Trypsin, sequencing peptides with

The peptides discussed so far are defined by a common genetic pattern or architectural feature, such as their sequence or disulfide bond pattern. In this section we discuss peptides that share a common mode of action but may arise from different peptide families. Proteinase inhibitors (Pis) come in an astounding range of sizes, from the smallest gene-encoded cyclic peptide known to date, sunflower trypsin inhibitor 1 (SFTI-1), ° a 14-residue cyclic peptide with a single disulfide bond, to squash inhibitors that are approximately 30 residues in size and feature the cystine knot motif, to 53-residue Pis found in Nicotiana... 

For example, chymotrypsin cleaves peptides on the C-terminal side of aromatic amino acid residues phenylalanine, tyrosine, and tryptophan, and to a lesser extent some other residues with bulky side-chains, e.g. Leu, Met, Asn, Gin. On the other hand, trypsin cleaves peptides on the C-terminal side of the basic residues arginine and lysine. Elastase usually catalyses hydrolysis of peptide bonds on the C-terminal side of neutral aliphatic amino acids, especially glycine or alanine. These three pancreatic enzymes are about 40% identical in their amino acid sequences, and their catalytic mechanisms are nearly identical. 

The folding pattern of cytochrome b5 is also found in the complex heme protein flavocytochrome b2 from yeast (Chapter 15)133 and probably also in liver sulfite oxidase134,135 Both are 58-kDa peptides which can be cleaved by trypsin to 11-kDa fragments that have spectroscopic similarities and sequence homology with cytochrome b5. Sulfite oxidase also has a molybdenum center (Section H). The 100-residue N-terminal portion of flavocytochrome b2 has the cytochrome b5 folding pattern but the next 386 residues form an eight-stranded (a / P)8 barrel that binds a molecule of FMN.133,136 All of these proteins pass electrons to cytochrome c. In contrast, the folding of cytochrome... 

From a rare fungus you have isolated an octapeptide that prevents baldness, and you wish to determine the peptide sequence. The amino acid composition is Lys(2), Asp, Tyr, Phe, Gly, Ser, Ala. Reaction of the intact peptide with FDNB yields DNP-alanine plus 2 moles of e-DNP-lysine on acid hydrolysis. Cleavage with trypsin yields peptides the compositions of which are (Lys, Ala, Ser) and (Gly, Phe, Lys), plus a dipeptide. Reaction with chymotrypsin releases free aspartic acid, a tetrapeptide with the composition (Lys, Ser, Phe, Ala), and a tripeptide the composition of which, following acid hydrolysis, is (Gly, Lys, Tyr). What is the sequence ... 

To establish the amino acid sequence unequivocally it is necessary to have peptides with overlapping sequences. This may be accomplished by determining the sequence of fragments obtained from treating a second aliquot of the protein with chymotrypsin. If these fragments are then treated with trypsin as a check, peptides identical to those obtained previously by successive treatment with trypsin and chymotrypsin are obtained. Other proteolytic enzymes, such as pepsin, subtilisin, and papain, with wider specificity than trypsin and chymotrypsin have proved useful in sequencing of some proteins. 

EXAMPLE 4.1 A peptide was cleaved into two smaller peptides with cyanogen bromide (CNBr) and into two different peptides by trypsin (Tryp). Their sequences were as follows ... 

Incubation of a protein fraction from blood plasma with trypsin gives rise to peptides with conspicuous biological effects. Pain, dilation of peripheral blood vessels, increased coronary flow and enhanced capillary permeability were observed on administration of these protein fragments [8]. In the early sixties the nonapeptide bradykinin and its precursors, kallidin and methionyl-kalUdin were isolated in pure form and their amino acid sequences determined soon after. 

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