Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins

Jan Kirrbach, Miriam Krugliak, Christian L. Ried, Philipp Pagel, Isaiah T. Arkin, Dieter Langosch*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Motivation: Most integral membrane proteins form dimeric or oligomeric complexes. Oligomerization is frequently supported by the noncovalent 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.

Original languageAmerican English
Pages (from-to)1623-1630
Number of pages8
JournalBioinformatics
Volume29
Issue number13
DOIs
StatePublished - 1 Jul 2013

Bibliographical note

Funding Information:
Funding: This work was supported by the Deutsche Forschungsgemeinschaft (grant La699/13-1 to D.L. and to I.A.), the Center for Integrative Protein Science Munich, the Deutsche Akademische Austauschdienst, and the TUM Graduate School.

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