Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
19 10 2023
19 10 2023
Historique:
received:
24
05
2022
accepted:
10
09
2023
medline:
23
10
2023
pubmed:
20
10
2023
entrez:
19
10
2023
Statut:
epublish
Résumé
Recent breakthroughs in highly accurate protein structure prediction using deep neural networks have made considerable progress in solving the structure prediction component of the 'protein folding problem'. However, predicting detailed mechanisms of how proteins fold into specific native structures remains challenging, especially for multidomain proteins constituting most of the proteomes. Here, we develop a simple structure-based statistical mechanical model that introduces nonlocal interactions driving the folding of multidomain proteins. Our model successfully predicts protein folding processes consistent with experiments, without the limitations of protein size and shape. Furthermore, slight modifications of the model allow prediction of disulfide-oxidative and disulfide-intact protein folding. These predictions depict details of the folding processes beyond reproducing experimental results and provide a rationale for the folding mechanisms. Thus, our physics-based models enable accurate prediction of protein folding mechanisms with low computational complexity, paving the way for solving the folding process component of the 'protein folding problem'.
Identifiants
pubmed: 37857633
doi: 10.1038/s41467-023-41664-1
pii: 10.1038/s41467-023-41664-1
pmc: PMC10587348
doi:
Substances chimiques
Proteins
0
Disulfides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6338Informations de copyright
© 2023. Springer Nature Limited.
Références
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13286-91
pubmed: 14595026
Proteins. 1995 Mar;21(3):167-95
pubmed: 7784423
J Mol Biol. 2007 Mar 9;366(5):1624-38
pubmed: 17222865
Adv Protein Chem. 1995;47:83-229
pubmed: 8561052
J Chem Phys. 2011 Mar 28;134(12):125102
pubmed: 21456702
Nat Struct Biol. 1999 Sep;6(9):825-31
pubmed: 10467093
J Am Chem Soc. 2008 Jan 23;130(3):796-7
pubmed: 18166059
Annu Rev Biophys Bioeng. 1983;12:183-210
pubmed: 6347038
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15969-74
pubmed: 25267632
J Mol Biol. 2001 Jul 6;310(2):311-25
pubmed: 11428892
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15863-4
pubmed: 25349434
Biochemistry. 1996 Sep 10;35(36):11734-46
pubmed: 8794754
Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18320-5
pubmed: 19020085
Nat Struct Biol. 1995 Aug;2(8):674-9
pubmed: 7552729
Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17880-5
pubmed: 24128764
PLoS One. 2015 Dec 14;10(12):e0145125
pubmed: 26658942
J Mol Biol. 2000 Mar 17;297(1):193-210
pubmed: 10704316
Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8625-30
pubmed: 18550823
Science. 2021 Aug 20;373(6557):871-876
pubmed: 34282049
EMBO J. 1999 Sep 1;18(17):4794-803
pubmed: 10469657
J Mol Biol. 2004 Jun 4;339(3):555-69
pubmed: 15147842
Molecules. 2022 Jul 12;27(14):
pubmed: 35889332
J Mol Biol. 2007 Apr 20;368(1):219-29
pubmed: 17331539
Proc Natl Acad Sci U S A. 2004 May 25;101(21):7976-81
pubmed: 15150406
Phys Rev Lett. 2002 Jun 24;88(25 Pt 1):258101
pubmed: 12097132
Fold Des. 1998;3(4):R81-91
pubmed: 9710577
Adv Protein Chem. 2000;53:209-82
pubmed: 10751946
Science. 1973 Jul 20;181(4096):223-30
pubmed: 4124164
FEBS Lett. 2002 Jun 19;521(1-3):77-80
pubmed: 12067730
J Chem Phys. 2013 Mar 14;138(10):105101
pubmed: 23514521
J Mol Biol. 2011 Jul 8;410(2):329-42
pubmed: 21554889
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7775-80
pubmed: 20385843
J Mol Biol. 1995 Nov 24;254(2):260-88
pubmed: 7490748
Nat Struct Biol. 1999 Nov;6(11):1016-24
pubmed: 10542092
Nat Struct Biol. 1999 Nov;6(11):1010-6
pubmed: 10542091
Proc Natl Acad Sci U S A. 2006 May 9;103(19):7298-303
pubmed: 16648265
Science. 2011 Oct 28;334(6055):517-20
pubmed: 22034434
Biochemistry. 2000 Apr 18;39(15):4207-16
pubmed: 10757967
J Mol Biol. 1998 Nov 13;283(5):1027-36
pubmed: 9799641
Biophys Physicobiol. 2016 Nov 18;13:281-293
pubmed: 28409080
Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):9890-5
pubmed: 26216963
Biophys Rev. 2018 Apr;10(2):163-181
pubmed: 29307002
J Mol Biol. 2007 Nov 23;374(2):528-46
pubmed: 17942114
J Chem Theory Comput. 2012 Nov 13;8(11):4646-56
pubmed: 26605620
Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11311-6
pubmed: 10500173
J Mol Biol. 1996 Nov 8;263(4):531-8
pubmed: 8918936
Bioinformatics. 2022 Mar 28;38(7):1881-1887
pubmed: 35099504
Acc Chem Res. 2017 Jan 17;50(1):105-111
pubmed: 28032989
J Chem Phys. 2009 Apr 14;130(14):145104
pubmed: 19368477
Protein Sci. 2002 May;11(5):1136-51
pubmed: 11967370
Nucleic Acids Res. 2020 Jan 8;48(D1):D376-D382
pubmed: 31724711
Nature. 1992 Jul 23;358(6384):302-7
pubmed: 1641003
Science. 1991 Sep 20;253(5026):1386-93
pubmed: 1716783
Proteins. 1989;6(2):87-103
pubmed: 2695928
Protein Eng Des Sel. 2014 Mar;27(3):65-72
pubmed: 24407015
J Mol Biol. 1998 Apr 17;277(5):997-1005
pubmed: 9571017
Science. 1993 Nov 5;262(5135):896-900
pubmed: 8235611
J Mol Biol. 2001 Jul 20;310(4):919-35
pubmed: 11453698
J Phys Chem B. 2018 Dec 13;122(49):11039-11047
pubmed: 30048131
J Mol Biol. 1992 Apr 5;224(3):805-18
pubmed: 1569558
J Am Chem Soc. 2011 Apr 13;133(14):5372-9
pubmed: 21417380
Annu Rev Biophys. 2008;37:289-316
pubmed: 18573083
Proteins. 2006 Feb 1;62(2):399-410
pubmed: 16302220
Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13865-70
pubmed: 18772375