title: Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Lehrstuhl für Chemie der Biopolymere, Technische Universität München, 85354 Freising, Germany.
authors: Jan
authors: J
authors: Kirrbach
authors: Miriam
authors: M
authors: Krugliak
authors: Christian L
authors: CL
authors: Ried
authors: Philipp
authors: P
authors: Pagel
authors: Isaiah T
authors: IT
authors: Arkin
authors: Dieter
authors: D
authors: Langosch
mesh_terms: D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D009154:Mutation; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry; D017386:Sequence Homology, Amino Acid
chemical_list: D008565:Membrane Proteins; D020543:Proteome