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Influence of induced fit in the interaction of Bacillus subtilis trp RNA‐binding attenuator protein and its RNA antiterminator target oligomer
Author(s) -
Flynn Peter F.,
Wendt Alice,
Gollnick Paul
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10243
Subject(s) - rna , tryptophan , trp operon , antitermination , chemistry , ternary complex , biophysics , bacillus subtilis , binding site , attenuator (electronics) , biochemistry , biology , rna polymerase , dna , lac operon , amino acid , genetics , physics , plasmid , gene , enzyme , bacteria , attenuation , optics
In the presence of excess tryptophan, tryptophan‐activated TRAP ( trp RNA‐binding attenuator protein) binds to a specific target in the trp ‐leader transcript, which induces the formation of a transcription terminator and transcription halts in the leader region. In the absence of tryptophan, TRAP does not bind RNA, an antiterminator forms, and the operon is expressed. Although the ternary complex involving TRAP ( Bacillus stearothermophilus ), tryptophan, and the RNA target has recently been crystallized, efforts to obtain structural data for the apo ‐form of TRAP (in any species) have not been successful. We have used multidimensional/multinuclear nuclear magnetic resonance (NMR) spectroscopy to probe the structure–function relationship in the TRAP‐activated system, and have obtained high‐resolution multidimensional/multinuclear NMR spectra of TRAP in all three of its functional states: tryptophan‐free or apo ‐TRAP, tryptophan‐activated TRAP, and tryptophan‐activated TRAP‐RNA ternary complex. Chemical shift perturbation analysis of the NMR data clarifies the interpretation of results obtained from previous crystal studies. Results presented herein demonstrate that tryptophan binding induces an essential structural change in TRAP that supports high‐affinity binding of the RNA target oligonucleotide. Proteins 2002;49:432–438. © 2002 Wiley‐Liss, Inc.