Collection of Soluble Variants of Membrane Proteins for Transcriptomics and Proteomics

Article type: Research Article

Authors: Möller, Steffen^; | Mix, Eilhard | Blüggel, Martin | Serrano-Fernández, Pablo | Koczan, Dirk | Kotsikoris, Vasilis^; | Kunz, Manfred | Watson, Michael | Pahnke, Jens | Illges, Harald^; | Kreutzer, Michael | Mikkat, Stefan^; | Thiesen, Hans-Jürgen | Glocker, Michael O. | Zettl, Uwe K. | Ibrahim, Saleh M.

Affiliations: 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 | University of Rostock, Core-facility Proteomics, Joachim-Jungius-Str. 9, 18055 Rostock, Germany

Note: [] Corresponding author. E-mail: [email protected]

Abstract: 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 support the identification of novel soluble variants by proteomics is provided.

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

Journal: In Silico Biology, vol. 5, no. 3, pp. 295-311, 2005