Peptide bonds surrounding

A unique aspect of using protein substrates is that the substrates themselves are so complex. Even a relatively small protein, having say 100 amino acids, has 99 potentially susceptible peptide bonds—and each of these bonds is expected to be unique. This hypothetical protein thus has 99 structurally unique substrates (potential sites for catalysis). The environment surrounding each of the protein s peptide bonds will be dependent on the tertiary structure of the protein, so one must consider, for example, native... 

Besides acids and alkalis, strong oxidants used to bleach silk also have the capacity to seriously degrade the fibres. The most significant reactions occur at tyrosine and threonine side-chains, resulting in their oxidation to acids and the breaking of surrounding peptide bonds cross-links are also generated, e.g. between lysine and tyrosine residues. 

In the active site of a protease, there are subsites labeled according to the peptide residue that they bind [81]. The point of peptide cleavage is between the peptide bond that binds residue Pj with residue P, . As a result, the residues that surround this position are labeled relative to the cleavage site as P2, Pj, P j, P 2, and so on. Therefore, the protein subsites occupied by residues Pj, Pp P p and P 2 are labeled as S2, Sj, S j, and S 2, respectively. 

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