Dissociation of yeast 80 S ribosomes by chaotropic salts

Visualization of conformational variability in the domains of long single-stranded RNA molecules

We demonstrate an application of atomic force microscopy (AFM) for the structural analysis of long single-stranded RNA (>1 kb), focusing on 28S ribosomal RNA (rRNA). Generally, optimization of the conditions required to obtain three-dimensional (3D) structures of long RNA molecules is a challenging or nearly impossible process. In this study, we overcome these limitations by developing a method using AFM imaging combined with automated, MATLAB-based image analysis algorithms for extracting information about the domain organization of single RNA molecules. We examined the 5 kb human 28S rRNA since it is the largest RNA molecule for which a 3D structure is available. As a proof of concept, we determined a domain structure that is in accordance with previously described secondary structural models. Importantly, we identified four additional small (200–300 nt), previously unreported domains present in these molecules. Moreover, the single-molecule nature of our method enabled us to report on the relative conformational variability of each domain structure identified, and inter-domain associations within subsets of molecules leading to molecular compaction, which may shed light on the process of how these molecules fold into the final tertiary structure.

Phosphorylation of yeast protein: Reduction of ribonucleic acid and isolation of yeast protein concentrate

Yeast nucleoproteins were chemically phosphorylated with phosphorus oxychloride (POCL(3)). Studies using (31)P nuclear magnetic resonance (NMR) spectroscopy, stability to pH and lysine estimation all indicated that the epsilon-amino group of lysine was the principal functional group phosphorylated. Phosphorylation of ca. 30% of the lysine residues resulted in removal of more than 85% of contaminant ribonucleic acid from protein precipitated at pH 4.2. Phosphorylation did not alter the amino acid composition of yeast proteins and was reversible under acidic conditions. Based on the data, a method for the preparation of phosphorylated yeast protein with low levels of nucleic acid is proposed.