Hydrolysis patterns and the production of peptide intermediates during protein degradation in marine systems

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) was used to evaluate the degradation of the protein bovine serum albumin (BSA) added to seawater. The production of peptides during degradation, the size of the peptides produced and the within-protein locations of protease attack were all monitored in an effort to evaluate whether specific types of proteases or specific peptide bond locations were targeted during BSA degradation. Analysis of products from the bacterial degradation of proteins in both seawater and sediment pore water revealed the creation and release of peptide intermediates into the medium. Peptides observed in seawater degradation experiments were all less than 40 amino acids long, whereas sedimentary digestions of the same protein generated peptide fragments in the pore water ranging from 110 to 508 amino acids in length. Neither of the environments demonstrated recurring cleavages adjacent to one amino acid or functional group that might be indicative of the action of a single protease. Instead, it appears that a mixture of bacterial proteases were involved in the degradation of protein. The MALDI-TOF-MS method presented, in combination with these results, can help us delineate some of the processes responsible in the initial stages of degradation and better understand how proteins are partitioned between dissolved and solid phases in marine systems.