Insights on protein thermal stability: a graph representation of molecular interactions.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 08 2019
01 08 2019
Historique:
received:
01
08
2018
revised:
29
10
2018
accepted:
07
12
2018
pubmed:
12
12
2018
medline:
17
6
2020
entrez:
12
12
2018
Statut:
ppublish
Résumé
Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity. Here, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In this approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and area under the receiver operating characteristic curve of 78%. Code is available upon request to edoardo.milanetti@uniroma1.it. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 30535291
pii: 5237552
doi: 10.1093/bioinformatics/bty1011
pmc: PMC6662296
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2569-2577Informations de copyright
© The Author(s) 2018. Published by Oxford University Press.
Références
Protein Eng. 2000 Mar;13(3):179-91
pubmed: 10775659
Nature. 2001 Feb 1;409(6820):641-5
pubmed: 11214326
Nature. 2001 Feb 22;409(6823):1092-101
pubmed: 11234023
Protein Eng. 2003 Apr;16(4):279-86
pubmed: 12736371
Biophys J. 2003 Oct;85(4):2641-9
pubmed: 14507727
Prog Nucleic Acid Res Mol Biol. 2003;74:37-81
pubmed: 14510073
Biophys J. 2004 Jan;86(1 Pt 1):85-91
pubmed: 14695252
Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3325-6
pubmed: 14993602
Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3747-52
pubmed: 15007165
Structure. 2005 Jun;13(6):857-60
pubmed: 15939017
Biophys J. 2005 Dec;89(6):4159-70
pubmed: 16150969
J Comput Chem. 2005 Dec;26(16):1781-802
pubmed: 16222654
Biophys Chem. 2006 Feb 1;119(3):256-70
pubmed: 16253416
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D204-6
pubmed: 16381846
Ann N Y Acad Sci. 2005 Dec;1066:12-33
pubmed: 16533916
Protein Sci. 2006 Jul;15(7):1569-78
pubmed: 16815912
J Am Chem Soc. 2007 May 2;129(17):5374-5
pubmed: 17411056
Science. 1985 Oct 11;230(4722):132-8
pubmed: 17842674
J Chem Inf Model. 2008 Jan;48(1):119-27
pubmed: 18161956
BMC Struct Biol. 2008 Feb 29;8:14
pubmed: 18312638
Comput Biol Chem. 2009 Dec;33(6):445-50
pubmed: 19896904
Biophys J. 2010 Feb 17;98(4):667-77
pubmed: 20159163
Biophys J. 2010 Apr 7;98(7):1109-18
pubmed: 20371310
Proteins. 2010 Sep;78(12):2699-706
pubmed: 20589630
J Am Chem Soc. 2010 Nov 17;132(45):16240-6
pubmed: 20979399
Biophys J. 2010 Dec 1;99(11):3704-15
pubmed: 21112295
J Biosci. 2011 Jun;36(2):253-63
pubmed: 21654080
J Chem Inf Model. 2011 Jul 25;51(7):1623-33
pubmed: 21662246
Crit Rev Biochem Mol Biol. 1990;25(4):281-305
pubmed: 2225910
J Biomol Struct Dyn. 2012;29(5):961-71
pubmed: 22292954
J Mol Biol. 2012 Apr 13;417(5):413-24
pubmed: 22342930
J Chem Inf Model. 2012 Dec 21;52(12):3144-54
pubmed: 23146088
J Chem Inf Model. 2013 Sep 23;53(9):2448-61
pubmed: 23962324
PLoS One. 2014 Mar 19;9(3):e91659
pubmed: 24646884
Biochim Biophys Acta. 2014 Dec;1844(12):2174-81
pubmed: 25172393
Nucleic Acids Res. 2015 Jan;43(Database issue):D376-81
pubmed: 25348408
PLoS One. 2014 Nov 13;9(11):e112751
pubmed: 25393107
Chemphyschem. 2015 Dec 1;16(17):3599-602
pubmed: 26426928
Sci Rep. 2016 Mar 18;6:23257
pubmed: 26988870
Nucleic Acids Res. 2016 Jul 8;44(W1):W375-82
pubmed: 27151201
Nature. 2016 Sep 14;537(7620):320-7
pubmed: 27629638
Philos Trans A Math Phys Eng Sci. 2016 Nov 13;374(2080):
pubmed: 27698032
Curr Opin Struct Biol. 2017 Feb;42:117-128
pubmed: 28040640
Sci Rep. 2017 Apr 24;7:46568
pubmed: 28436442
Nat Commun. 2017 May 18;8:15428
pubmed: 28516908
J Biomol Struct Dyn. 2018 Sep;36(12):3265-3273
pubmed: 28952426
Bioinformatics. 2017 Nov 1;33(21):3415-3422
pubmed: 29036273
Biochemistry. 1979 Dec 11;18(25):5698-703
pubmed: 518863
Biopolymers. 1983 Dec;22(12):2577-637
pubmed: 6667333
Eur J Biochem. 1994 Mar 15;220(3):981-5
pubmed: 8143751
Proteins. 1996 Jan;24(1):81-91
pubmed: 8628735
J Mol Biol. 1997 Jun 20;269(4):631-43
pubmed: 9217266
Fold Des. 1997;2(4):S40-6
pubmed: 9269567