Cooperative and directional folding of the preQ1 riboswitch aptamer domain

J Am Chem Soc. 2011 Mar 30;133(12):4196-9. doi: 10.1021/ja110411m. Epub 2011 Mar 4.

Abstract

Riboswitches are cis-acting RNA fragments that regulate gene expression by sensing cellular levels of the associated small metabolites. In bacteria, the class I preQ(1) riboswitch allows the fine-tuning of queuosine biosynthesis in response to the intracellular concentration of the queuosine anabolic intermediate preQ(1). When binding preQ(1), the aptamer domain undergoes a significant degree of secondary and tertiary structural rearrangement and folds into an H-type pseudoknot. Conformational "switching" of the riboswitch aptamer domain upon recognizing its cognate metabolite plays a key role in the regulatory mechanism of the preQ(1) riboswitch. We investigate the folding mechanism of the preQ(1) riboswitch aptamer domain using all-atom Go̅-model simulations. The folding pathway of such a single domain is found to be cooperative and sequentially coordinated, as the folding proceeds in the 5' → 3' direction. This kinetically efficient folding mechanism suggests a fast ligand-binding response in competition with RNA elongation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aptamers, Nucleotide / chemistry*
  • Aptamers, Nucleotide / genetics
  • Bacillus subtilis / genetics
  • Kinetics
  • Nucleic Acid Conformation
  • Nucleoside Q / chemistry*
  • Nucleoside Q / genetics
  • Riboswitch*

Substances

  • Aptamers, Nucleotide
  • Riboswitch
  • Nucleoside Q