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Protein Folding Studies on the Ribosomal Protein S6: the Role of Entropy in Nucleation
Umeå University, Faculty of Science and Technology, Chemistry.
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

One of the most challenging tasks remaining in the field of biochemistry is the one of understanding how the information within the amino acid sequence of proteins translates into a unique structure. Solving this problem would lead to endless possibilities for application in the medical and biotechnology industry.

Many decades ago scientists realized that the process that facilitates the folding of a polypeptide chain could not be random and happen by chance; there needs to be direction in the folding free energy landscape. This landscape is defined by the thermodynamic factors entropy and enthalpy. The contribution made by enthalpy i.e. the contact energies from intra- and intermolecular interactions have been extensively investigated by various mutational studies. The influence of entropy on the other hand, is less well understood. My work focuses on the effect of altering the entropic components of forming the various parts of a known protein scaffold. This is done by genetic engineering in combination with biophysical characterisation and analysis. The results show effects on protein folding rates as well as on the pathway for nucleation and emphasis the ability of the folding landscape to readjust to entropic variations. Proteins are therefore not required to fold along a unique route to their final structure but can do so in several ways. The folding pathways we observe today have hence likely evolved as an adaptation to biological demands.

Place, publisher, year, edition, pages
Umeå: Kemi , 2005. , 150 p.
Keyword [en]
Biochemistry, protein folding, circular permutation, topology, connectivity, entropy, protein stability, chevron plot
Keyword [sv]
Biokemi
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:umu:diva-535ISBN: 91-7305-890-4 (print)OAI: oai:DiVA.org:umu-535DiVA: diva2:143745
Public defence
2005-06-03, KB3A9, KBC, Umeå universitet, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2005-05-10 Created: 2005-05-10 Last updated: 2009-08-13Bibliographically approved
List of papers
1. Folding of circular permutants with decreased contact order: general trend balanced by protein stability
Open this publication in new window or tab >>Folding of circular permutants with decreased contact order: general trend balanced by protein stability
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2001 (English)In: Journal of Molecular Biology, ISSN 0022-2836, Vol. 314, no 4, 891-900 p.Article in journal (Refereed) Published
Abstract [en]

To examine the influence of contact order and stability on the refolding rate constant for two-state proteins, we have analysed the folding kinetics of the small β-α-β protein S6 and two of its circular permutants with relative contact orders of 0.19, 0.15 and 0.12. Data reveal a small but significant increase of the refolding rate constant (log kf) with decreasing contact order. At the same time, the decreased contact order is correlated to losses in global stability and alterations of the folding nucleus. When the differences in stability are accounted for by addition of Na2SO4 or by comparison of the folding kinetics at the transition mid-point, the dependence between log kf and contact order becomes stronger and follows the general correlation for two-state proteins. The observation emphasizes the combined action of topology and stability in controlling the rate constant of protein folding.

Keyword
protein folding, rate constants, two-state proteins, topology, protein stability
Identifiers
urn:nbn:se:umu:diva-8780 (URN)doi:10.1006/jmbi.2001.5186 (DOI)
Note
Jeanette Hargbo.Available from: 2008-02-12 Created: 2008-02-12 Last updated: 2009-08-13Bibliographically approved
2. Complete change of the protein folding transition state upon circular permutation
Open this publication in new window or tab >>Complete change of the protein folding transition state upon circular permutation
2002 (English)In: Nature Structural Biology, ISSN 1072-8368, Vol. 9, 818-22 p.Article in journal (Refereed) Published
Abstract [en]

Reversing the loop lengths of the small protein S6 by circular permutation has a dramatic effect on the transition state structure: it changes from globally diffuse to locally condensed. The phenomenon arises from a biased dispersion of the contact energies. Stability data derived from point mutations throughout the S6 structure show that interactions between residues that are far apart in sequence are stronger than those that are close. This entropy compensation drives all parts of the protein to fold simultaneously and produces the diffuse transition-state structure typical for two-state proteins. In the circular permutant, where strong contacts and short sequence separations are engineered to concur, the transition state becomes atypically condensed and polarized. Taken together with earlier findings that S6 may also fold by a 'collapsed' trajectory with an intermediate, the results suggest that this protein may fold by a multiplicity of mechanisms. The observations indicate that the diffuse transition state of S6 is not required for folding but could be an evolutionary development to optimize cooperativity.

Identifiers
urn:nbn:se:umu:diva-8790 (URN)doi:10.1038/nsb847 (DOI)
Note
Jeanette HargboAvailable from: 2008-02-12 Created: 2008-02-12 Last updated: 2009-08-13Bibliographically approved
3. Qualitative assessment of φ values for proteins with complex folding free energy profiles
Open this publication in new window or tab >>Qualitative assessment of φ values for proteins with complex folding free energy profiles
Manuscript (Other academic)
Identifiers
urn:nbn:se:umu:diva-4586 (URN)
Available from: 2005-05-10 Created: 2005-05-10 Last updated: 2010-01-13Bibliographically approved
4. Panning for the minimal protein folding nucleus through loop-entropy perturbations
Open this publication in new window or tab >>Panning for the minimal protein folding nucleus through loop-entropy perturbations
Manuscript (Other academic)
Identifiers
urn:nbn:se:umu:diva-4587 (URN)
Available from: 2005-05-10 Created: 2005-05-10 Last updated: 2010-01-13Bibliographically approved

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