| The goal of this thesis was to take a step-wise approach in advancing and merging the field of marine organic geochemistry into the field of proteomics. Investigations of protein dynamics in marine systems have historically focused on the evaluation of degradation rates and the quantification of amino acid concentrations. Both of these approaches loose nearly all information on the size, sequence, and degradation mechanisms. In order to evaluate how proteinaceous material naturally persists in marine sedimentary systems, the original protein or peptide must be examined intact. Once this is accomplished, enzymatic processes, degradation mechanisms, and eventual preservation of proteins and peptides can be more accurately addressed. Using mass spectrometry the analysis of degradation patterns of a known protein by natural bacterial assemblages from marine sediments were completed. Results demonstrate that the carboxyl and amine end of proteins are remineralized, leaving the center, or core, of the protein behind in the system to either undergo further degradation or long term preservation in the sediments. Once a non-hydrolytic method for extracting natural proteins from marine sediments was established, the protein component was isolated from four Washington coast margin sediments to examine the size distribution and the amino acid chemistry of the remaining fragments. Each size fraction of the base-soluble component has a unique amino acid composition, regardless of where on the margin the sediment was collected. Based on the amino acid signatures of the various size fractions, this study suggests that the larger size fractions represent intact, or near intact, proteins. Examinations of bulk amino acid character in sediments demonstrated that offshore and down-core amino acid distributions opposed one another, suggesting two environmental mechanisms were at work. Oxygen exposure time controls the bulk signature of the amino acids present within the sediments, whereas sub/an-oxic degradation plays a minor role in changing the final distribution of those amino acids. These findings suggest that intact cores of proteins are present in the sediments after extensive degradation and mass spectrometry has the potential to sequence and evaluate fragments from natural marine systems. |
