During my research i came across a peptide* in a research article# which is surprisingly stable to proteolytic enzymes with normal amino acids. Its an antimicrobial peptide which is resistant to the proteolytic enzymes pepsin, trypsin, chymotrypsin, proteinase K and pronase and broad pH stability. How can this be possible that these enzyme are not able to act at their specific site even though no protecting group is present.

* MACQCPDAISGWTHTDYQCHGLENKMYRHVYAICMNGTQVYCRTEWGSSC

# http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031498

2012P Identification, purification and characterization of laterosporulin, a novel bacteriocin produced by Brevibacillus sp. strain GI-9.pdf

The stability of a peptide also depends on its tertiary structure. If the peptide is not denatured, proteases may not be able to access the cleavage sites. Also it depends a bit on how you assess whether there was proteolysis or not (e.g. searching for fragments or indirectly via activity assays). Peptides may retain biology activity to some extent, even after cleavage.

I have not read the paper but looking at the sequence there are quite a few cysteins (allowing for disulphide bonds). Moreover they generally do not ionize well and yield low signals in MS, which may limit identification of fragments.

But in addition we see a number of hydrophobic residues, such as tryptophane and tyrosine, so my guess (without any close analysis) is really that tertiary structure may inhibit cleavage.