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Folding of the Ribosomal protein S6: The role of sequence connectivity, overlapping foldons, and parallel pathways
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. (Mikael Oliveberg)
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.
Keyword [en]
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
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-29963ISBN: 978-91-7155-939-5 (print)OAI: oai:DiVA.org:su-29963DiVA: diva2:236575
Public defence
2009-10-24, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
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
List of papers
1. Identification of the minimal protein-folding nucleus through loop-entropy perturbations.
Open this publication in new window or tab >>Identification of the minimal protein-folding nucleus through loop-entropy perturbations.
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2006 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 103, no 11, 4083-4088 p.Article in journal (Refereed) Published
Abstract [en]

To explore the plasticity and structural constraints of the protein-folding nucleus we have constructed through circular permutation four topological variants of the ribosomal protein S6. In effect, these topological variants represent entropy mutants with maintained spatial contacts. The proteins were characterized at two complementary levels of detail: by φ-value analysis estimating the extent of contact formation in the transition-state ensemble and by Hammond analysis measuring the site-specific growth of the folding nucleus. The results show that, although the loop-entropy alterations markedly influence the appearance and structural location of the folding nucleus, it retains a common motif of one helix docking against two strands. This nucleation motif is built around a shared subset of side chains in the center of the hydrophobic core but extends in different directions of the S6 structure following the permutant-specific differences in local loop entropies. The adjustment of the critical folding nucleus to alterations in loop entropies is reflected by a direct correlation between the φ-value change and the accompanying change in local sequence separation.

Keyword
circular permutations, phi-values, transition state
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:su:diva-29976 (URN)10.1073/pnas.0508863103 (DOI)
Available from: 2009-09-25 Created: 2009-09-25 Last updated: 2017-12-13Bibliographically approved
2. Common motifs and topological effects in the protein folding transition state.
Open this publication in new window or tab >>Common motifs and topological effects in the protein folding transition state.
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2006 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, ISSN 0022-2836, Vol. 359, no 4, 1075-1085 p.Article in journal (Refereed) Published
Abstract [en]

Through extensive experiment, simulation, and analysis of protein S6 (IRIS), we find that variations in nucleation and folding pathway between circular permutations are determined principally by the restraints of topology and specific nucleation, and affected by changes in chain entropy. Simulations also relate topological features to experimentally measured stabilities. Despite many sizable changes in Φ values and the structure of the transition state ensemble that result from permutation, we observe a common theme: the critical nucleus in each of the mutants share a subset of residues that can be mapped to the critical nucleus residues of the wild-type. Circular permutations create new N and C termini, which are the location of the largest disruption of the folding nucleus, leading to a decrease in both Φ values and the role in nucleation. Mutant nuclei are built around the wild-type nucleus but are biased towards different parts of the S6 structure depending on the topological and entropic changes induced by the location of the new N and C termini.

Keyword
ensemble, simulatoin, circular permutation, protein S6
Identifiers
urn:nbn:se:su:diva-29977 (URN)10.1016/j.jmb.2006.04.015 (DOI)
Available from: 2009-09-25 Created: 2009-09-25 Last updated: 2017-12-13Bibliographically approved
3. Changes of protein folding pathways by circular permutation. Overlapping nuclei promote global cooperativity.
Open this publication in new window or tab >>Changes of protein folding pathways by circular permutation. Overlapping nuclei promote global cooperativity.
2008 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 283, no 41, 27904-27915 p.Article in journal (Refereed) Published
Abstract [en]

The evolved properties of proteins are not limited to structure and stability but also include their propensity to undergo local conformational changes. The latter, dynamic property is related to structural cooperativity and is controlled by the folding-energy landscape. Here we demonstrate that the structural cooperativity of the ribosomal protein S6 is optimized by geometric overlap of two competing folding nuclei: they both include the central beta-strand 1. In this way, folding of one nucleus catalyzes the formation of the other, contributing to make the folding transition more concerted overall. The experimental evidence is provided by an extended set of circular permutations of S6 that allows quantitative analysis of pathway plasticity at the level of individual side chains. Because similar overlap between competing nuclei also has been discerned in other proteins, we hypothesize that the coupling of several small nuclei into extended "supernuclei" represents a general principle for propagating folding cooperativity across large structural distances.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:su:diva-29978 (URN)10.1074/jbc.M801776200 (DOI)000259719200061 ()
Available from: 2009-09-25 Created: 2009-09-25 Last updated: 2017-12-13Bibliographically approved
4. The HD-exchange motions of S6 are insensitive to reversal of the protein-folding pathway
Open this publication in new window or tab >>The HD-exchange motions of S6 are insensitive to reversal of the protein-folding pathway
(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
protein dynamics, circular permutation, transition state, energy landscape
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-30002 (URN)
Available from: 2009-09-28 Created: 2009-09-28 Last updated: 2010-01-14Bibliographically approved

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