Protein structure bulges

Richardson JS, Getzoff ED, Richardson DC (1978) The / -bulge a common small unit of nonrepetitive protein structure. Proc Natl Acad Sci USA 75 2574-2578... 

Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

Figure 10.7. Schematic representation of the Rev protein, emphasizing its two key functional domains. The secondary structure of the RRE, highlighting the Rev biding site, is shown. Residues essential for RRE are in bold. The intervening bulge contains two non-Watson-Crick base pairs, G48 G71 and G47 A73, and a bulged base U72. ...

Unpaired bases may bulge at various points in double-stranded stems of longer palindromes. These imperfect palindromes in the DNA are responsible for much of the tertiary structure of the various kinds of RNA. The tertiary structure, in turn, often determines the interaction of the RNA with enzymes and other proteins. 

Transfer RNA (tRNA) has the lowest molecular weight, that is, near 28,000. Its function is to activate amino acids for protein biosynthesis. It has a unique cloverleaf structure (Figure 10.29), and there are sections of double-helix, bulges, and hairpin turns. Of all RNAs, it has the highest number of unusual bases (10-15%). Thus, the hairpin arm pointing east contains pseudouridine W and is... 

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