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A global topology map of the Saccharomyces cerevisiae membrane proteome
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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 30, 11142-11147 p.Article in journal (Refereed) Published
Abstract [en]

The yeast Saccharomyces cerevisiae is, arguably, the best understood eukaryotic model organism, yet comparatively little is known about its membrane proteome. Here, we report the cloning and expression of 617 S. cerevisiae membrane proteins as fusions to a C-terminal topology reporter and present experimentally constrained topology models for 546 proteins. By homology, the experimental topology information can be extended to ≈15,000 membrane proteins from 38 fully sequenced eukaryotic genomes.

Place, publisher, year, edition, pages
2006. Vol. 103, no 30, 11142-11147 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:su:diva-24329DOI: 10.1073/pnas.0604075103OAI: oai:DiVA.org:su-24329DiVA: diva2:197243
Note
Part of urn:nbn:se:su:diva-6875Available from: 2007-05-24 Created: 2007-05-15 Last updated: 2017-12-13Bibliographically approved
In thesis
1. Topology Prediction of Membrane Proteins: Why, How and When?
Open this publication in new window or tab >>Topology Prediction of Membrane Proteins: Why, How and When?
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Membrane proteins are of broad interest since they constitute a large fraction of the proteome in all organisms, up to 20-30%. They play a crucial role in many cellular processes mediating information flow and molecular transport across otherwise nearly impermeable membranes. Traditional three-dimensional structural analyses of membrane proteins are difficult to perform, which makes studies of other structural aspects important. The topology of an α-helical membrane protein is a two-dimensional description of how the protein is embedded in the membrane and gives valuable information on both structure and function.

This thesis is focused on predicting the topology of α-helical membrane proteins and on assessing and improving the prediction accuracy. Reliability scores have been derived for a number of prediction methods, and have been integrated into the widely used TMHMM predictor. The reliability score makes it possible to estimate the trustworthiness of a prediction.

Mapping the full topology of a membrane protein experimentally is time-consuming and cannot be done on a genome-wide scale. However, determination of the location of one part of a membrane protein relative to the membrane is feasible. We have analyzed the impact of incorporating such experimental information a priori into TMHMM predictions and show that the accuracy increases significantly. We further show that the C-terminal location of a membrane protein (inside or outside) is the optimal information to use as a constraint in the predictions.

By combining experimental techniques for determining the C-terminal location of membrane proteins with topology predictions, we have produced reliable topology models for the majority of all membrane proteins in the model organisms E. coli and S. cerevisiae. The results were further expanded to ~15,000 homologous proteins in 38 fully sequenced eukaryotic genomes. This large set of reliable topology models should be useful, in particular as the structural data for eukaryotic membrane proteins is very limited.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik, 2007. 61 p.
Keyword
membrane protein, topology prediction, bioinformatics
National Category
Theoretical Chemistry
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-6875 (URN)91-7155-397-5 (ISBN)
Public defence
2007-06-15, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00
Opponent
Supervisors
Available from: 2007-05-24 Created: 2007-05-15Bibliographically approved
2. What’s in? What’s out? And how did it get there?: Studies on topologies and insertion of membrane proteins
Open this publication in new window or tab >>What’s in? What’s out? And how did it get there?: Studies on topologies and insertion of membrane proteins
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Because of their hydrophobic and hydrophilic nature and the need for a lipid bilayer for retaining the native structure, membrane proteins are hard to study. Nevertheless, they are important, as many of our diseases are related to membrane proteins and around 60% of the different pharmaceutical drugs are directed against a membrane proteins [1]. There are many ways to study a protein, you can study function, structure, how the protein is targeted and inserted into its specific organelle, the interactions with other proteins or ligands etc. In the absence of a high-resolution structure, a topology model for a membrane protein is often useful. We have obtained reliable topologies for 546 of the membrane proteins going through the secretory pathways in S. cerevisiae by combining experimental data with topology prediction programs. In addition we have produced topology models for over 15,000 membrane proteins from 38 sequenced eukaryotic genomes using homology to the experimentally determined group.

We also examined the growth rates and tolerance to certain stress conditions for our large set of clones that over-express membrane proteins. This provides important information both for structural studies of membrane proteins where large amounts of protein is needed for further studies, and for getting some insight in the function of specific proteins. Finally we have studied the integration of membrane proteins by the Tim23 translocon in the inner membrane of mitochondria. We have investigated the hydrophobicity required for efficient integration of transmembrane (TM) helices by Tim23. From this data we have derived an in vivo hydrophobicity scale for the insertion of different amino acids into the inner membrane of the mitochondria, and have made a comparison with a previously determined hydrophobicity scale for the ER translocon Sec61. We concluded that charged residues flanking the TM segment are of major importance for insertion into the membrane.

We therefore further investigated the importance of charged residues flanking the first, weakly hydrophobic, TM segment in the mitochondrial inner membrane protein Mgm1p with regard to membrane insertion by the Tim23 complex.

Place, publisher, year, edition, pages
Stockholm: Department of biochemistry and biophysics, Stockholm University, 2010. 72 p.
Keyword
membrane protein, topology, yeast, mitochondria, TIM23
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-42321 (URN)978-91-7447-138-0 (ISBN)
Public defence
2010-10-22, 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 3: Manuscript. Paper 4: ManuscriptAvailable from: 2010-09-30 Created: 2010-08-24 Last updated: 2012-01-09Bibliographically approved

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