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Biological Chemistry

Editor-in-Chief: Brüne, Bernhard

Editorial Board: Buchner, Johannes / Lei, Ming / Ludwig, Stephan / Sies, Helmut / Thomas, Douglas D. / Turk, Boris / Wittinghofer, Alfred

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IMPACT FACTOR 2017: 3.022

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Volume 389, Issue 9


Docking of tryptophan analogs to trytophanyl-tRNA synthetase: implications for non-canonical amino acid incorporations

M. Kamran Azim
  • 1H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Nediljko Budisa
Published Online: 2008-08-19 | DOI: https://doi.org/10.1515/BC.2008.133


Non-canonical amino acids (NAA), as building blocks for peptides and proteins during ribosomal translation, represent a nearly infinite supply of novel functions. The specific selection, activation and tRNA-charging of amino acids by aminoacyl-tRNA synthetases (AARS) in the aminoacylation reaction are essential steps. In most cases, aminoacylation of NAA is a good indication that the related amino acid will participate in ribosomal translation as well. However, testing the translational capacity of amino acid analogs has technical limitations. Therefore, a rapid and reliable in silico test for NAA recognition by AARS would be advantageous in experimental design. We chose tryptophanyl-tRNA synthetase from Escherichia coli as a model system for docking studies with various tryptophan analogs using the FlexX-Pharm strategy. We were able to calculate relative binding energies for Trp analogs in TrpRS that correlate well with their translational activities in E. coli. In particular, FlexX-Pharm predicted the binding sites of fluoro-, amino-, hydroxyl- and aza-containing Trp analogs within 1.5 Å of Trp in the homology model of E. coli TrpRS. Therefore, the use of ligand docking prior to NAA incorporation experiments might provide a straightforward means for determining NAA that can be efficiently incorporated into a protein.

Keywords: FlexX-Pharm; ligand docking; non-natural amino acids; protein engineering

About the article

Corresponding author

Received: 2008-01-09

Accepted: 2008-05-22

Published Online: 2008-08-19

Published in Print: 2008-09-01

Citation Information: Biological Chemistry, Volume 389, Issue 9, Pages 1173–1182, ISSN (Online) 1437-4315, ISSN (Print) 1431-6730, DOI: https://doi.org/10.1515/BC.2008.133.

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