Dawn of a New Era for Membrane Protein Design.
Journal
Biodesign research
ISSN: 2693-1257
Titre abrégé: Biodes Res
Pays: United States
ID NLM: 9918469288306676
Informations de publication
Date de publication:
2022
2022
Historique:
received:
28
01
2022
accepted:
20
03
2022
medline:
15
4
2022
pubmed:
15
4
2022
entrez:
18
10
2023
Statut:
epublish
Résumé
A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.
Identifiants
pubmed: 37850134
doi: 10.34133/2022/9791435
pii: 9791435
pmc: PMC10521746
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
9791435Informations de copyright
Copyright © 2022 Shahin Sowlati-Hashjin et al.
Déclaration de conflit d'intérêts
The authors declare that they have no conflicts of interest.
Références
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
Cell Syst. 2020 Oct 21;11(4):402-411.e4
pubmed: 32971019
Science. 2019 Mar 29;363(6434):1418-1423
pubmed: 30923216
Nature. 1994 Jan 20;367(6460):243-9
pubmed: 8121489
Nat Struct Mol Biol. 2021 Sep;28(9):762-770
pubmed: 34518698
J Phys Chem B. 2021 Aug 19;125(32):9130-9144
pubmed: 34365794
Elife. 2018 Jun 21;7:
pubmed: 29927385
Nature. 2016 Sep 14;537(7620):320-7
pubmed: 27629638
Biochemistry. 2006 Sep 26;45(38):11324-32
pubmed: 16981692
Nat Chem Biol. 2020 Jan;16(1):77-86
pubmed: 31792443
Front Mol Biosci. 2020 Aug 07;7:129
pubmed: 32850948
Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):7051-7056
pubmed: 29915030
J Chem Theory Comput. 2017 Jul 11;13(7):3077-3084
pubmed: 28618232
Angew Chem Int Ed Engl. 2016 Jun 20;55(26):7364-8
pubmed: 27122231
J Biol Phys. 2016 Jan;42(1):133-46
pubmed: 26264478
J Mol Graph. 1996 Dec;14(6):354-60, 376
pubmed: 9195488
Biophys J. 1993 Dec;65(6):2455-60
pubmed: 7508762
Neuron. 2017 Aug 2;95(3):504-529
pubmed: 28772120
Mol Cell Biol. 2010 Nov;30(22):5432-43
pubmed: 20837704
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14808-13
pubmed: 18812512
Brief Bioinform. 2021 May 20;22(3):
pubmed: 32743637
Q Rev Biophys. 2010 Feb;43(1):65-158
pubmed: 20667175
J Am Chem Soc. 2010 Nov 10;132(44):15516-8
pubmed: 20945900
J Mol Biol. 2012 May 25;419(1-2):89-101
pubmed: 22391420
Nat Chem. 2021 Dec;13(12):1192-1199
pubmed: 34795436
Science. 1988 May 27;240(4856):1177-81
pubmed: 2453923
Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10988-E10997
pubmed: 30373828
ChemMedChem. 2018 Jul 6;13(13):1300-1302
pubmed: 29679519
J Comput Chem. 2016 Apr 5;37(9):836-47
pubmed: 26666582
RSC Chem Biol. 2020 Dec 8;2(2):503-512
pubmed: 34458796
Nature. 2017 Jul 6;547(7661):68-73
pubmed: 28607487
Nat Methods. 2021 Apr;18(4):346-357
pubmed: 33828274
Bioinformatics. 2006 Mar 1;22(5):623-5
pubmed: 16397007
Biochem Soc Symp. 2001;(68):111-23
pubmed: 11573342
Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4175-84
pubmed: 25253890
Sci Rep. 2019 Nov 4;9(1):15978
pubmed: 31685855
Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):E3959-E3968
pubmed: 29632192
Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2848-52
pubmed: 18287056
Nat Methods. 2016 Dec;13(12):1036-1042
pubmed: 27798611
Mol Pharmacol. 2018 Apr;93(4):251-258
pubmed: 29298813
Nat Commun. 2013;4:2415
pubmed: 24026014
Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):9632-7
pubmed: 26199411
Nature. 2018 Mar 22;555(7697):428-430
pubmed: 29565377
Curr Opin Struct Biol. 2008 Oct;18(5):581-6
pubmed: 18674618
Cell. 2019 Jul 25;178(3):748-761.e17
pubmed: 31280962
Nature. 2019 Jan;565(7738):186-191
pubmed: 30626941
Curr Opin Struct Biol. 2018 Feb;48:74-82
pubmed: 29136528
Biophys J. 2002 Jan;82(1 Pt 1):509-16
pubmed: 11751337
Nature. 2014 Aug 21;512(7514):276-81
pubmed: 25119048
Chem Commun (Camb). 2019 May 7;55(38):5431-5434
pubmed: 30916680
J Chem Theory Comput. 2016 Jan 12;12(1):405-13
pubmed: 26631602
Chembiochem. 2017 Sep 19;18(18):1807-1813
pubmed: 28703362
Cell. 2016 Feb 11;164(4):780-91
pubmed: 26830878
J Chem Theory Comput. 2011 Sep 13;7(9):3001-3011
pubmed: 22046108
Curr Protoc Neurosci. 2010 Jan;Chapter 4:Unit 4.33
pubmed: 20066658
PLoS Comput Biol. 2012;8(10):e1002708
pubmed: 23093919
ACS Synth Biol. 2014 Dec 19;3(12):892-902
pubmed: 24611683
Nat Biotechnol. 2020 Feb;38(2):165-168
pubmed: 31844291
Biophys J. 2010 Dec 15;99(12):3880-6
pubmed: 21156129
J Am Chem Soc. 2006 Mar 1;128(8):2697-704
pubmed: 16492056
Structure. 2012 Jan 11;20(1):5-14
pubmed: 22244752
Philos Trans R Soc Lond B Biol Sci. 2017 Aug 5;372(1726):
pubmed: 28630153
Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):64-9
pubmed: 18165312
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
J Struct Biol. 2017 Mar;197(3):350-353
pubmed: 28115258
Bioinformatics. 2020 May 1;36(9):2909-2911
pubmed: 31930403
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Biophys J. 2018 Mar 13;114(5):1091-1102
pubmed: 29539396
Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15102-7
pubmed: 25288768
J Phys Chem B. 2021 Jan 14;125(1):169-183
pubmed: 33373220
BMC Biol. 2009 Aug 13;7:50
pubmed: 19678920
Science. 2021 Feb 19;371(6531):
pubmed: 33602829
Nat Struct Mol Biol. 2015 May;22(5):362-9
pubmed: 25895059
Acta Pharmacol Sin. 2016 Jan;37(1):34-43
pubmed: 26657056
Nat Commun. 2019 Oct 29;10(1):4918
pubmed: 31664022
PLoS Comput Biol. 2009 Jul;5(7):e1000440
pubmed: 19609355
Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22146-22156
pubmed: 32848056
J Biomol Screen. 2010 Apr;15(4):441-6
pubmed: 20208034
Curr Oncol Rep. 2022 Jan;24(1):23-31
pubmed: 35059997
J Biol Chem. 2006 Feb 24;281(8):5042-9
pubmed: 16354667
Prog Mol Biol Transl Sci. 2020;170:177-213
pubmed: 32145945
PLoS Comput Biol. 2014 Jan;10(1):e1003417
pubmed: 24415929
J Mol Biol. 2021 Oct 1;433(20):167154
pubmed: 34271008
Science. 2021 Dec 17;374(6574):1509-1513
pubmed: 34735217
Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1198-203
pubmed: 18202181
ACS Synth Biol. 2017 Nov 17;6(11):2042-2055
pubmed: 28771312
J Am Chem Soc. 2009 Mar 25;131(11):3794-5
pubmed: 19292479
Biophys J. 2018 Sep 18;115(6):1116-1129
pubmed: 30197180
PLoS Comput Biol. 2011 Jul;7(7):e1002096
pubmed: 21789034
J Mol Biol. 2019 Aug 9;431(17):3353-3365
pubmed: 31220459
PLoS Comput Biol. 2017 Oct 23;13(10):e1005786
pubmed: 29059183
Nucleic Acids Res. 2012 Jan;40(Database issue):D370-6
pubmed: 21890895
Nat Biotechnol. 2020 Dec;38(12):1415-1420
pubmed: 32632300
Nat Commun. 2018 May 16;9(1):1950
pubmed: 29769519
Nat Protoc. 2021 Dec;16(12):5357-5376
pubmed: 34707255
Nat Nanotechnol. 2022 Jan;17(1):67-75
pubmed: 34811552
J Phys Chem B. 2012 Mar 8;116(9):2934-42
pubmed: 22339391
Front Bioinform. 2021 Apr 09;1:646581
pubmed: 36303794
IUCrJ. 2019 Oct 17;6(Pt 6):996-1006
pubmed: 31709055
J Chem Theory Comput. 2012 Aug 14;8(8):2905-11
pubmed: 26592129
Angew Chem Int Ed Engl. 2021 Aug 16;60(34):18680-18687
pubmed: 34042235
Biochim Biophys Acta. 2012 Mar;1818(3):617-26
pubmed: 22155685
Biochim Biophys Acta Biomembr. 2022 Feb 1;1864(1):183777
pubmed: 34537214
Expert Opin Drug Discov. 2011 Jan;6(1):17-32
pubmed: 22328899
Science. 2007 Mar 30;315(5820):1817-22
pubmed: 17395823
J Mol Biol. 2015 Jan 16;427(1):190-204
pubmed: 25205552
Arch Biochem Biophys. 1997 Mar 1;339(1):107-14
pubmed: 9056240
Anal Chem. 2019 Jan 2;91(1):482-504
pubmed: 30481456
J Am Chem Soc. 2007 Jan 24;129(3):512-8
pubmed: 17227013
Nucleic Acids Res. 2018 Jul 2;46(W1):W368-W373
pubmed: 29718451
J Chem Inf Model. 2018 Nov 26;58(11):2193-2202
pubmed: 30336018
J Biol Chem. 2021 Jan-Jun;296:100558
pubmed: 33744284
Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1511-1516
pubmed: 29378944
Nat Methods. 2014 May;11(5):585-92
pubmed: 24658140
Biophys J. 2011 Sep 7;101(5):1130-8
pubmed: 21889450
Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21614-8
pubmed: 19966228
J Am Chem Soc. 2018 Apr 4;140(13):4543-4551
pubmed: 29547697
Nat Commun. 2019 May 21;10(1):2260
pubmed: 31113958
Trends Biochem Sci. 2017 May;42(5):329-330
pubmed: 28363673
BMC Bioinformatics. 2013 Sep 18;14:276
pubmed: 24047460
Science. 2018 Mar 2;359(6379):1042-1046
pubmed: 29496880
J Biomol Screen. 2008 Jun;13(5):424-9
pubmed: 18567842
Methods Mol Biol. 2012;819:469-86
pubmed: 22183552
Nature. 2020 Sep;585(7823):129-134
pubmed: 32848250
Nat Commun. 2020 Aug 28;11(1):4331
pubmed: 32859914
Chem Rev. 2021 Oct 27;121(20):12384-12444
pubmed: 34297541