Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching.

Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding.

In-cell NMR spectroscopy in Escherichia coli.

A living cell is a complex system that contains many biological macromolecules and small molecules necessary for survival, in a relatively small volume. It is within this crowded and complex cellular environment that proteins function making in-cell studies of protein structure and binding interactions an exciting and important area of study. Nuclear magnetic resonance (NMR) spectroscopy is a particularly attractive method for in-cell studies of proteins since it provides atomic-level data noninvasively in solution.