ISB Home

- Article -

Volume 5

Full article

In Silico Biology 5, 0028 (2005); ©2005, Bioinformation Systems e.V.  

Collection of soluble variants of membrane proteins for transcriptomics and proteomics

Steffen Möller1,2,*, Eilhard Mix3, Martin Blüggel4, Pablo Serrano-Fernández1, Dirk Koczan1, Vasilis Kotsikoris1,5, Manfred Kunz5, Michael Watson6, Jens Pahnke7, Harald Illges8,9, Michael Kreutzer2, Stefan Mikkat2,10, Hans-Jürgen Thiesen1, Michael O. Glocker2, Uwe K. Zettl3 and Saleh M. Ibrahim1

University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany
 University of Rostock, Proteome Center Rostock, Joachim-Jungius-Str. 9, 18055 Rostock, Germany
University of Rostock, Department of Neurology, Gehlsheimer Str. 20, 18147 Rostock, Germany
Protagen AG, Emil-Figge-Str. 76 A, 44227 Dortmund, Germany
University of Rostock, Department of Dermatology, Augustenstr. 20, 18055 Rostock, Germany
Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN, UK
Department of Pathology, University Hospital Zurich, Schmelzbergstrasse 1, 8091 Zürich, Switzerland
University of Konstanz, Department of Biology, Immunology, Universitätsstr. 10, 78457 Konstanz, Germany
 Biotechnologie Institut Thurghau, Konstanzer Str. 19, 8274 Tägerwilen, Switzerland
10University of Rostock, Core-facility Proteomics, Joachim-Jungius-Str. 9, 18055 Rostock, Germany

* Corresponding author; Email:

Edited by E. Wingender; received January 04, 2005; revised and accepted March 16, 2005; published April 05, 2005


The existence of a soluble splice variant for a gene encoding a transmembrane protein suggests that this gene plays a role in intercellular signalling, particularly in immunological processes. Also, the absence of a splice variant of a reported soluble variant suggests exclusive control of the solubilisation by proteolytic cleavage. Soluble splice variants of membrane proteins may also be interesting targets for crystallisation as their structure may be expected to preserve, at least partially, their function as integral membrane proteins, whose structures are most difficult to determine.

This paper presents a dataset derived from the literature in an attempt to collect all reported soluble variants of membrane proteins, be they splice variants or shedded. A list of soluble variants is derived in silico from Ensembl. These are checked on their presence in multiple organisms and their number of membranespanning regions is inspected. The findings then are confirmed by a comparison with identified proteins of a recent global proteomics study of human blood plasma. Finally, a tool to determine novel soluble variants by proteomics is provided.


Keywords: soluble membrane proteins, splice variants, mass spectrometry, proteolytic cleavage, ectodomain shedding, human, mouse, rat, immune response