Robust AMBER Force Field Parameters for Glutathionylated Cysteines.
AMBER force field parameters
S-glutathionylation
molecular dynamics simulations
post-translational modifications
redox modifications
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
09 Oct 2023
09 Oct 2023
Historique:
received:
19
09
2023
revised:
02
10
2023
accepted:
07
10
2023
medline:
2
11
2023
pubmed:
14
10
2023
entrez:
14
10
2023
Statut:
epublish
Résumé
S-glutathionylation is an oxidative post-translational modification, which is involved in the regulation of many cell signaling pathways. Increasing amounts of studies show that it is crucial in cell homeostasis and deregulated in several pathologies. However, the effect of S-glutathionylation on proteins' structure and activity is poorly understood, and a drastic lack of structural information at the atomic scale remains. Studies based on the use of molecular dynamics simulations, which can provide important information about modification-induced modulation of proteins' structure and function, are also sparse, and there is no benchmarked force field parameters for this modified cysteine. In this contribution, we provide robust AMBER parameters for S-glutathionylation, which we tested extensively against experimental data through a total of 33 μs molecular dynamics simulations. We show that our parameter set efficiently describes the global and local structural properties of S-glutathionylated proteins. These data provide the community with an important tool to foster new investigations into the effect of S-glutathionylation on protein dynamics and function, in a common effort to unravel the structural mechanisms underlying its critical role in cellular processes.
Identifiants
pubmed: 37834470
pii: ijms241915022
doi: 10.3390/ijms241915022
pmc: PMC10573104
pii:
doi:
Substances chimiques
Cysteine
K848JZ4886
Glutathione
GAN16C9B8O
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Références
Int J Mol Sci. 2020 Oct 30;21(21):
pubmed: 33143095
Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):26057-26065
pubmed: 31772010
Nature. 2010 Dec 23;468(7327):1115-8
pubmed: 21179168
J Chem Theory Comput. 2015 Aug 11;11(8):3696-713
pubmed: 26574453
J Biol Chem. 2011 Aug 5;286(31):27515-27
pubmed: 21632542
Nutrients. 2019 Aug 20;11(8):
pubmed: 31434242
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
FEBS Lett. 2018 Mar;592(6):1030-1041
pubmed: 29453875
Biochem J. 2014 Aug 15;462(1):39-52
pubmed: 24825169
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13086-91
pubmed: 16916935
Curr Opin Pharmacol. 2007 Aug;7(4):381-91
pubmed: 17662654
Front Plant Sci. 2014 Dec 23;5:712
pubmed: 25566286
Trends Biochem Sci. 2009 Feb;34(2):85-96
pubmed: 19135374
Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):619-25
pubmed: 15299791
Endocrinology. 2009 Mar;150(3):1122-31
pubmed: 18988672
Biochim Biophys Acta. 2009 Aug;1794(8):1218-23
pubmed: 19362171
Biochem Pharmacol. 2002 Sep;64(5-6):1057-64
pubmed: 12213605
Arch Biochem Biophys. 2021 Jun 15;704:108890
pubmed: 33894196
Phys Chem Chem Phys. 2022 Nov 9;24(43):26371-26397
pubmed: 36285789
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
J Phys Chem B. 2009 Oct 8;113(40):13279-90
pubmed: 19757835
Biochemistry (Mosc). 2023 Jul;88(7):924-943
pubmed: 37751864
J Chem Theory Comput. 2015 Apr 14;11(4):1864-74
pubmed: 26574392
Nat Methods. 2022 Jun;19(6):679-682
pubmed: 35637307
Free Radic Biol Med. 2007 Sep 15;43(6):883-98
pubmed: 17697933
Int J Mol Sci. 2023 Mar 14;24(6):
pubmed: 36982600
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Antioxid Redox Signal. 2013 Oct 20;19(12):1305-20
pubmed: 23541030
Free Radic Biol Med. 2018 May 20;120:204-216
pubmed: 29578070
Fungal Genet Biol. 2021 Mar;148:103506
pubmed: 33450403
Antioxid Redox Signal. 2012 Mar 15;16(6):496-505
pubmed: 21929356
Mol Interv. 2007 Dec;7(6):313-24
pubmed: 18199853
Int J Mol Sci. 2020 Apr 24;21(8):
pubmed: 32344771
Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3780-5
pubmed: 15004285
Proteins. 2008 Nov 15;73(3):765-83
pubmed: 18498103
Cell. 2014 Mar 13;156(6):1235-1246
pubmed: 24630725
J Mol Biol. 2009 Jan 23;385(3):889-901
pubmed: 18992757
J Biol Chem. 2009 Apr 3;284(14):9299-310
pubmed: 19158074
J Mol Biol. 2012 Jul 13;420(3):190-203
pubmed: 22522127
Curr Opin Chem Biol. 2023 Aug;75:102326
pubmed: 37245422
Biophys J. 2017 Dec 5;113(11):2354-2363
pubmed: 29211989
Oxid Med Cell Longev. 2013;2013:972913
pubmed: 23766865