Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins

Hoang Linh Nguyen, Dang Lan Pham, Edward P. O'Brien, Mai Suan Li

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The antibiotic activity of erythromycin, which reversibly binds to a site within the bacterial ribosome exit tunnel, against many gram positive microorganisms indicates that it effectively inhibits the production of proteins. Similar to other macrolides, the activity of erythromycin is far from universal, as some peptides can bypass the macrolide-obstructed exit tunnel and become partially or fully synthesized. It is unclear why, at the molecular level, some proteins can be synthesized while others cannot. Here, we use steered molecular dynamics simulations to examine how erythromycin inhibits synthesis of the peptide ErmCL but not the peptide H-NS. By pulling these peptides through the exit tunnel of the E.coli ribosome with and without erythromycin present, we find that erythromycin directly interacts with both nascent peptides, but the force required for ErmCL to bypass erythromycin is greater than that of H-NS. The largest forces arise three to six residues from their N-terminus as they start to bypass Erythromycin. Decomposing the interaction energies between erythromycin and the peptides at this point, we find that there are stronger electrostatic and dispersion interactions with the more C-terminal residues of ErmCL than with H-NS. These results suggest that erythromycin slows or stalls synthesis of ErmCL compared to H-NS due to stronger interactions with particular residue positions along the nascent protein.

Original languageEnglish (US)
Article number6460
JournalScientific reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Erythromycin
Static Electricity
Peptides
Proteins
Macrolides
Ribosomes
Molecular Dynamics Simulation
Escherichia coli
Anti-Bacterial Agents

All Science Journal Classification (ASJC) codes

  • General

Cite this

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title = "Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins",
abstract = "The antibiotic activity of erythromycin, which reversibly binds to a site within the bacterial ribosome exit tunnel, against many gram positive microorganisms indicates that it effectively inhibits the production of proteins. Similar to other macrolides, the activity of erythromycin is far from universal, as some peptides can bypass the macrolide-obstructed exit tunnel and become partially or fully synthesized. It is unclear why, at the molecular level, some proteins can be synthesized while others cannot. Here, we use steered molecular dynamics simulations to examine how erythromycin inhibits synthesis of the peptide ErmCL but not the peptide H-NS. By pulling these peptides through the exit tunnel of the E.coli ribosome with and without erythromycin present, we find that erythromycin directly interacts with both nascent peptides, but the force required for ErmCL to bypass erythromycin is greater than that of H-NS. The largest forces arise three to six residues from their N-terminus as they start to bypass Erythromycin. Decomposing the interaction energies between erythromycin and the peptides at this point, we find that there are stronger electrostatic and dispersion interactions with the more C-terminal residues of ErmCL than with H-NS. These results suggest that erythromycin slows or stalls synthesis of ErmCL compared to H-NS due to stronger interactions with particular residue positions along the nascent protein.",
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Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins. / Nguyen, Hoang Linh; Pham, Dang Lan; O'Brien, Edward P.; Li, Mai Suan.

In: Scientific reports, Vol. 8, No. 1, 6460, 01.12.2018.

Research output: Contribution to journalArticle

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