Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation.
MD simulations
flavoproteins
redox potential
thermodynamic integration
Journal
Molecules (Basel, Switzerland)
ISSN: 1420-3049
Titre abrégé: Molecules
Pays: Switzerland
ID NLM: 100964009
Informations de publication
Date de publication:
11 Aug 2023
11 Aug 2023
Historique:
received:
30
06
2023
revised:
07
08
2023
accepted:
09
08
2023
medline:
28
8
2023
pubmed:
26
8
2023
entrez:
26
8
2023
Statut:
epublish
Résumé
Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from
Identifiants
pubmed: 37630271
pii: molecules28166016
doi: 10.3390/molecules28166016
pmc: PMC10459689
pii:
doi:
Substances chimiques
Flavodoxin
0
Flavoproteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : European Union
ID : PE_00000019 "HEAL ITALIA"
Références
J Comput Chem. 2005 Dec;26(16):1701-18
pubmed: 16211538
Biomolecules. 2021 Jul 27;11(8):
pubmed: 34439771
Appl Microbiol Biotechnol. 2013 Jun;97(12):5177-88
pubmed: 23640366
Phys Rev Lett. 2003 Oct 3;91(14):140601
pubmed: 14611511
Chem Sci. 2019 Dec 2;11(4):1140-1152
pubmed: 34084371
Molecules. 2022 Feb 05;27(3):
pubmed: 35164342
J Comput Chem. 2012 Jun 30;33(17):1467-77
pubmed: 22528559
J Biotechnol. 2006 Aug 5;124(4):670-89
pubmed: 16712999
Biochim Biophys Acta Bioenerg. 2019 Mar 1;1860(3):233-258
pubmed: 30419202
Biochemistry. 1997 Feb 11;36(6):1259-80
pubmed: 9063874
J Phys Chem B. 2015 Apr 30;119(17):5386-91
pubmed: 25856548
Biochemistry. 2001 Jul 31;40(30):8686-95
pubmed: 11467928
Biochemistry. 1990 Nov 13;29(45):10364-75
pubmed: 2261478
J Phys Chem A. 2008 Dec 18;112(50):13053-7
pubmed: 18828581
Biochemistry. 1998 Jul 7;37(27):9668-78
pubmed: 9657679
J Comput Aided Mol Des. 2012 May;26(5):569-76
pubmed: 22350568
J Phys Chem B. 2010 Nov 25;114(46):14907-15
pubmed: 20961131
Biochemistry. 1995 Mar 14;34(10):3183-92
pubmed: 7880813
Chembiochem. 2005 Apr;6(4):738-46
pubmed: 15747387
Biochemistry. 1994 Dec 27;33(51):15298-308
pubmed: 7803393
Methods Mol Biol. 2021;2280:135-155
pubmed: 33751433
J Phys Chem B. 2011 Apr 7;115(13):3632-41
pubmed: 21410212
J Am Chem Soc. 2003 Dec 24;125(51):15789-95
pubmed: 14677969
J Chem Inf Model. 2022 Oct 10;62(19):4748-4759
pubmed: 36126254
ACS Cent Sci. 2018 Dec 26;4(12):1708-1718
pubmed: 30648154
Eur J Biochem. 1984 Feb 1;138(3):481-9
pubmed: 6692831
J Mol Biol. 1977 Nov 25;117(1):195-225
pubmed: 599565
J Biol Chem. 2007 Aug 31;282(35):25240-6
pubmed: 17602164
J Comput Chem. 2017 Jul 5;38(18):1612-1621
pubmed: 28470751
J Chem Inf Model. 2011 Apr 25;51(4):947-58
pubmed: 21417269
Appl Environ Microbiol. 2004 Feb;70(2):873-82
pubmed: 14766567
Biochemistry. 1999 Sep 21;38(38):12377-86
pubmed: 10493805
Antioxid Redox Signal. 2014 May 20;20(15):2372-415
pubmed: 23875805
Biochemistry. 1996 Dec 17;35(50):15980-8
pubmed: 8973168
Biophys J. 2010 May 19;98(10):2309-16
pubmed: 20483340
J Chem Inf Model. 2017 Dec 26;57(12):2911-2937
pubmed: 29243483
Curr Opin Biotechnol. 2000 Aug;11(4):369-76
pubmed: 10975456
Biochemistry. 2001 Nov 13;40(45):13548-55
pubmed: 11695902
Biochemistry. 1999 Jun 1;38(22):7168-76
pubmed: 10353827
J Chem Phys. 2007 Jan 7;126(1):014101
pubmed: 17212484
J Comput Chem. 2013 Sep 30;34(25):2135-45
pubmed: 23832629
J Comput Chem. 2019 Dec 15;40(32):2834-2842
pubmed: 31471978
J Mol Biol. 1991 Mar 5;218(1):195-208
pubmed: 2002503
Commun Chem. 2021 May 11;4(1):61
pubmed: 36697634
Curr Opin Struct Biol. 2016 Dec;41:19-26
pubmed: 27266331
J Chem Theory Comput. 2013 Sep 10;9(9):3889-99
pubmed: 26592384
Biochemistry. 1994 Jul 19;33(28):8505-14
pubmed: 8031784