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Updated: May 11, 2026

Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
Published on: May 26, 2011
Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins
Jan Kirrbach1, Miriam Krugliak, Christian L Ried
1Lehrstuhl für Chemie der Biopolymere, Technische Universität München, 85354 Freising, Germany.
Motivation:
Most integral membrane proteins form dimeric or oligomeric complexes. Oligomerization is frequently supported by the non-covalent interaction of transmembrane helices. It is currently not clear how many high-affinity transmembrane domains (TMD) exist in a proteome and how specific their interactions are with respect to preferred contacting faces and their underlying residue motifs.
Results:
We first identify a threshold of 55% sequence similarity, which demarcates the border between meaningful alignments of TMDs and chance alignments. Clustering the human single-span membrane proteome using this threshold groups ~40% of the TMDs. The homotypic interaction of the TMDs representing the 33 largest clusters was systematically investigated under standardized conditions. The results reveal a broad distribution of relative affinities. High relative affinity frequently coincides with (i) the existence of a preferred helix-helix interface and (ii) sequence specificity as indicated by reduced affinity after mutating conserved residues.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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