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Updated: Jul 24, 2026

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
Published on: August 7, 2021
Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation
Chiansan Ma1, Nathan A Baker, Simpson Joseph
1Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA. chiansan@yale.edu
Abstract:
The binding of paromomycin and similar antibiotics to the small (30S) ribosomal subunit has been studied using continuum electrostatics methods. Crystallographic information from a complex of paromomycin with the 30S subunit was used as a framework to develop structures of similar antibiotics in the same ribosomal binding site. Total binding energies were calculated from electrostatic properties obtained by solution of the Poisson-Boltzmann equation combined with a surface area-dependent apolar term. These computed results showed good correlation with experimental data. Additionally, calculation of the ribosomal electrostatic potential in the paromomycin binding site provided insight into the electrostatic mechanisms for aminoglycoside binding and clues for the rational design of more effective antibiotics.
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