Preparation of Proteoglycans for N-Terminal and Internal Amino Acid Sequence Analysis

Abstract

Amino acid sequence analysis of proteoglycans is performed using many of the same methods that are used for conventional proteins and glycoproteins, with some specific modifications that result from the glycosaminoglycans that are attached to the protein core. Amino acid sequence analysis of proteoglycans is more challenging than for conventional proteins for two reasons. First, because proteoglycans are large molecules, they have the same problems that are inherent in sequence analysis of larger proteins. The higher molecular weight provides for relatively high levels of nonspecific cleavage of the protein during Edman chemistry, resulting in a rapidly increasing background. Second, the presence of glycosaminoglycans, which tend to bind water, can exacerbate the problem of nonspecific hydrolysis of peptide bonds to such an extent that it may be impossible to obtain an N-terminal on a proteoglycan that is over 70% glycosaminoglycan. In an ideal situation, it is difficult to determine more than 10 amino acids from the N-terminal of an intact proteoglycan.