Collection of soluble variants of membrane proteins for transcriptomics and proteomics.
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.
University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany. moeller@pzr.uni-rostock.de
Steffen
S
Möller
Eilhard
E
Mix
Martin
M
Blüggel
Pablo
P
Serrano-Fernández
Dirk
D
Koczan
Vasilis
V
Kotsikoris
Manfred
M
Kunz
Michael
M
Watson
Jens
J
Pahnke
Harald
H
Illges
Michael
M
Kreutzer
Stefan
S
Mikkat
Hans-Jürgen
HJ
Thiesen
Michael O
MO
Glocker
Uwe K
UK
Zettl
Saleh M
SM
Ibrahim
D000818:Animals; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D011381:Programming Languages; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics*; D012995:Solubility
D008565:Membrane Proteins; D012333:RNA, Messenger