Genetic interaction mapping informs integrative structure determination of protein complexes.
Journal
Science (New York, N.Y.)
ISSN: 1095-9203
Titre abrégé: Science
Pays: United States
ID NLM: 0404511
Informations de publication
Date de publication:
11 12 2020
11 12 2020
Historique:
received:
14
10
2019
revised:
23
07
2020
accepted:
23
10
2020
entrez:
11
12
2020
pubmed:
12
12
2020
medline:
3
2
2021
Statut:
ppublish
Résumé
Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.
Identifiants
pubmed: 33303586
pii: 370/6522/eaaz4910
doi: 10.1126/science.aaz4910
pmc: PMC7946025
mid: NIHMS1671864
pii:
doi:
Substances chimiques
Histones
0
Multiprotein Complexes
0
Saccharomyces cerevisiae Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NHLBI NIH HHS
ID : P01 HL089707
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM127029
Pays : United States
Organisme : NINDS NIH HHS
ID : U54 NS100717
Pays : United States
Organisme : NCRR NIH HHS
ID : U54 RR020839
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008284
Pays : United States
Organisme : NIGMS NIH HHS
ID : U54 GM103520
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM098101
Pays : United States
Organisme : NIGMS NIH HHS
ID : P01 GM105473
Pays : United States
Organisme : NIGMS NIH HHS
ID : P50 GM082250
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209891
Pays : United States
Organisme : NIAID NIH HHS
ID : P50 AI150476
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM084279
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM118061
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM083960
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI135990
Pays : United States
Organisme : NIGMS NIH HHS
ID : P50 GM081879
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM123159
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM084448
Pays : United States
Organisme : NIH HHS
ID : DP5 OD009180
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM126900
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM109824
Pays : United States
Organisme : NIH HHS
ID : S10 OD021596
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Références
Structure. 2017 Sep 5;25(9):1317-1318
pubmed: 28877501
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Nature. 2005 Jul 14;436(7048):294-8
pubmed: 16015338
Cell. 2009 Aug 21;138(4):774-86
pubmed: 19703402
Protein Sci. 2014 Jun;23(6):747-59
pubmed: 24639379
PLoS Comput Biol. 2010 Mar 05;6(3):e1000694
pubmed: 20221255
Nat Methods. 2017 Jun;14(6):577-580
pubmed: 28481362
Cell Rep. 2013 Jun 27;3(6):2168-78
pubmed: 23746449
Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12186-12191
pubmed: 27729520
Cell. 2005 Nov 18;123(4):581-92
pubmed: 16286007
Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4088-4098
pubmed: 32034103
Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1380-7
pubmed: 22307589
Science. 2010 Jan 22;327(5964):425-31
pubmed: 20093466
Bioinformatics. 2012 Dec 15;28(24):3282-9
pubmed: 23093611
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Genetics. 2008 Aug;179(4):1769-84
pubmed: 18579506
Annu Rev Biochem. 2008;77:443-77
pubmed: 18318657
Cell. 2014 Aug 28;158(5):1123-1135
pubmed: 25171412
Bioinformatics. 2004 Jun 12;20(9):1453-4
pubmed: 14871861
Elife. 2015 Sep 24;4:
pubmed: 26402457
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
pubmed: 11752295
Nature. 2012 Sep 20;489(7416):452-5
pubmed: 22914091
Nat Struct Mol Biol. 2020 Sep;27(9):822-828
pubmed: 32719457
Curr Opin Struct Biol. 2014 Oct;28:96-104
pubmed: 25173450
Mol Cell Proteomics. 2015 Jan;14(1):162-76
pubmed: 25381059
Cell. 1996 Mar 22;84(6):843-51
pubmed: 8601308
J Mol Biol. 1993 Dec 5;234(3):779-815
pubmed: 8254673
Cell. 1991 Jun 14;65(6):1023-31
pubmed: 2044150
EMBO J. 2000 May 15;19(10):2323-31
pubmed: 10811623
Mol Cell Biol. 2005 Nov;25(22):10060-70
pubmed: 16260619
Mol Cell. 2015 Sep 3;59(5):794-806
pubmed: 26340423
Nature. 2012 May 20;486(7402):276-9
pubmed: 22699623
Anal Biochem. 1984 Apr;138(1):141-3
pubmed: 6731838
Bioinformatics. 2014 Sep 1;30(17):2524-6
pubmed: 24794931
Nature. 2007 Nov 29;450(7170):695-701
pubmed: 18046406
Trends Biochem Sci. 2011 Apr;36(4):179-82
pubmed: 21345680
Cell. 2019 May 30;177(6):1384-1403
pubmed: 31150619
Science. 2014 May 30;344(6187):1023-8
pubmed: 24876496
Curr Opin Struct Biol. 2017 Oct;46:110-121
pubmed: 28735108
Protein Sci. 2006 Nov;15(11):2507-24
pubmed: 17075131
Genes Dev. 2015 Jun 15;29(12):1326-40
pubmed: 26109053
Genome Biol. 2014;15(12):550
pubmed: 25516281
EMBO J. 2001 Sep 17;20(18):5207-18
pubmed: 11566884
Genome Biol. 2006;7(7):R63
pubmed: 16859555
Bioinformatics. 2013 Feb 1;29(3):407-8
pubmed: 23242262
Chem Rev. 2015 Mar 25;115(6):2376-418
pubmed: 25688442
Nat Chem Biol. 2020 Jun;16(6):653-659
pubmed: 32152544
Science. 2004 Jan 16;303(5656):343-8
pubmed: 14645854
Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10080-5
pubmed: 17540730
Curr Protoc Mol Biol. 2001 May;Chapter 13:Unit13.12
pubmed: 18265096
Mol Cell. 2012 Jun 8;46(5):691-704
pubmed: 22681890
J Chem Theory Comput. 2016 Apr 12;12(4):1799-805
pubmed: 26771390
Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):12902-7
pubmed: 11687631
Nature. 2010 May 20;465(7296):363-7
pubmed: 20436457
Science. 2017 May 26;356(6340):
pubmed: 28495876
Nat Protoc. 2014 Aug;9(8):1867-81
pubmed: 25010907
Bioinformatics. 2004 Nov 22;20(17):3246-8
pubmed: 15180930
Cell. 2018 Mar 22;173(1):11-19
pubmed: 29570991
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Cell. 2008 Sep 19;134(6):1066-78
pubmed: 18805098
Nucleic Acids Res. 2012 Oct;40(19):9941-52
pubmed: 22848102
Mol Cell. 2006 Jul 7;23(1):109-19
pubmed: 16818235
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jun 1;61(Pt 6):541-5
pubmed: 16511091
Bioessays. 2014 Jul;36(7):706-13
pubmed: 24842270
Proteins. 2018 Mar;86 Suppl 1:51-66
pubmed: 29071738
J Biol Chem. 2010 Apr 9;285(15):11704-13
pubmed: 20139424
Nat Biotechnol. 2018 Jul;36(6):512-520
pubmed: 29734294
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Mol Cell Proteomics. 2014 Nov;13(11):2927-43
pubmed: 25161197
Mol Cell Proteomics. 2007 Mar;6(3):439-50
pubmed: 17200106
Nature. 2019 Dec;576(7785):149-157
pubmed: 31634902
EMBO J. 2001 Dec 17;20(24):7137-48
pubmed: 11742990
Bioinformatics. 2007 Sep 1;23(17):2345-7
pubmed: 17623706
Science. 2013 Feb 22;339(6122):913-5
pubmed: 23430643
PLoS Comput Biol. 2017 Jan 5;13(1):e1005324
pubmed: 28056090
Methods Enzymol. 2010;470:205-31
pubmed: 20946812
Methods. 2006 Dec;40(4):344-52
pubmed: 17101447
PLoS Biol. 2012 Jan;10(1):e1001244
pubmed: 22272186
Genetics. 2017 Dec;207(4):1263-1273
pubmed: 29084817
Curr Opin Struct Biol. 2016 Oct;40:163-185
pubmed: 27939973
Cell. 2013 Nov 7;155(4):817-29
pubmed: 24209620
Biophys J. 2017 Dec 5;113(11):2344-2353
pubmed: 29211988
Science. 2001 Oct 5;294(5540):93-6
pubmed: 11588250
J Biol Chem. 2013 Mar 29;288(13):9126-34
pubmed: 23389035
Proteins. 2003 Feb 1;50(2):272-82
pubmed: 12486721
Mol Cell. 2008 Dec 5;32(5):735-46
pubmed: 19061648
Nucleic Acids Res. 2011 Jan;39(Database issue):D411-9
pubmed: 21071423
Elife. 2014 May 01;3:e02030
pubmed: 24842992
Proteins. 2018 Mar;86 Suppl 1:113-121
pubmed: 28940798
Science. 2012 Sep 14;337(6100):1348-52
pubmed: 22984071
Biopolymers. 1983 Dec;22(12):2577-637
pubmed: 6667333
Science. 2011 Dec 16;334(6062):1518-24
pubmed: 22174245
Nature. 2018 Aug;560(7720):607-612
pubmed: 30135578
Bioinformatics. 2010 Apr 1;26(7):966-8
pubmed: 20147306
Cell. 2006 Nov 17;127(4):831-46
pubmed: 17110340
Structure. 2015 Jul 7;23(7):1156-67
pubmed: 26095030
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Elife. 2018 Apr 11;7:
pubmed: 29638215
Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11751-11756
pubmed: 29078326
Structure. 2014 Sep 2;22(9):1239-1251
pubmed: 25087511
Methods. 2001 Dec;25(4):402-8
pubmed: 11846609
Curr Biol. 2006 Jul 11;16(13):1280-9
pubmed: 16815704
PLoS One. 2011;6(12):e28766
pubmed: 22163331
Science. 2012 Aug 17;337(6096):816-21
pubmed: 22745249
Nat Rev Genet. 2020 Jun;21(6):339-354
pubmed: 32060427
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
Proc R Soc Lond A Math Phys Sci. 1946;186(1007):453-61
pubmed: 20998741
Nat Genet. 2019 Jul;51(7):1170-1176
pubmed: 31209393
J Biol Chem. 2005 Mar 18;280(11):9879-86
pubmed: 15632126
F1000Res. 2014 Jul 01;3:149
pubmed: 25352980
Nature. 2007 Nov 29;450(7170):683-94
pubmed: 18046405
Nat Genet. 2019 Jul;51(7):1177-1186
pubmed: 31209395
Cell. 2005 Nov 18;123(4):593-605
pubmed: 16286008
Nucleic Acids Res. 2018 Jul 2;46(W1):W432-W437
pubmed: 29790960
Proteins. 2003 Jul 1;52(1):88-91
pubmed: 12784372
Structure. 2018 Jun 5;26(6):894-904.e2
pubmed: 29657133
Cell. 2006 Dec 1;127(5):941-54
pubmed: 17129781
Mol Cell. 2018 Jun 21;70(6):1054-1066.e4
pubmed: 29932900
Phys Rev Lett. 1986 Nov 24;57(21):2607-2609
pubmed: 10033814
EMBO J. 2010 Feb 17;29(4):717-26
pubmed: 20094031
Mol Cell. 2007 Mar 9;25(5):703-12
pubmed: 17320445
Proteins. 2018 Mar;86 Suppl 1:67-77
pubmed: 28845538
Nature. 2018 Mar 22;555(7697):475-482
pubmed: 29539637
Science. 2019 Jul 12;365(6449):185-189
pubmed: 31296772
Cell. 2010 May 28;141(5):739-45
pubmed: 20510918
Nature. 2020 Jul;583(7816):459-468
pubmed: 32353859
Science. 2005 Jul 8;309(5732):303-6
pubmed: 16002620
Nucleic Acids Res. 2014 Jan;42(2):870-81
pubmed: 24163256
Protein Sci. 2018 Jan;27(1):14-25
pubmed: 28710774
J Am Chem Soc. 2005 Nov 23;127(46):16026-7
pubmed: 16287280
Nature. 2007 Apr 12;446(7137):806-10
pubmed: 17314980
Nat Methods. 2017 Jun;14(6):573-576
pubmed: 28319113
Cell. 2013 Aug 15;154(4):775-88
pubmed: 23932120
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W363-7
pubmed: 15980490
Science. 2020 Dec 4;370(6521):
pubmed: 33060197
Mol Cell. 2020 Apr 16;78(2):197-209.e7
pubmed: 32084337
Nature. 2006 Jul 6;442(7098):86-90
pubmed: 16728976