Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain.
Journal
Current opinion in biotechnology
ISSN: 1879-0429
Titre abrégé: Curr Opin Biotechnol
Pays: England
ID NLM: 9100492
Informations de publication
Date de publication:
10 2019
10 2019
Historique:
received:
31
08
2018
revised:
25
01
2019
accepted:
04
02
2019
pubmed:
10
3
2019
medline:
11
2
2020
entrez:
10
3
2019
Statut:
ppublish
Résumé
Metabolic models containing kinetic information can answer unique questions about cellular metabolism that are useful to metabolic engineering. Several kinetic modeling frameworks have recently been developed or improved. In addition, techniques for systematic identification of model structure, including regulatory interactions, have been reported. Each framework has advantages and limitations, which can make it difficult to choose the most appropriate framework. Common limitations are data availability and computational time, especially in large-scale modeling efforts. However, recently developed experimental techniques, parameter identification algorithms, as well as model reduction techniques help alleviate these computational bottlenecks. Opportunities for additional improvements may come from the rich literature in catalysis and chemical networks. In all, kinetic models are positioned to make significant impact in cellular engineering.
Identifiants
pubmed: 30851632
pii: S0958-1669(18)30155-1
doi: 10.1016/j.copbio.2019.02.005
pmc: PMC6731160
mid: NIHMS1034805
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
24-30Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM008449
Pays : United States
Informations de copyright
Copyright © 2019 Elsevier Ltd. All rights reserved.
Références
BMC Syst Biol. 2015 Aug 19;9:48
pubmed: 26286864
Bioinformatics. 2008 Mar 15;24(6):848-54
pubmed: 18267948
J R Soc Interface. 2013 Dec 04;11(91):20130505
pubmed: 24307566
J Proteomics. 2016 Mar 16;136:222-33
pubmed: 26825536
BMC Syst Biol. 2012 Jun 22;6:75
pubmed: 22727112
Nat Commun. 2018 Jan 12;9(1):184
pubmed: 29330441
Metab Eng. 2018 Jan;45:158-170
pubmed: 29233745
PLoS Comput Biol. 2007 Oct;3(10):1871-78
pubmed: 17922568
Metab Eng. 2012 Nov;14(6):672-86
pubmed: 23026121
Cell Syst. 2015 Oct 28;1(4):283-92
pubmed: 27136057
Integr Biol (Camb). 2015 Aug;7(8):895-903
pubmed: 25855352
BMC Bioinformatics. 2017 Jan 21;18(1):52
pubmed: 28109249
Bioinformatics. 2014 Oct 15;30(20):2991-2
pubmed: 25005749
BMC Syst Biol. 2017 Feb 13;11(1):17
pubmed: 28193218
Cell. 2018 Jan 11;172(1-2):358-372.e23
pubmed: 29307493
Metab Eng. 2011 Jan;13(1):60-75
pubmed: 21075211
Mol Syst Biol. 2017 Jan 3;13(1):903
pubmed: 28049137
BMC Syst Biol. 2014 May 03;8:52
pubmed: 24885656
Metab Eng. 2016 Jan;33:158-168
pubmed: 26474788
PLoS Comput Biol. 2017 Jul 20;13(7):e1005444
pubmed: 28727725
Science. 2016 Oct 28;354(6311):
pubmed: 27789812
Nat Commun. 2016 Dec 20;7:13806
pubmed: 27996047
Mol Syst Biol. 2017 Jan 16;13(1):907
pubmed: 28093455
Metab Eng. 2009 Jan;11(1):20-30
pubmed: 18718548
BMC Syst Biol. 2016 Jun 06;10(1):40
pubmed: 27266508
Biophys J. 2010 Jan 20;98(2):175-85
pubmed: 20338839
Biophys J. 2006 Feb 15;90(4):1453-61
pubmed: 16299075
BMC Bioinformatics. 2017 Jan 3;18(1):2
pubmed: 28049424
Biotechnol J. 2013 Jul;8(7):768-75
pubmed: 23813763
Eur J Biochem. 2004 Aug;271(16):3348-59
pubmed: 15291812
Biotechnol J. 2013 Sep;8(9):1090-104
pubmed: 23450699
Metab Eng. 2014 Sep;25:63-71
pubmed: 24972370
PLoS Comput Biol. 2013;9(1):e1002888
pubmed: 23382663
Biotechnol Adv. 2017 Dec;35(8):981-1003
pubmed: 28916392
PLoS Comput Biol. 2016 Jul 28;12(7):e1005039
pubmed: 27467583
J Cheminform. 2015 Aug 28;7:44
pubmed: 26322134
Sci Rep. 2016 Jul 15;6:29635
pubmed: 27417285
Biosystems. 2018 Jul;169-170:20-25
pubmed: 29857031
Trends Biotechnol. 2010 Aug;28(8):391-7
pubmed: 20646768
Nat Genet. 2007 Nov;39(11):1369-75
pubmed: 17952072
Synth Syst Biotechnol. 2017 Nov 15;2(4):243-252
pubmed: 29552648
Biophys J. 2008 Dec 15;95(12):5606-17
pubmed: 18820235
PLoS Comput Biol. 2016 Mar 10;12(3):e1004800
pubmed: 26963521
Nat Biotechnol. 2013 Apr;31(4):357-61
pubmed: 23455438
PLoS Comput Biol. 2014 Apr 24;10(4):e1003580
pubmed: 24762745
Curr Opin Chem Biol. 2017 Feb;36:15-23
pubmed: 28064089
Biophys J. 2017 Sep 5;113(5):1150-1162
pubmed: 28877496
Bioinformatics. 2005 Apr 15;21(8):1603-9
pubmed: 15613400
Bull Math Biol. 2017 Jul;79(7):1449-1486
pubmed: 28656491
Metab Eng. 2017 May;41:144-151
pubmed: 28389394
Metab Eng. 2016 Sep;37:46-62
pubmed: 27113440
NPJ Syst Biol Appl. 2018 May 29;4:19
pubmed: 29872542