Optimizing HSQC experiment for the observation of exchange broadened signals in RNA–protein complexes

Abstract : Sites for interaction in protein–RNA complexes are often regions of conformational exchange. Although the study of exchange processes could bring valuable information about the recognition mode between protein and RNA, chemical exchange can be detrimental to the NMR spectra quality, resulting in broad, very weak or even unobservable signals. In the present report, we used CPMG–like experiments to improve HSQC spectra of an RNA–protein complex in fast exchange on the chemical shift time scale. The use of such improvement will allow us to handle the resolution of the three-dimensional structure of the complex by NMR.