Sequencing Larger Proteins

Larger proteins cannot be sequenced by the Edman sequencing because of the less than perfect efficiency of the method. A strategy called divide and conquer successfully cleaves the larger protein into smaller, practical amino acids. This is done by using a certain chemical or enzyme which can cleave the protein at specific amino acid residues. The separated peptides can be isolated by chromatography. Then they can be sequenced using the Edman method, because of their smaller size.

In order to put together all the sequences of the different peptides, a method of overlapping peptides is used. The strategy of divide and conquer followed by Edman sequencing is used again a second time, but using a different enzyme or chemical to cleave it into different residues. This allows two different sets of amino acid sequences of the same protein, but at different points. By comparing these two sequences and examining for any overlap between the two, the sequence can be known for the original protein.

For example, trypsin can be used on the initial peptide to cleave it at the carboxyl side of arginine and lysine residues. Using trypsin to cleave the protein and sequencing them individually with Edman degradation will yield many different individual results. Although the sequence of each individual cleaved amino acid segment is known, the order is scrambled. Chymotrypsin, which cleaves on the carboxyl side of aromatic and other bulky nonpolar residues, can be used. The sequence of these segments overlap with those of the trypsin. They can be overlapped to find the original sequence of the initial protein. However, this method is limited in analyzing larger sized proteins (more than 100 amino acids) because of secondary hydrogen bond interference. Other weak intermolecular bonding such as hydrophobic interactions cannot be properly predicted. Only the linear sequence of a protein can be properly predicted assuming the sequence is small enough.