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Int. J. Mol. Sci. 2013, 14(11), 22741-22752; doi:10.3390/ijms141122741
Article

Small Molecule Binding, Docking, and Characterization of the Interaction between Pth1 and Peptidyl-tRNA

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Received: 9 October 2013 / Revised: 31 October 2013 / Accepted: 12 November 2013 / Published: 19 November 2013
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Abstract

Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding of piperonylpiperazine, a small molecule constituent of a combinatorial synthetic library common to most compounds with inhibitory activity, was mapped to Pth1 via NMR spectroscopy. We also report computational docking results, modeling piperonylpiperazine binding based on chemical shift perturbation mapping. Overall these studies promote Pth1 as a novel antibiotic target, contribute to understanding how Pth1 interacts with its substrate, advance the current model for cleavage, and demonstrate feasibility of small molecule inhibition.
Keywords: peptidyl-tRNA hydrolase; small angle neutron scattering; enzyme-substrate complex; docking; inhibition peptidyl-tRNA hydrolase; small angle neutron scattering; enzyme-substrate complex; docking; inhibition
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Hames, M.C.; McFeeters, H.; Holloway, W.B.; Stanley, C.B.; Urban, V.S.; McFeeters, R.L. Small Molecule Binding, Docking, and Characterization of the Interaction between Pth1 and Peptidyl-tRNA. Int. J. Mol. Sci. 2013, 14, 22741-22752.

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