Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding.
Riboswitches are gene-regulating RNAs that are usually found in the 5'-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg(2+), Ca(2+), and Mn(2+) facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.
Lipfert
Jan
J
Department of Physics, Stanford University, Stanford, California 94305, USA.
Sim
Adelene Y L
AY
Herschlag
Daniel
D
Doniach
Sebastian
S
D020121:5' Untranslated Regions; D052157:Aptamers, Nucleotide / Q000737:chemistry; D001483:Base Sequence; D001665:Binding Sites; D002413:Cations, Divalent / Q000737:chemistry; D005998:Glycine / Q000737:chemistry*; D017665:Hydroxyl Radical / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D053838:Scattering, Small Angle
D020121:5' Untranslated Regions; D052157:Aptamers, Nucleotide; D002413:Cations, Divalent; D008024:Ligands; D012329:RNA, Bacterial; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; D017665:Hydroxyl Radical; D005998:Glycine