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