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Identification of novel sphingolipid-binding motifs in mammalian membrane proteins
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. (Gunnar von Heijne)
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Specific interactions between transmembrane proteins and sphingolipids is a poorly understood phenomenon, and only a couple of instances have been identified. The best characterized example is the sphingolipid-binding motif VXXTLXXIY found in the transmembrane helix of the vesicular transport protein p24. Here, we have used a simple motif- probability algorithm (MOPRO) to identify proteins that contain putative sphingolipid-binding motifs in a dataset comprising full proteomes from mammalian organisms. Four selected candidate proteins all tested positive for sphingolipid binding in a photoaffinity assay. The putative sphingolipid-binding motifs are noticeably enriched in the 7TM family of G-protein coupled receptors, predominantly in transmembrane helix 6. 

Keyword [en]
sphingolipid;, transmembrane helix
National Category
Bioinformatics (Computational Biology)
Research subject
Biochemistry towards Bioinformatics
Identifiers
URN: urn:nbn:se:su:diva-101791OAI: oai:DiVA.org:su-101791DiVA: diva2:705529
Available from: 2014-03-17 Created: 2014-03-17 Last updated: 2014-03-24
In thesis
1. Protein Interactions from the Molecular to the Domain Level
Open this publication in new window or tab >>Protein Interactions from the Molecular to the Domain Level
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes.

Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes.

The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level.

In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2014. 52 p.
Keyword
Protein interactions, protein domains, membrane proteins
National Category
Bioinformatics (Computational Biology)
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-101795 (URN)978-91-7447-854-9 (ISBN)
Public defence
2014-04-25, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
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Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

Available from: 2014-04-03 Created: 2014-03-17 Last updated: 2014-07-07Bibliographically approved

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