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Structure, prediction, evolution and genome wide studies of membrane proteins
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

α-helical membrane proteins constitute 20-30% of all proteins in a cell and are involved in many essential cellular functions. The structure is only known for a few hundred of them, which makes structural models important. The most common structural model of a membrane protein is the topology which is a two-dimensional representation of the structure.

This thesis is focused on three different aspects of membrane protein structure: improving structural predictions of membrane proteins, improving the level of detail of structural models and the concept of dual topology.

It is possible to improve topology models of membrane proteins by including experimental information in computer predictions. This was first performed in Escherichia coli and, by using homology, it was possible to extend the results to 225 prokaryotic organisms. The improved models covered ~80% of the membrane proteins in E. coli and ~30% of other prokaryotic organisms.

However, the traditional topology concept is sometimes too simple for complex membrane protein structures, which create a need for more detailed structural models. We created two new machine learning methods, one that predicts more structural features of membrane proteins and one that predicts the distance to the membrane centre for the amino acids. These methods improve the level of detail of the structural models.

The final topic of this thesis is dual topology and membrane protein evolution. We have studied a class of membrane proteins that are suggested to insert either way into the membrane, i.e. have a dual topology. These protein families might explain the frequent occurrence of internal symmetry in membrane protein structures.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik , 2007. , 47 p.
National Category
Theoretical Chemistry
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-7027ISBN: 978-91-7155-489-5 (print)OAI: oai:DiVA.org:su-7027DiVA: diva2:197500
Public defence
2007-09-24, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2007-08-31 Created: 2007-08-29 Last updated: 2011-09-23Bibliographically approved
List of papers
1. Global topology analysis of the Escherichia coli inner membrane proteome
Open this publication in new window or tab >>Global topology analysis of the Escherichia coli inner membrane proteome
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2005 In: Science, ISSN 0193-4511, Vol. 308, no 5726, 1321-1323 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24420 (URN)
Note
Part of urn:nbn:se:su:diva-7027Available from: 2007-08-31 Created: 2007-08-29Bibliographically approved
2. Experimentally constrained topology models for 51,208 bacterial inner membrane proteins.
Open this publication in new window or tab >>Experimentally constrained topology models for 51,208 bacterial inner membrane proteins.
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2005 (English)In: J Mol Biol, ISSN 0022-2836, Vol. 352, no 3, 489-94 p.Article in journal (Refereed) Published
Keyword
Algorithms, Bacteria/chemistry/genetics, Bacterial Proteins/*chemistry/genetics, Databases; Genetic, Escherichia coli/chemistry/genetics, Escherichia coli Proteins/chemistry/genetics, Membrane Proteins/*chemistry/genetics, Models; Molecular, Open Reading Frames, Protein Structure; Secondary
Identifiers
urn:nbn:se:su:diva-18890 (URN)16120447 (PubMedID)
Available from: 2007-12-27 Created: 2007-12-27 Last updated: 2011-01-12Bibliographically approved
3. A study of the membrane-water interface region of membrane proteins
Open this publication in new window or tab >>A study of the membrane-water interface region of membrane proteins
2005 In: Journal of Molecular Biology, ISSN 0022-2836, Vol. 346, no 1, 377-385 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24422 (URN)
Note
Part of urn:nbn:se:su:diva-7027Available from: 2007-08-31 Created: 2007-08-29Bibliographically approved
4. Structural classification and prediction of reentrant regions in α-helical transmembrane proteins: Application to complete genomes
Open this publication in new window or tab >>Structural classification and prediction of reentrant regions in α-helical transmembrane proteins: Application to complete genomes
2006 In: Journal of Molecular Biology, ISSN 0022-2836, Vol. 361, no 3, 591-603 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24423 (URN)
Note
Part of urn:nbn:se:su:diva-7027Available from: 2007-08-31 Created: 2007-08-29Bibliographically approved
5. ZPRED: Predicting the distance to the membrane center for residues in α-helical membrane proteins
Open this publication in new window or tab >>ZPRED: Predicting the distance to the membrane center for residues in α-helical membrane proteins
2006 In: Bioinformatics, ISSN 1367-4803, Vol. 22, no 14, e191-196 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24424 (URN)
Note
Part of urn:nbn:se:su:diva-7027Available from: 2007-08-31 Created: 2007-08-29Bibliographically approved
6. Identification and evolution of dual-topology membrane proteins
Open this publication in new window or tab >>Identification and evolution of dual-topology membrane proteins
2006 (English)In: Nature Structural & Molecular Biology, ISSN 1545-9993, E-ISSN 1545-9985, Vol. 13, no 2, 112-116 p.Article in journal (Refereed) Published
Abstract [en]

Integral membrane proteins are generally believed to have unique membrane topologies. However, it has been suggested that dual-topology proteins that adopt a mixture of two opposite orientations in the membrane may exist. Here we show that the membrane orientations of five dual-topology candidates identified in Escherichia coli are highly sensitive to changes in the distribution of positively charged residues, that genes in families containing dual-topology candidates occur in genomes either as pairs or as singletons and that gene pairs encode two oppositely oriented proteins whereas singletons encode dual-topology candidates. Our results provide strong support for the existence of dual-topology proteins and shed new light on the evolution of membrane-protein topology and structure.

National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-23012 (URN)10.1038/nsmb1057 (DOI)
Available from: 2006-10-29 Created: 2006-10-29 Last updated: 2011-09-23Bibliographically approved

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