title: Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes.
abstract: We have performed a comparative analysis of amino acid distributions in predicted integral membrane proteins from a total of 107 genomes. A procedure for identification of membrane spanning helices was optimized on a homology-reduced data set of 170 multi-spanning membrane proteins with experimentally determined topologies. The optimized method was then used for extraction of highly reliable partial topologies from all predicted membrane proteins in each genome, and the average biases in amino acid distributions between loops on opposite sides of the membrane were calculated. The results strongly support the notion that a biased distribution of Lys and Arg residues between cytoplasmic and extra-cytoplasmic segments (the positive-inside rule) is present in most if not all organisms.
authors: Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden.
authors: Johan
authors: J
authors: Nilsson
authors: Bengt
authors: B
authors: Persson
authors: Gunnar
authors: G
authors: von Heijne
mesh_terms: D000596:Amino Acids / Q000032:analysis*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D030562:Databases, Protein; D016678:Genome; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics*; D017017:Methanococcus; D016366:Open Reading Frames; D011487:Protein Conformation
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D008565:Membrane Proteins