Earlier we have shown that positions of ribonucleotides in the nucleotide-Hfq complexes correlate with the available structural and biochemical data. Our results have demonstrated that it is possible to determine single-stranded RNA-binding sites on the protein surface using a soaking procedure followed by structure determination of the nucleotide-protein complexes. In order to test our approach, RNA-binding proteins CspB from Bacillus subtilis and Rop from Escherichia coli were chosen. AMP and GMP affinities to the proteins have been also estimated by measuring of fluorescence changes during titration of the AMP-MANT and GMP-MANT solution by appropriate proteins.
RNA binding, X-ray diffraction analysis, transcription regulation, translation regulation, fluorescent analogs of nucleotides
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