An enumerative algorithm for de novo design of proteins with diverse pocket structures.
NTF2-like proteins
high-throughput screening
protein design
protein pockets
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876
Informations de publication
Date de publication:
08 09 2020
08 09 2020
Historique:
pubmed:
26
8
2020
medline:
28
10
2020
entrez:
26
8
2020
Statut:
ppublish
Résumé
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
Identifiants
pubmed: 32839327
pii: 2005412117
doi: 10.1073/pnas.2005412117
pmc: PMC7486743
doi:
Substances chimiques
Nucleocytoplasmic Transport Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
22135-22145Informations de copyright
Copyright © 2020 the Author(s). Published by PNAS.
Déclaration de conflit d'intérêts
The authors declare no competing interest.
Références
BMC Bioinformatics. 2013 Nov 19;14:327
pubmed: 24246060
J Mol Biol. 2011 Jan 28;405(4):1079-100
pubmed: 20932976
Nature. 2017 Oct 5;550(7674):74-79
pubmed: 28953867
Nucleic Acids Res. 2002 May 15;30(10):e43
pubmed: 12000848
Nature. 2013 Sep 12;501(7466):212-216
pubmed: 24005320
Methods Mol Biol. 2008;426:419-35
pubmed: 18542881
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048
pubmed: 28430426
Sci Rep. 2018 Nov 1;8(1):16189
pubmed: 30385875
Proc Natl Acad Sci U S A. 1978 Jun;75(6):2574-8
pubmed: 275827
Nature. 2016 Sep 14;537(7620):320-7
pubmed: 27629638
J Am Chem Soc. 2012 Oct 3;134(39):16197-206
pubmed: 22871159
Curr Opin Struct Biol. 2009 Apr;19(2):145-55
pubmed: 19327982
Nature. 2002 Apr 11;416(6881):657-60
pubmed: 11948354
Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):E5478-85
pubmed: 26396255
Curr Opin Struct Biol. 2015 Aug;33:16-26
pubmed: 26093060
J Chem Inf Model. 2010 Apr 26;50(4):589-603
pubmed: 20205445
Nature. 2015 Dec 24;528(7583):580-4
pubmed: 26675729
Proteins. 2016 Feb;84(2):201-16
pubmed: 26575337
Science. 2016 May 6;352(6286):687-90
pubmed: 27151863
BMC Struct Biol. 2015 Oct 22;15:21
pubmed: 26492857
Protein Sci. 2017 Dec;26(12):2426-2437
pubmed: 28980354
J Biol Chem. 2019 Dec 13;294(50):19436-19443
pubmed: 31699898
Nature. 2018 Sep;561(7724):485-491
pubmed: 30209393
Science. 2017 Jan 13;355(6321):201-206
pubmed: 28082595
Science. 2017 Jul 14;357(6347):168-175
pubmed: 28706065
Nucleic Acids Res. 2016 Mar 18;44(5):e43
pubmed: 26553805
PLoS One. 2011;6(8):e24109
pubmed: 21909381
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
Nucleic Acids Res. 2014 Jan;42(Database issue):D304-9
pubmed: 24304899
Nature. 2012 Nov 8;491(7423):222-7
pubmed: 23135467
Nucleic Acids Res. 2005 Apr 22;33(7):2302-9
pubmed: 15849316
Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17668-73
pubmed: 17971437
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
pubmed: 19461840
Nat Methods. 2020 Jul;17(7):665-680
pubmed: 32483333
Fold Des. 1998;3(6):449-55
pubmed: 9889161
PLoS One. 2011;6(5):e19230
pubmed: 21603656