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Size Distribution and Amino Acid Chemistry of Base-extractable Proteins from Washington Coast Sediments

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Abstract

Proteinaceous components from four Washington coast margin sediments were extracted with base, fractionated into one of four size classes (<3 kDa, 3–10 kDa, 10–100 kDa, >100 kDa), and analyzed for their amino acid contents. Base-extracted material accounts for ~30% of the total hydrolyzable amino acids (THAA) and each size fraction has a unique composition, regardless of where the sediment was collected (shelf or upper slope). The <3 kDa size fraction (~10% of base-extractable THAA) is relatively enriched in glycine (~30 mol%), lysine (~5 mol%), and non-protein amino acids (~5 mol%). Glycine and non-protein amino acids are common degradation products, and lysine is very surface active. We suggest that the <3 kDa size fraction, therefore, represents a diagenetic mixture of fragments produced during the degradation of larger proteins. The 3–10 and 10–100 kDa size fractions (~10% and 42% of base-extractable THAA, respectively) have similar amino acid distributions dominated by aspartic acid (~30 mol%). Enrichments in Asp is likely due to both preservation of Asp-rich proteins and the production of Asp during degradation. The >100 kDa size fraction (~38% of base-extractable THAA) is not dominated by any particular amino acid and can not be modeled by mixing the amino acid compositions of the other size fractions. We propose that the larger size fractions (10–100 kDa and >100 kDa) represent intact, or near intact, proteins. Estimates of isoelectric points and relative hydrophobicity suggest the base-extractable proteins are primarily acidic and have globular structures. Statistical comparisons to several known proteins indicates that the base-extractable component is most similar to planktonic cytoplasmic proteins.

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  1. School of Oceanography, University of Washington, Seattle, WA, 98103, USA

    Brook L. Nunn & Richard G. Keil

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Nunn, B., Keil, R. Size Distribution and Amino Acid Chemistry of Base-extractable Proteins from Washington Coast Sediments. Biogeochemistry 75, 177–200 (2005). https://doi.org/10.1007/s10533-004-6546-9

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