title: Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome.
abstract: BACKGROUND
  Membrane proteins are key components in a large spectrum of diverse functions and thus account for the major proportion of the drug-targeted portion of the genome. From a structural perspective, the α-helical transmembrane proteins can be categorized into major groups based on the number of transmembrane helices and these groups are often associated with specific functions. When compared to the well-characterized seven-transmembrane containing proteins (7TM), other TM groups are less explored and in particular the 4TM group. In this study, we identify the complete 4TM complement from the latest release of the human genome and assess the 4TM structure group as a whole. We functionally characterize this dataset and evaluate the resulting groups and ubiquitous functions, and furthermore describe disease and drug target involvement.
  
  
  RESULTS
  We classified 373 proteins, which represents ~7 % of the human membrane proteome, and includes 69 more proteins than our previous estimate. We have characterized the 4TM dataset based on functional, structural, and/or evolutionary similarities. Proteins that are involved in transport activity constitute 37 % of the dataset, 23 % are receptor-related, and 13 % have enzymatic functions. Intriguingly, proteins involved in transport are more than double the 15 % of transporters in the entire human membrane proteome, which might suggest that the 4TM topological architecture is more favored for transporting molecules over other functions. Moreover, we found an interesting exception to the ubiquitous intracellular N- and C-termini localization that is found throughout the entire membrane proteome and 4TM dataset in the neurotransmitter gated ion channel families. Overall, we estimate that 58 % of the dataset has a known association to disease conditions with 19 % of the genes possibly involved in different types of cancer.
  
  
  CONCLUSIONS
  We provide here the most robust and updated classification of the 4TM complement of the human genome as a platform to further understand the characteristics of 4TM functions and to explore pharmacological opportunities.
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
authors.forename: Misty M
authors.initials: MM
authors.lastname: Attwood
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
authors.forename: Arunkumar
authors.initials: A
authors.lastname: Krishnan
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
authors.forename: Valentina
authors.initials: V
authors.lastname: Pivotti
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
authors.forename: Samira
authors.initials: S
authors.lastname: Yazdi
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
authors.forename: Markus Sällman
authors.initials: MS
authors.lastname: Almén
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden. helgi.schioth@neuro.uu.se.|Institutionen för neurovetenskap, BMC, Box 593, 751 24, Uppsala, Sweden. helgi.schioth@neuro.uu.se.
authors.forename: Helgi B
authors.initials: HB
authors.lastname: Schiöth
mesh_terms: D015894:Genome, Human; D006801:Humans; D008565:Membrane Proteins / Q000145:classification / Q000235:genetics*; D020543:Proteome / Q000235:genetics
chemical_list: D008565:Membrane Proteins; D020543:Proteome
keywords: 4TM; Cancer; Drug targets; Four transmembrane; Function; Human proteome; Structure function; Topology prediction