this ability to manipulate the folding pathway to demonstrate that the dynamic motions of the S6 structure are independent of how the protein folds. The HD-exchange protection factors remain the same upon complete reversal of the folding order. The phenomenon arises because the HD-exchange motions and the high-energy excitations controlling the folding pathway occur at separated free-energy levels: the Boltzmann distribution of unproductive unfolding attempts samples all unfolding channels in parallel, even those that end up in excessively high barriers. Accordingly, the findings provide a simple rationale for how to interpret native-state dynamics without the need to invoke fluctuations off the normal unfolding reaction coordinate.

Keyword [en]
protein dynamics, circular permutation, transition state, energy landscape
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:su:diva-30002OAI: diva2:240407
Available from: 2009-09-28 Created: 2009-09-28 Last updated: 2010-01-14Bibliographically approved
In thesis
1. Folding of the Ribosomal protein S6: The role of sequence connectivity, overlapping foldons, and parallel pathways
Open this publication in new window or tab >>Folding of the Ribosomal protein S6: The role of sequence connectivity, overlapping foldons, and parallel pathways
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

To investigate how protein folding is affected by sequence connectivity five topological variants of the ribosomal protein S6 were constructed through circular permutation.  In these constructs, the chain connectivity (i.e. the order of secondary-structure elements) is changed without changing the native-state topology.  The effects of the permutations on the folding process were then characterised by φ-value analysis, which estimates the extent of contact formations in the transition-state ensemble.  The results show that the folding nuclei of the wild-type and permutant proteins comprises a common motif of one α-helix docking against two β-sheets, i.e. the minimal structure for folding.  However, this motif is recruited in different parts of the S6 structure depending on the permutation, either in the α1 or α2 half of the protein.  This minimal structure is not unique for S6 but can also be seen in other proteins.  As an effect of the dual nucleation possibilities, the transition-state changes describe a competition between two parallel pathways, which both include the central β-stand 1.  This strand constitutes thus a structural overlap between the two competing nuclei.  As similar overlap between competing nuclei is also seen in other proteins, I hypothesise that the coupling of several small nuclei into extended ‘super nuclei’ represents a general principle for propagating folding cooperativity across large structural distances.  Moreover, I demonstrate by NMR analysis that the existence of multiple folding nuclei renders the H/D-exchange kinetics independent of the folding pathway.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2009. 94 p.
protein folding, protein stability, two-state folding, S6, chevron plot, transition state, parallell pathways, foldon, two-channel landscape, protein engineering, H/D-exchange
National Category
Biochemistry and Molecular Biology
Research subject
urn:nbn:se:su:diva-29963 (URN)978-91-7155-939-5 (ISBN)
Public defence
2009-10-24, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper IV: ManuscriptAvailable from: 2009-10-01 Created: 2009-09-23 Last updated: 2009-09-29Bibliographically approved

Open Access in DiVA

No full text

Search in DiVA

By author/editor
Haglund, Ellinor
By organisation
Department of Biochemistry and Biophysics
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 44 hits
ReferencesLink to record
Permanent link

Direct link