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Protein Science, Vol 7, Issue 4 1029-1038, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

E. WALLIN and G. VON-HEIJNE
Department of Biochemistry, Stockholm University, S-106 91 Stockholm, Sweden

We have carried out detailed statistical analyses of integral membrane proteins of the helix-bundle class from eubacterial, archaean, and eukaryotic organisms for which genome-wide sequence data are available. Twenty to 30% of all ORFs are predicted to encode membrane proteins, with the larger genomes containing a higher fraction than the smaller ones. Although there is a general tendency that proteins with a smaller number of transmembrane segments are more prevalent than those with many, uni-cellular organisms appear to prefer proteins with 6 and 12 transmembrane segments, whereas Caenorhabditis elegans and Homo sapiens have a slight preference for proteins with seven transmembrane segments. In all organisms, there is a tendency that membrane proteins either have many transmembrane segments with short connecting loops or few transmembrane segments with large extra-membraneous domains. Membrane proteins from all organisms studied, except possibly the archaeon Methanococcus jannaschii, follow the so-called ``positive-inside'' rule; i.e., they tend to have a higher frequency of positively charged residues in cytoplasmic than in extra-cytoplasmic segments. segments.
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