Collection of soluble variants of membrane proteins for transcriptomics and proteomics

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

Research output: Contribution to journalArticlepeer-review

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 determine novel soluble variants by proteomics is provided.
Original languageEnglish
Pages (from-to)295-311
Number of pages17
JournalIn Silico Biology
Volume5
Issue number3
Publication statusPublished - 2005

Keywords

  • Animals
  • Humans
  • Membrane Proteins
  • Programming Languages
  • Proteomics
  • RNA, Messenger
  • Solubility

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