Chapter 14. Examples of Homonuclear 2D Experiments

Amino Acids

Proteins

Ubiquitin, a small protein ( 8.5kd ) present in all eukaryotic cells . It contains a highly conserved sequence of 76 amino acids that is identical in a wide variety of sources including humans, fish, and insects. It participates in diverse cellular functions, such as protein degradation, chromatin structure, and heat shock, by conjugation to other proteins through the carboxy terminus. This protein is highly conserved in evolution : yeast and human ubiquitin differ at only 3 of 76 residues. The carboxyl-terminal glycine of ubiquitin becomes covalently attached to the ε-amino group of lysine residues of proteins destined to be degraded.

The energy for the formation of these isopeptide bonds comes from ATP. Three enzymes- E1 : ubiquitin activating enzyme、 E2 : ubiquitin-carrier protein、 E3 : ubiquitin-protein ligase- participate in the conjugation of ubiquitin to protein. First, the terminal carboxylate group of ubiquitin becomes linked to a sulfhydryl group of E1 by a thioester bond. Activated ubiquitin is then shuttled to a sulfhydryl of E2. Finally, E3 catalyzes the transfer of ubiquitin from E2 to the target protein. A protein tagged for destriction usually acquires several molecules of ubiquitin. Theε-amino group of a lysine residue of one ubiquitin molecule can become linked to the terminal carboxylate of another. This ubiquitinylated protein is degraded by an ATP-powered 26S protease complex and ubiquitin is then recycled; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns. ( From J Mol Biol 194: 531-44 (1987) )