title: The evolution of domain arrangements in proteins and interaction networks.
abstract: Proteins are composed of domains, which are conserved evolutionary units that often also correspond to functional units and can frequently be detected with reasonable reliability using computational methods. Most proteins consist of two or more domains, giving rise to a variety of combinations of domains. Another level of complexity arises because proteins themselves can form complexes with small molecules, nucleic acids and other proteins. The networks of both domain combinations and protein interactions can be conceptualised as graphs, and these graphs can be analysed conveniently by computational methods. In this review we summarise facts and hypotheses about the evolution of domains in multi-domain proteins and protein complexes, and the tools and data resources available to study them.
authors.affiliation: Bioinformatics Division, School of Biological Sciences, University of Münster, Schlossplatz 4, 48143 Münster, Germany. january@uni-muenster.de
authors.forename: E
authors.initials: E
authors.lastname: Bornberg-Bauer
authors.forename: F
authors.initials: F
authors.lastname: Beaussart
authors.forename: S K
authors.initials: SK
authors.lastname: Kummerfeld
authors.forename: S A
authors.initials: SA
authors.lastname: Teichmann
authors.forename: J
authors.initials: J
authors.lastname: Weiner
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics / Q000502:physiology; D019143:Evolution, Molecular; D014644:Genetic Variation; D006801:Humans; D046912:Multiprotein Complexes / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics* / Q000502:physiology; D011506:Proteins / Q000235:genetics* / Q000502:physiology
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins
references.citation: Circulation. 2013 Jun 4;127(22):2222-30
references.pmid: 23733968
references.citation: Diabetes Metab J. 2015 Oct;39(5):353-62
references.pmid: 26566492
references.citation: Nat Rev Endocrinol. 2012 Jan 24;8(4):237-45
references.pmid: 22271188
references.citation: JAMA. 2011 Jun 22;305(24):2556-64
references.pmid: 21693744
references.citation: Nat Genet. 2003 Jun;34(2):154-6
references.pmid: 12730697
references.citation: Herz. 2014 Jun;39(4):466-9
references.pmid: 23925411
references.citation: Lancet. 2010 May 29;375(9729):1875-84
references.pmid: 20462635
references.citation: Arterioscler Thromb Vasc Biol. 2008 Jul;28(7):1225-36
references.pmid: 18565848
references.citation: Eur Heart J. 2013 Dec;34(45):3478-90a
references.pmid: 23956253
references.citation: J Clin Endocrinol Metab. 2013 Apr;98(4):1622-30
references.pmid: 23450048
references.citation: Circulation. 2013 Nov 26;128(22):2364-71
references.pmid: 24170386
references.citation: Lancet. 2015 Jan 24;385(9965):341-50
references.pmid: 25282520
references.citation: J Am Coll Cardiol. 2014 Apr 8;63(13):1278-88
references.pmid: 24509273
references.citation: N Engl J Med. 2015 Oct 29;373(18):1720-32
references.pmid: 26510021
references.citation: Atherosclerosis. 2009 Mar;203(1):1-7
references.pmid: 18649882
references.citation: N Engl J Med. 2010 Apr 29;362(17):1563-74
references.pmid: 20228404
references.citation: Circulation. 2001 Dec 18;104(25):3046-51
references.pmid: 11748098
references.citation: Diabetes. 2001 Feb;50(2):315-21
references.pmid: 11272142
references.citation: Lancet. 2008 Jan 12;371(9607):117-25
references.pmid: 18191683
references.citation: N Engl J Med. 2014 May 8;370(19):1809-19
references.pmid: 24678979
references.citation: N Engl J Med. 2006 Mar 23;354(12 ):1264-72
references.pmid: 16554528
references.citation: N Engl J Med. 2015 Apr 16;372(16):1489-99
references.pmid: 25773378
references.citation: Lancet. 2010 Feb 27;375(9716):735-42
references.pmid: 20167359
references.citation: JAMA. 2015 Mar 10;313(10):1029-36
references.pmid: 25756439
references.citation: Eur Heart J. 2015 Sep 21;36(36):2415-24
references.pmid: 25971287
references.citation: Lancet. 2015 Jan 24;385(9965):351-61
references.pmid: 25262344
references.citation: Diabetes. 2003 May;52(5):1210-4
references.pmid: 12716754
references.citation: Diabetologia. 2015 Sep;58(9):2051-5
references.pmid: 26049403
references.citation: N Engl J Med. 2015 Apr 16;372(16):1500-9
references.pmid: 25773607
references.citation: Metabolism. 2014 Dec;63(12):1469-79
references.pmid: 25242435
references.citation: N Engl J Med. 2015 Jun 18;372(25):2387-97
references.pmid: 26039521
references.citation: Eur Radiol. 2016 May;26(5):1420-30
references.pmid: 26304802
references.citation: N Engl J Med. 2008 Nov 20;359(21):2195-207
references.pmid: 18997196
references.citation: Ann Intern Med. 2015 Jul 7;163(1):40-51
references.pmid: 25915661
references.citation: Cardiovasc Diabetol. 2010 Aug 30;9:44
references.pmid: 20804545
references.citation: J Lipid Res. 2007 Jun;48(6):1336-42
references.pmid: 17337758
references.citation: Atherosclerosis. 2011 Jul;217(1):3-46
references.pmid: 21882396