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Co-factor dependent conformational switching of GTPases
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. (Ehrenberg)
Laboratoire d’Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. (Ehrenberg)
2008 (English)In: Biophysical Journal, ISSN 0006-3495, Biophysical J, ISSN 0006-3495, Vol. 95, no 4, 1704-1715 p.Article in journal (Refereed) Published
Abstract [en]

This theoretical work covers structural and biochemical aspects of nucleotide binding and GDP/GTP exchange of GTP hydrolases belonging to the family of small GTPases. Current models of GDP/GTP exchange regulation are often based on two specific assumptions. The first is that the conformation of a GTPase is switched by the exchange of the bound nucleotide from GDP to GTP or vice versa. The second is that GDP/GTP exchange is regulated by a guanine nucleotide exchange factor, which stabilizes a GTPase conformation with low nucleotide affinity. Since, however, recent biochemical and structural data seem to contradict this view, we present a generalized scheme for GTPase action. This novel ansatz accounts for those important cases when conformational switching in addition to guanine nucleotide exchange requires the presence of cofactors, and gives a more nuanced picture of how the nucleotide exchange is regulated. The scheme is also used to discuss some problems of interpretation that may arise when guanine nucleotide exchange mechanisms are inferred from experiments with analogs of GTP, like GDPNP, GDPCP, and GDP gamma S.

Place, publisher, year, edition, pages
2008. Vol. 95, no 4, 1704-1715 p.
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
URN: urn:nbn:se:uu:diva-97263DOI: 10.1529/biophysj.107.127290ISI: 000257889400014PubMedID: 18502805OAI: oai:DiVA.org:uu-97263DiVA: diva2:172122
Available from: 2008-05-07 Created: 2008-05-07 Last updated: 2009-10-19Bibliographically approved
In thesis
1. A Few Strokes to the Family Portrait of Translational GTPases
Open this publication in new window or tab >>A Few Strokes to the Family Portrait of Translational GTPases
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Protein biosynthesis is a core process in all living organisms. Assembly of the protein chain from aminoacids is catalysed by the ribosome, ancient and extremely complex macromolecular machine. Several different classes of accessory molecules are involved in translation, and one set of them, called translational GTPases (trGTPases), was in the focus of this work.

In this thesis properties of two trGTPases– EF-G and eRF3 - were studied by means of direct biochemical experiments. EF-G is a bacterial trGTPase involved in two steps of translation: translocation and ribosomal recycling. Translocation is a process of the ribosomal movement along the mRNA, and recycling as the step when upon completion of the protein ribosome is released from the mRNA via splitting in two ribosomal subunits. We found that off the ribosome EF-G has similar affinities to GDP and GTP, and thus given the predominance of the latter in the cell, EF-G should be present mostly in the complex with GTP. However, binding to the ribosome increases factors affinity to GTP drastically, ensuring that it is in the GTP-bound state. GDP can not promote neither translocation, not recycling, and GDPNP can not promote recycling. It can, however, promote translocation, but in so doing it results in an intermediate ribosomal state and translocation process can be reversed by addition of GDP, which is not the case for the EF-G•GTP-catalyzed reaction.

The second trGTPase we investigated is eukaryotic termination factor eRF3. This protein together with another factor, eRF1, is involved translation termination, which is release of the synthesized protein from the ribosome. We demonstrateed, that eRF3 alone has basically no propensity to bind GTP and thus resides in the GDP-bound state. Complex formation between eRF1 and eRF3 promotes GTP binding by the latter, resulting in the formation of the ternary complex eRF1•eRF3•GTP, which in turn is catalyzing the termination event.

Experimental investigations of trGTPases where rationalized within a generalized thermodynamical framework, accommoding the existent experimental observations, both structural and biochemical.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2008. 86 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 435
Molecular biology, translation, GTPase, EF-G, eRF3, Molekylärbiologi
urn:nbn:se:uu:diva-8844 (URN)978-91-554-7210-8 (ISBN)
Public defence
2008-05-28, B21, ICM BMC, Husargatan 3, Uppsala, 13:00
Available from: 2008-05-07 Created: 2008-05-07Bibliographically approved

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