The Exchangeable Yeast Ribosomal Acidic Protein YP2β Shows Characteristics of a Partly Folded State under Physiological Conditions

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Abstract
The eukaryotic acidic ribosomal P proteins, contrary to the standard r-proteins which are rapidly degraded in the cytoplasm, are found forming a large cytoplasmic pool that exchanges with the ribosome-bound proteins during translation. The native structure of the P proteins in solution is therefore an essential determinant of the protein−protein interactions that take place in the exchange process. In this work, the structure of the ribosomal acidic protein YP2β from Saccharomyces cerevisiae has been investigated by fluorescence spectroscopy, circular dichroism (CD), nuclear magnetic resonance (NMR), and sedimentation equilibrium techniques. We have established the fact that YP2β bears a 22% α-helical secondary structure and a noncompact tertiary structure under physiological conditions (pH 7.0 and 25 °C); the hydrophobic core of the protein appears to be solvent-exposed, and very low cooperativity is observed for heat- or urea-induced denaturation. Moreover, the 1H-NMR spectra show a small signal dispersion, and virtually all the amide protons exchange with the solvent on a very short time scale, which is characteristic of an open structure. At low pH, YP2β maintains its secondary structure content, but there is no evidence for tertiary structure. 2,2,2-Trifluoroethanol (TFE) induces a higher amount of α-helical structure but also disrupts any trace of the remaining tertiary fold. These results indicate that YP2β may have a flexible structure in the cytoplasmic pool, with some of the characteristics of a “molten globule”, and also point out the physiological relevance of such flexible protein states in processes other than protein folding.