Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
13-21053S
Grantová Agentura České Republiky
DBI13-58737
National Science Foundation
DBI16-59726
National Science Foundation
APVV-16-0600
Agentúra na Podporu Výskumu a Vývoja
LM2015055
Ministerstvo Školství, Mládeže a Tělovýchovy
LM2010005
Ministerstvo Školství, Mládeže a Tělovýchovy
2018
MoA between the Institute of Microbiology, Czech Academy of Sciences, and the College of Biomedical Sciences, Larkin University.
PubMed
32397647
PubMed Central
PMC7248756
DOI
10.3390/molecules25092247
PII: molecules25092247
Knihovny.cz E-zdroje
- Klíčová slova
- entropy, global motion, ligand binding, molecular evolution, salt bridges,
- MeSH
- alosterická regulace MeSH
- arginin chemie metabolismus MeSH
- Bacillus subtilis chemie genetika metabolismus MeSH
- bakteriální proteiny chemie genetika metabolismus MeSH
- entropie MeSH
- Escherichia coli chemie genetika metabolismus MeSH
- fylogeneze MeSH
- konformace proteinů, alfa-helix MeSH
- konformace proteinů, beta-řetězec MeSH
- proteinové domény MeSH
- regulon genetika MeSH
- represorové proteiny chemie genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- simulace molekulární dynamiky MeSH
- vazba proteinů MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- arginin MeSH
- ArgR protein, Bacteria MeSH Prohlížeč
- bakteriální proteiny MeSH
- represorové proteiny MeSH
Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.
College of Biomedical Sciences Larkin University Miami FL 33169 USA
Department of Chemistry Princeton University Princeton NJ 08544 USA
Faculty of Sciences University of South Bohemia 37005 Ceske Budejovice Czechia
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