title: Evolution: a guide to perturb protein function and networks.
abstract: Protein interactions give rise to networks that control cell fate in health and disease; selective means to probe these interactions are therefore of wide interest. We discuss here Evolutionary Tracing (ET), a comparative method to identify protein functional sites and to guide experiments that selectively block, recode, or mimic their amino acid determinants. These studies suggest, in principle, a scalable approach to perturb individual links in protein networks.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. lichtarge@bcm.edu
authors.forename: Olivier
authors.initials: O
authors.lastname: Lichtarge
authors.forename: Angela
authors.initials: A
authors.lastname: Wilkins
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D019143:Evolution, Molecular; D019204:GTP-Binding Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D011506:Proteins; D019204:GTP-Binding Proteins
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5330-5
references.pmid: 17372228
references.citation: Proteins. 2006 Apr 1;63(1):87-99
references.pmid: 16397893
references.citation: FEBS Lett. 2008 Apr 9;582(8):1266-70
references.pmid: 18282479
references.citation: J Mol Biol. 2008 Dec 5;384(1):109-19
references.pmid: 18804117
references.citation: J Mol Biol. 2009 Feb 6;385(5):1470-80
references.pmid: 18845160
references.citation: Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):13-20
references.pmid: 8552589
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8634-9
references.pmid: 16731632
references.citation: PLoS Comput Biol. 2009 Jan;5(1):e1000266
references.pmid: 19148270
references.citation: PLoS Comput Biol. 2007 Jul;3(7):e119
references.pmid: 17630824
references.citation: Cell. 2009 Aug 21;138(4):774-86
references.pmid: 19703402
references.citation: J Mol Biol. 2004 Mar 5;336(5):1265-82
references.pmid: 15037084
references.citation: Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1483-8
references.pmid: 10677488
references.citation: PLoS Biol. 2005 Dec;3(12):e405
references.pmid: 16279839
references.citation: J Neurosci. 2006 Dec 6;26(49):12727-34
references.pmid: 17151276
references.citation: Bioinformatics. 2006 Aug 15;22(16):2049-50
references.pmid: 16809388
references.citation: Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7787-92
references.pmid: 20385837
references.citation: J Mol Biol. 1998 Apr 3;277(3):635-46
references.pmid: 9533885
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W526-30
references.pmid: 17537808
references.citation: J Biol Chem. 2006 Jan 13;281(2):1261-73
references.pmid: 16280323
references.citation: Nature. 2007 Dec 13;450(7172):1001-9
references.pmid: 18075579
references.citation: J Mol Biol. 2004 Nov 19;344(2):303-10
references.pmid: 15522285
references.citation: Bioinformatics. 2008 Nov 1;24(21):2445-52
references.pmid: 18776193
references.citation: Nat Struct Biol. 2001 Mar;8(3):234-7
references.pmid: 11224568
references.citation: Methods Enzymol. 2004;383:66-93
references.pmid: 15063647
references.citation: J Struct Funct Genomics. 2009 Apr;10(2):181-91
references.pmid: 19194785
references.citation: Protein Sci. 2006 Jun;15(6):1530-6
references.pmid: 16672239
references.citation: Nature. 2009 Nov 12;462(7270):182-8
references.pmid: 19907488
references.citation: J Mol Biol. 2007 Jun 8;369(3):863-79
references.pmid: 17451744
references.citation: Bioinformatics. 2009 Jun 15;25(12):1513-20
references.pmid: 19357097
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3764-9
references.pmid: 19228942
references.citation: Nat Struct Mol Biol. 2004 Apr;11(4):371-9
references.pmid: 15034550
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9215-20
references.pmid: 19470646
references.citation: PLoS One. 2008 May 07;3(5):e2136
references.pmid: 18461181
references.citation: BMC Bioinformatics. 2009 Apr 13;10:107
references.pmid: 19361344
references.citation: J Mol Biol. 2008 Jul 4;380(2):415-24
references.pmid: 18514737
references.citation: N Engl J Med. 2010 Apr 1;362(13):1181-91
references.pmid: 20220177
references.citation: Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12473-8
references.pmid: 11606719
references.citation: Proteins. 2003 Aug 1;52(2):225-35
references.pmid: 12833546
references.citation: J Mol Biol. 2002 Feb 8;316(1):139-54
references.pmid: 11829509
references.citation: J Mol Biol. 2005 Jul 15;350(3):402-15
references.pmid: 15946684
references.citation: J Biol Chem. 2004 Feb 27;279(9):8126-32
references.pmid: 14660595
references.citation: Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):352-7
references.pmid: 9419379
references.citation: Protein Sci. 2009 Jan;18(1):180-95
references.pmid: 19177362
references.citation: Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7507-11
references.pmid: 8755504
references.citation: Science. 2008 Oct 17;322(5900):438-42
references.pmid: 18927392
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W489-94
references.pmid: 17553829
references.citation: J Mol Biol. 2003 Aug 1;331(1):263-79
references.pmid: 12875851
references.citation: J Biol Chem. 2006 Sep 8;281(36):26745-53
references.pmid: 16809340
references.citation: J Mol Biol. 2003 Feb 7;326(1):255-61
references.pmid: 12547207
references.citation: BMC Bioinformatics. 2008 Jan 11;9:17
references.pmid: 18190718
references.citation: Science. 2007 Nov 23;318(5854):1258-65
references.pmid: 17962520
references.citation: J Comput Chem. 2009 Jul 30;30(10):1545-614
references.pmid: 19444816
references.citation: J Mol Biol. 1996 Mar 29;257(2):342-58
references.pmid: 8609628
references.citation: Protein Sci. 1996 Jun;5(6):1001-13
references.pmid: 8762132
references.citation: Bioinformatics. 2010 Mar 1;26(5):617-24
references.pmid: 20080507
references.citation: Bioinformatics. 2009 Jun 1;25(11):1426-7
references.pmid: 19307237
references.citation: J Mol Biol. 1996 Jul 26;260(4):604-20
references.pmid: 8759323
references.citation: Mol Pharmacol. 2010 Mar;77(3):405-15
references.pmid: 20038610
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21149-54
references.pmid: 19923431
references.citation: J Mol Biol. 2006 Aug 4;361(1):195-208
references.pmid: 16831445
references.citation: J Mol Biol. 2004 Oct 1;342(5):1487-504
references.pmid: 15364576
references.citation: Curr Opin Genet Dev. 2006 Feb;16(1):71-7
references.pmid: 16377176
references.citation: Bioinformatics. 2010 Apr 1;26(7):964-5
references.pmid: 20139468
references.citation: J Mol Biol. 1997 Dec 5;274(3):325-37
references.pmid: 9405143
references.citation: Cell. 2006 May 19;125(4):801-14
references.pmid: 16713569
references.citation: J Mol Biol. 2005 Aug 19;351(3):614-26
references.pmid: 16019027
references.citation: FEBS Lett. 2009 Jun 5;583(11):1759-65
references.pmid: 19269289
references.citation: Nature. 2009 Apr 16;458(7240):859-64
references.pmid: 19370028
references.citation: PLoS Comput Biol. 2008 Sep 26;4(9):e1000181
references.pmid: 18818722
references.citation: Brief Bioinform. 2009 Jul;10(4):378-91
references.pmid: 19324930
references.citation: Nat Rev Drug Discov. 2006 Dec;5(12):993-6
references.pmid: 17139284
references.citation: Curr Opin Struct Biol. 2009 Feb;19(1):31-8
references.pmid: 19157855
references.citation: J Mol Biol. 2009 Jan 16;385(2):381-92
references.pmid: 19041878
references.citation: Proteins. 2009 Mar;74(4):948-60
references.pmid: 18767161
references.citation: J Mol Biol. 2006 Mar 10;356(5):1263-74
references.pmid: 16412461
references.citation: Genome Biol. 2008 Jan 16;9(1):R9
references.pmid: 18199329
references.citation: Bioinformatics. 2006 Jul 1;22(13):1656-7
references.pmid: 16644792
references.citation: PLoS Comput Biol. 2009 Jan;5(1):e1000267
references.pmid: 19165315
references.citation: Nat Struct Mol Biol. 2007 Apr;14(4):301-7
references.pmid: 17351632
references.citation: Proteins. 2006 Feb 1;62(2):479-88
references.pmid: 16304646
references.citation: J Mol Biol. 2007 Aug 31;371(5):1392-404
references.pmid: 17603074
references.citation: Development. 2004 Apr;131(8):1679-89
references.pmid: 15084454
references.citation: Bioinformatics. 2005 Apr 15;21(8):1487-94
references.pmid: 15613384
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12724-9
references.pmid: 16129838
references.citation: Science. 1995 Jan 20;267(5196):383-6
references.pmid: 7529940
references.citation: J Mol Biol. 2010 Mar 12;396(5):1451-73
references.pmid: 20036248
references.citation: Trends Endocrinol Metab. 2009 Jan;20(1):25-33
references.pmid: 19056296
references.citation: Bioinformatics. 2003 Jan;19(1):163-4
references.pmid: 12499312
references.citation: Traffic. 2009 Aug;10(8):1019-33
references.pmid: 19515093
references.citation: Proteins. 2006 Oct 1;65(1):111-23
references.pmid: 16894615
references.citation: Science. 1997 Jan 17;275(5298):381-4
references.pmid: 8994033
references.citation: BMC Struct Biol. 2006 Sep 24;6:19
references.pmid: 16995956
references.citation: PLoS Comput Biol. 2009 Dec;5(12):e1000585
references.pmid: 19997483
references.citation: J Mol Biol. 2007 Oct 26;373(3):801-10
references.pmid: 17868687