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J Am Chem Soc. 2002 Feb 20;124(7):1438-42.

Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation.

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Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.


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.

[Indexed for MEDLINE]

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