An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches
نویسندگان
چکیده
منابع مشابه
Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches.
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply four prediction tools to a class of double glycine riboswitches that can bind two ligands cooperatively. A novel method (BPPalign), RMdetect, JAR3D, and Ros...
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Site-directed spin labeling with continuous wave electron paramagnetic resonance (EPR) spectroscopy was utilized to characterize dynamic features of the kink-turn motif formed through a leader-linker interaction in the Vibrio cholerae glycine riboswitch. Efficient incorporation of spin-labels into select sites within the phosphate backbone of the leader-linker region proceeded via splinted liga...
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A set of 12 fluorogenic glycine riboswitches with different thermodynamic and kinetic response properties was engineered. For the design of functional riboswitches, a three-part RNA approach was applied based on the idea of linking a RNA sensor, transmitter and actuator part together. For the RNA sensor and actuator part, we used the tandem glycine aptamer structure from Bacillus subtillis, and...
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Signal transduction upon binding of a ligand to a membrane protein can occur not only via allosteric conformational changes but also through fluctuations. We report a numerical study on the influence of conformational fluctuations on the cooperativity of a binding reaction in a simple model of an integral membrane receptor consisting of transmembrane helices. We find that small fluctuations lat...
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In this issue of Chemistry & Biology, Trausch and Batey report a discrepancy between ligand binding affinity and the effect of transcription termination in a THF riboswitch, raising some important questions about our current understanding of ligand-dependent RNA switches.
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ژورنال
عنوان ژورنال: RNA
سال: 2012
ISSN: 1355-8382
DOI: 10.1261/rna.031286.111