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Theoretical studies of Membrane Proteins: Properties, Prediction Methods and Genome-wide analysis
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
1999 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Membrane proteins are a large and important class of proteins. They are responsible for several of the key functions in a living cell, e.g. transport of nutrients and ions, cell-cell signaling, and cell-cell adhesion.

Despite their importance it has not been possible to study their structure and organization in much detail because of the difficulty to obtain 3D structures.

In this thesis theoretical studies of membrane protein sequences and structures have been carried out by analyzing existing experimental data. The data comes from several sources including sequence databases, genome sequencing projects, and 3D structures. Prediction of the membrane spanning regions by hydrophobicity analysis is a key technique used in several of the studies. A novel method for this is also presented and compared to other methods.

The primary questions addressed in the thesis are: What properties are common to all membrane proteins? What is the overall architecture of a membrane protein? What properties govern the integration into the membrane? How many membrane proteins are there and how are they distributed in different organisms? Several of the findings have now been backed up by experiments.

An analysis of the large family of G-protein coupled receptors pinpoints differences in length and amino acid composition of loops between proteins with and without a signal peptide and also differences between extra- and intracellular loops. Known 3D structures of membrane proteins have been studied in terms of hydrophobicity, distribution of secondary structure and amino acid types, position specific residue variability, and differences between loops and membrane spanning regions.

An analysis of several fully and partially sequenced genomes from eukaryotes, prokaryotes, and archaea has been carried out. Several differences in the membrane protein content between organisms were found, the most important being the total number of membrane proteins and the distribution of membrane proteins with a given number of transmembrane segments. Of the properties that were found to be similar in all organisms, the most obvious is the bias in the distribution of positive charges between the extra- and intracellular loops.

Finally, an analysis of homologues to membrane proteins with known topology uncovered two related, multi-spanning proteins with opposite predicted orientations. The predicted topologies were verified experimentally, providing a first example of "divergent topology evolution".

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik , 1999. , 48 p.
Keyword [en]
Biochemistry, Biology
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:su:diva-30ISBN: 91-7265-012-5 (print)OAI: oai:DiVA.org:su-30DiVA: diva2:192167
Public defence
1999-11-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00
Opponent
Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved
List of papers
1. Properties of N-terminal tails in G-protein coupled receptors - a statistical study
Open this publication in new window or tab >>Properties of N-terminal tails in G-protein coupled receptors - a statistical study
1995 In: Protein engineering, ISSN 1460-213X, Vol. 8, 693-698 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23454 (URN)
Note
Part of urn:nbn:se:su:diva-30Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved
2. Prediction of transmembrane α-helices in prokaryotic membrane proteins: the dense alignment surface method
Open this publication in new window or tab >>Prediction of transmembrane α-helices in prokaryotic membrane proteins: the dense alignment surface method
Show others...
1997 In: Protein engineering, ISSN 1460-213X, Vol. 10, 673-676 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23455 (URN)
Note
Part of urn:nbn:se:su:diva-30Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved
3. Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria.
Open this publication in new window or tab >>Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria.
Show others...
1997 In: Protein science, ISSN 1469-896X, Vol. 6, no 4, 808-815 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23456 (URN)
Note
Part of urn:nbn:se:su:diva-30Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved
4. Architecture of β-barrel membrane proteins: Analysis of trimeric porins
Open this publication in new window or tab >>Architecture of β-barrel membrane proteins: Analysis of trimeric porins
Show others...
1998 In: Protein science, ISSN 1469-896X, Vol. 7, no 9, 2026-2032 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23457 (URN)
Note
Part of urn:nbn:se:su:diva-30Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved
5. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms.
Open this publication in new window or tab >>Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms.
1998 In: Protein science, ISSN 1469-896X, Vol. 7, no 4, 1029-1038 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23458 (URN)
Note
Part of urn:nbn:se:su:diva-30Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved
6. Divergent evolution of membrane protein topology: The Escherichia coli RnfA and RnfE homologues.
Open this publication in new window or tab >>Divergent evolution of membrane protein topology: The Escherichia coli RnfA and RnfE homologues.
1999 In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, Vol. 96, no 15, 8540-8544 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23459 (URN)
Note
Part of urn:nbn:se:su:diva-30Available from: 2004-01-29 Created: 2004-01-29Bibliographically approved

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