Abstract
The interaction of a highly conserved secondary structural RNA motif of Halobacterium halobium and Escherichia coli 23S ribosomal RNAs with the peptidyl transferase inhibitor antibiotic amicetin has been investigated by proton NMR spectroscopy and molecular modelling. The NMR spectra of the synthetic 35mer RNA motifs revealed spectral features characteristic of a stable, well folded A-RNA type tertiary conformation, including resolved resonances assigned to unpaired bases located in the middle of the motif strongly implicated in amicetin binding. Addition of amicetin to the 35mer RNA samples was accompanied by significant and discrete changes to the spectra which can be qualitatively interpreted to the changes induced to the local conformation of the RNA motifs arising from the formation of a specific complex with amicetin. These results are also supported by the unconstrained molecular model of RNA-amicetin complex which highlights potential interactions between the two molecular components.
Similar content being viewed by others
Article PDF
References
Mankin AS . Ribosomal antibiotics. Mol Biol 35: 509–520 ( 2001)
Vazquez D . Inhibitors of Protein Biosynthesis. Springer-Verlag, Berlin ( 1979)
Hermann T . Chemical and functional diversity of small molecule ligands for RNA. Biopolymers 70: 4–18 ( 2003)
Kirillov S, Porse BT, Vester B, Wooley P, Garrett RA . Movement of the 3′-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics. FEBS Lett 406: 223–233 ( 1997)
Vester B, Garrett RA . The importance of highly conserved nucleotides in the binding region of chlorampenicol at the peptidyl transfer center of Escherichia coli 23S ribosomal RNA. EMBO J 7: 3577–3587 ( 1988)
Cundliffe E . Involvement of specific portions of rRNA in defined ribosomal functions: a study utilizing antibiotics. In Structure, Function and Genetics of Ribosomes Ed., B. Hardesty et al., pp. 586–604, Springer-Verlag, New York ( 1986)
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA . The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905–920 ( 2000)
Carter AP, Clemens WM, Brodersen DE, Morgan-Warren RE, Wimberley B, Ramakrishnan V . Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340–348 ( 2000)
Schlunzen F, Zarivach R, Harms J, Bashan A, Tocil A, Albercht R, Yonath A, Franceshi F . Structural basis for the interaction of antibiotics with peptidyl transferase center in eubacteria. Nature 413: 814–818 ( 2001)
Hansen J, Moore PB, Steitz TA . Structures of five antibiotics bound at the peptidyl transferase centre of the large ribosomal subunit. J Mol Biol 330: 1061–1075 ( 2003)
Polacek N, Mankin AS . The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit Rev Biochem Mol Biol 40: 285–311 ( 2005)
Leviev IG, Fonseca CR, Phan H, Garrett RA, Heilek G, Noller HF, Mankin AS . A conserved secondary structural motif in the 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide formation. EMBO J 13: 1682–1686 ( 1994)
Smith JL, Sundaralingam M . The structure of the antibiotic amicetin consisting of nucleobase, disaccharide and amino acid moieties. Acta Cryst B37: 1095–1101 ( 1981)
Tan GT, DeBlasio A, Mankin AS . Mutations in the peptidyl transferase centre of 23S rRNA reveal the site of action of sparsomycin, a universal inhibitor of translation. J Mol Biol 261: 222–230 ( 1996)
Phelan M, Banks RJ, Conn GL, Ramesh V . NMR studies of the structure and Mg2+ binding properties of a conserved ‘hammerhead’ RNA motif of EMCV picornavirus RNA. Nucleic Acids Res 32: 4715–4724 ( 2004)
Gallego J, Varani G . Targeting RNA with small-molecule drugs: therapeutic promise and chemical challenges. Acc Chem Res 34: 836–884 ( 2001)
Zuker M . Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415 ( 2003)
Wüthrich K . NMR of Proteins and Nucleic Acids. John Wiley & Sons, New York ( 1986)
Piotto M, Saudek V, Sklenar V . Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR 2: 661–665 ( 1992)
Brunger AT . X-PLOR Version 3.1 Manual. Yale University Press New Haven USA, Connecticut ( 1992)
Miller JL, Cheatham TE, Kollman PA . Simulation of nucleic acids. In Oxford Handbook of Nucleic Acids. Ed., S. Neidle, pp. 99–115, Oxford University Press, USA ( 1999)
Ennifar E, Nikulin A, Tishchenko S, Serganov A, Nevskaya N, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P . The crystal structure of UUCG tetraloop. J Mol Biol 304: 35–42 ( 2000)
Varani G, Cheong C, Tinoco I . Structure of an unusually stable RNA hairpin. Biochemistry 30: 3280–3289 ( 1991)
Gray DM, Huang SH, Johnson KH . Absorption and circular dichroism of nucleic acid duplexes and triplexes. Methods Enzymol 261: 271–299 ( 1995)
Donarski JA . Synthesis and NMR studies of the binding of amicetin antibiotic to conserved secondary structural RNA motifs of 23S ribosomal RNAs. Ph.D. Thesis, UMIST ( 2004)
Varani G, Aboul-ela F, Allain FHT . NMR investigation of RNA structure. Progress in NMR Spectroscopy 29: 51–127 ( 1996)
Jiang F, Fiala R, Live D, Kumar A, Pate DJ . RNA folding topology and intermolecular contacts in the AMP-RNA aptamer complex. Biochemistry 35: 13250–13266 ( 1996)
Bocharov EV, Gudkov AT, Budovskaya EV, Arseniev AS . Conformational independence of N- and C-domains in ribosomal protein L7/L12 and in the complex with protein L10. FEBS Lett 423: 347–350 ( 1988)
Ramesh V, Frederick RO, Syed SEH, Gibson CF, Yang JC, Roberts GCK . The interactions of Escherichia coli trp repressor with tryptophan and with an operator oligonucleotide. NMR studies using selective 15N-labelled protein. Eur J Biochem 225: 601–608 ( 1994)
Levy SB . Antibiotic Resistance: An Ecological Imbalance. Abstracts of papers of Symp on Antibiotic resistance: origins, evolution, selection and spread Ciba Foundation, No. 207, London ( 1996)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Donarski, J., Shammas, C., Banks, R. et al. NMR and Molecular Modelling Studies of the Binding of Amicetin Antibiotic to Conserved Secondary Structural Motifs of 23S Ribosomal RNAs. J Antibiot 59, 177–183 (2006). https://doi.org/10.1038/ja.2006.25
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/ja.2006.25