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Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations

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  • Zhou Gong
  • Yunjie Zhao
  • Changjun Chen
  • Yong Duan
  • Yi Xiao

Abstract

Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Bacillus subtilis is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ1 entrance. The dynamic picture further suggests that the specific recognition of preQ1 by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ1 binding.

Suggested Citation

  • Zhou Gong & Yunjie Zhao & Changjun Chen & Yong Duan & Yi Xiao, 2014. "Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-12, March.
    • Handle: RePEc:plo:pone00:0092247
    DOI: 10.1371/journal.pone.0092247
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    References listed on IDEAS

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    1. Zhou Gong & Yunjie Zhao & Changjun Chen & Yi Xiao, 2012. "Computational Study of Unfolding and Regulation Mechanism of preQ1 Riboswitches," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-8, September.
    2. Alexander Serganov & Lili Huang & Dinshaw J. Patel, 2008. "Structural insights into amino acid binding and gene control by a lysine riboswitch," Nature, Nature, vol. 455(7217), pages 1263-1267, October.
    3. Wade Winkler & Ali Nahvi & Ronald R. Breaker, 2002. "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression," Nature, Nature, vol. 419(6910), pages 952-956, October.
    4. Robert T. Batey & Sunny D. Gilbert & Rebecca K. Montange, 2004. "Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine," Nature, Nature, vol. 432(7015), pages 411-415, November.
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