Mapping the Human Single-Span Membrane Proteome for Self-Interacting Transmembrane Domains

Abstract

Single-span membrane proteins comprise more than 10% of the human proteome. Most of those integral membrane proteins form non-covalent functional complexes that are frequently supported by sequence-specific interaction of transmembrane domains (TMDs) [1]. It has been suggested that non-covalent membrane protein multimerization may substitute for the frequently observed multi-domain organization of soluble proteins. To date, only a few dimerization motifs such as the GxxxG motif are known. Even those motifs are highly depending on the sequence context.Here, we investigate biologically relevant sequence similarities of human single-span membrane proteins and use them to construct clusters of homologous TMDs. Using the ToxR system [2] it is possible to experimentally determine the self-interaction of one representative TMD for each group. Amino acids which are conserved in the alignment of each cluster's TMDs were replaced to identify their importance for homotypic interaction.We are able to group almost half of all bitopic TMD sequences into clusters. Most sequences from large clusters exhibit medium to high self-interaction as shown by the ToxR system. From those findings one can assume specifically interacting TMDs to be highly represented in the human proteome. Almost half of the investigated clusters include a conserved GxxxG or SmallxxxSmall like motif which was found to be important for interaction, if not exclusively. In some cases extracellular domains are by far not as similar as their corresponding TMDs. This raises the question about the origin and development of TMDs by convergent or divergent evolution.[1] Langosch, Arkin; Interaction and conformational dynamics of membrane-spanning protein helices. Protein Sci. 2009, 18, 1343-1358.[2] Kolmar et al.; Membrane insertion of the bacterial signal transduction protein ToxR and requirements of transcription activation studied by modular replacement of different protein substructures. EMBO J, 1995, 14, 3895-3904.