Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria.
Journal
Biophysical journal
ISSN: 1542-0086
Titre abrégé: Biophys J
Pays: United States
ID NLM: 0370626
Informations de publication
Date de publication:
04 01 2022
04 01 2022
Historique:
received:
10
05
2021
revised:
17
09
2021
accepted:
29
11
2021
pubmed:
6
12
2021
medline:
19
3
2022
entrez:
5
12
2021
Statut:
ppublish
Résumé
Understanding the relationship between protein structures and their function is still an open question that becomes very challenging when allostery plays an important functional role. Allosteric proteins, in fact, exploit different ranges of motions (from sidechain local fluctuations to long-range collective motions) to effectively couple distant binding sites, and of particular interest is whether allosteric proteins of the same families with similar functions and structures also necessarily share the same allosteric mechanisms. Here, we compared the early dynamics initiating the allosteric communication of a prototypical allosteric enzyme from two different organisms, i.e., the imidazole glycerol phosphate synthase (IGPS) enzymes from the thermophilic bacteria and the yeast, working at high and room temperatures, respectively. By combining molecular dynamics simulations and network models derived from graph theory, we found rather distinct early allosteric dynamics in the IGPS from the two organisms, involving significatively different allosteric pathways in terms of both local and collective motions. Given the successful prediction of key allosteric residues in the bacterial IGPS, whose mutation disrupts its allosteric communication, the outcome of this study paves the way for future experimental studies on the yeast IGPS that could foster therapeutic applications by exploiting the control of IGPS enzyme allostery.
Identifiants
pubmed: 34864045
pii: S0006-3495(21)03881-9
doi: 10.1016/j.bpj.2021.11.2888
pmc: PMC8758406
pii:
doi:
Substances chimiques
imidazole glycerol phosphate synthase
EC 3.5.1.-
Aminohydrolases
EC 3.5.4.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
119-130Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM106121
Pays : United States
Informations de copyright
Copyright © 2021 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Références
Cell. 2004 Feb 6;116(3):417-29
pubmed: 15016376
Proteins. 2008 Mar;70(4):1294-312
pubmed: 17876828
Structure. 2019 Apr 2;27(4):566-578
pubmed: 30744993
Philos Trans R Soc Lond B Biol Sci. 2018 Jun 19;373(1749):
pubmed: 29735740
BMC Syst Biol. 2018 Jul 31;12(1):80
pubmed: 30064421
J Biol Chem. 2021 Sep;297(3):101061
pubmed: 34384784
Curr Opin Struct Biol. 2018 Jun;50:1-8
pubmed: 29080471
J Phys Chem B. 2019 Apr 25;123(16):3452-3461
pubmed: 30943726
Methods Mol Biol. 2021;2253:137-151
pubmed: 33315222
PLoS Comput Biol. 2013;9(5):e1003046
pubmed: 23696718
J Comput Chem. 2004 Jul 15;25(9):1157-74
pubmed: 15116359
Cell Chem Biol. 2019 Nov 21;26(11):1501-1514.e9
pubmed: 31495713
Biochemistry. 2016 Nov 29;55(47):6484-6494
pubmed: 27797506
Proc Natl Acad Sci U S A. 2012 May 29;109(22):E1428-36
pubmed: 22586084
Biophys J. 2001 Jan;80(1):505-15
pubmed: 11159421
Acta Naturae. 2015 Oct-Dec;7(4):34-45
pubmed: 26798490
Methods Mol Biol. 2012;796:385-98
pubmed: 22052502
Mol Pharmacol. 1999 Apr;55(4):778-86
pubmed: 10101037
Front Mol Biosci. 2018 Feb 06;5:4
pubmed: 29468164
Biophys J. 2005 Jul;89(1):475-87
pubmed: 15849257
J Biol Chem. 2005 Jul 29;280(30):27477-80
pubmed: 15932877
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
Nat Commun. 2020 Jul 31;11(1):3862
pubmed: 32737291
Chem Rev. 2016 Jun 8;116(11):6503-15
pubmed: 26876046
Chem Rev. 2016 Jun 8;116(11):6588-606
pubmed: 26726755
Biochemistry. 2020 Jul 28;59(29):2729-2742
pubmed: 32633500
J Chem Theory Comput. 2019 Apr 9;15(4):2116-2126
pubmed: 30836000
Biochemistry. 2003 Jun 17;42(23):7003-12
pubmed: 12795595
Biophys Rev. 2020 Feb;12(1):155-174
pubmed: 31838649
Proteins. 1993 Dec;17(4):412-25
pubmed: 8108382
Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3414-E3423
pubmed: 28396388
Nature. 1986 Nov 6-12;324(6092):80-4
pubmed: 3537803
PLoS One. 2019 Jul 26;14(7):e0220061
pubmed: 31348798
Phys Life Rev. 2013 Mar;10(1):1-26
pubmed: 23199577
J Chem Phys. 2020 Oct 7;153(13):134104
pubmed: 33032427
Nat Struct Biol. 2003 Jan;10(1):59-69
pubmed: 12483203
Structure. 2001 Oct;9(10):987-97
pubmed: 11591353
Chem Biol. 2012 Dec 21;19(12):1589-99
pubmed: 23261602
J Chem Theory Comput. 2020 May 12;16(5):3385-3395
pubmed: 32251581
Biophys Rev. 2020 Apr;12(2):443-452
pubmed: 32198636
Curr Protoc Protein Sci. 2016 Nov 1;86:2.9.1-2.9.37
pubmed: 27801516
Structure. 2002 Feb;10(2):185-93
pubmed: 11839304
Biochemistry. 2001 Jan 30;40(4):876-87
pubmed: 11170408
Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12201-E12208
pubmed: 30530700
Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303
pubmed: 29788355
Sci Rep. 2016 Aug 01;6:30750
pubmed: 27476470
Methods Mol Biol. 2014;1084:193-226
pubmed: 24061923
Nat Commun. 2021 May 12;12(1):2748
pubmed: 33980881
Front Physiol. 2016 Aug 26;7:375
pubmed: 27616995
J Phys Chem Lett. 2021 May 6;12(17):4262-4267
pubmed: 33904738
Biochemistry. 2007 Feb 27;46(8):2156-73
pubmed: 17261030
J Chem Inf Model. 2019 May 28;59(5):2394-2406
pubmed: 30763088
Nat Rev Drug Discov. 2002 Mar;1(3):198-210
pubmed: 12120504
Biophys J. 2010 Oct 6;99(7):2245-54
pubmed: 20923659
Proteins. 2006 Mar 1;62(4):1053-61
pubmed: 16355416