The amide bond is the essential structural motif of the protein backbone. The hydrolysis reaction of amides, often used as a model for the cleavage of peptide bonds, is thus of primary concern for living systems. The hydrolysis of non-activated amides is very slow and in most cases undetectable. An amide bond’s stability is ascribed to its partial double bond character, caused by the delocalization between the nitrogen lone pair and the π* orbital of CO bond. As a consequence, amides show a characteristic short C-N bond length and a rigid planar conformation. This stability also has important chemical consequences, a low reactivity toward nucleophilic attacks on the carbon and important basicity shifts of the nitrogen with respect to amines. (more…)

Many proteins are synthesized in biologically inactive forms, and are activated in post-translational processes such as proteolytic cleavage. This process is usually catalyzed by external proteins, but some proteins are able to self-catalyze the reactions without the need for any other protein or cofactor. We are interested in one of this post-translational process, known as protein splicing. In protein splicing, a segment of an inactive protein, the intein (internal protein), is excised from the rest of the protein, and the two flanking domains, the C- and N-exteins, join each other, forming a biologically active protein (see Figure).