Trypsin specificity

Rothman and Byrne 46) have used tryptic digestion to determine whether the subunits of alkaline phosphatase are identical. Since trypsin specifically cleaves at lysyl and arginyl residues, there will be as many peptides formed as there are arginine and lysine residues if the mono-... 

Frequently a third enzymatic digestion is necessary to eliminate all the possible ambiguities. Using trypsin as a proteolysis enzyme allows one partially to distinguish Lys from Gin, two isobars. In fact, the trypsin specifically cleaves on the C-terminal side of Lys and Arg, so all the amino acids with mass 128 ending a peptide can be identified as Lys. However, the absence of a cleavage cannot be used as proof in identifying an amino acid... 

Trypsin specificity. In addition to breaking peptide bonds, trypsin can break ester bonds, producing a carboxylic acid and an alcohol. 

For tissue engineering and regenerative medicine, stem cells should be effectively cultured in vitro [130, 131]. Novel thermoresponsive MD-NC gels could be applied in cell culture and cell harvesting without trypsinization, specifically using mesenchymal stem cells (MSCs) [132]. The composition of the MD-NC gel (the ratio of the two monomer types and the clay content) was found to determine its... 

Gunther, R., Thust, S., Hofmann, H. J., Bordusa, F. (2000). Trypsin-specific acyl-4-guanidi-nophenyl esters for a-chymotrypsin-catalysed reactions. Eur.. Biochem., 267,3496-3501. 

Phenylmethanesulfonyl fluoride (PMSF) [329-98-6] M 174.2, m 90-91 , 92-93 . Purified by recrystn from ""CgHe, pet ether or CHCl3-pet ether. [Davies and Dick J Chem Soc 483 1932 cf Tullock and Coffman J Org Chem 23 2016 I 960.] It is a general protease inhibitor (specific for trypsin and chymotrypsin) and is a good substitute for diisopropylphosphoro floridate [Fahrney and Gould 7 Am Chem Soc 85 997 1963]. 

Even though these enzymes have no absolute specificity, many of them show a preference for a particular side chain before the scissile bond as seen from the amino end of the polypeptide chain. The preference of chymotrypsin to cleave after large aromatic side chains and of trypsin to cleave after Lys or Arg side chains is exploited when these enzymes are used to produce peptides suitable for amino acid sequence determination and fingerprinting. In each case, the preferred side chain is oriented so as to fit into a pocket of the enzyme called the specificity pocket. 

This is nicely illustrated by members of the chymotrypsin superfamily the enzymes chymotrypsin, trypsin, and elastase have very similar three-dimensional structures but different specificity. They preferentially cleave adjacent to bulky aromatic side chains, positively charged side chains, and small uncharged side chains, respectively. Three residues, numbers 189, 216, and 226, are responsible for these preferences (Figure 11.11). Residues 216... 

Residue 189 is at the bottom of the specificity pocket. In trypsin the Asp residue at this position interacts with the positively charged side chains Lys or Arg of a substrate. This accounts for the preference of trypsin to cleave adjacent to these residues. In chymotrypsin there is a Ser residue at position 189, which does not interfere with the binding of the substrate. Bulky aromatic groups are therefore preferred by chymotrypsin since such side chains fill up the mainly hydrophobic specificity pocket. It has now become clear, however, from site-directed mutagenesis experiments that this simple picture does not tell the whole story. 

Figure 11.11 Schematic diagrams of the specificity pockets of chymotrypsin, trypsin and elastase, illustrating the preference for a side chain adjacent to the scisslle bond In polypeptide substrates. Chymotrypsin prefers aromatic side chains and trypsin prefers positively charged side chains that can interact with Asp 189 at the bottom of the specificity pocket. The pocket is blocked in elastase, which therefore prefers small uncharged side chains.

The Asp 189-Lys mutation in trypsin causes unexpected changes in substrate specificity... 

Asp 189 at the bottom of the substrate specificity pocket interacts with Lys and Arg side chains of the substrate, and this is the basis for the preferred cleavage sites of trypsin (see Figures 11.11 and 11.12). It is almost trivial to infer, from these observations, that a replacement of Asp 189 with Lys would produce a mutant that would prefer to cleave substrates adjacent to negatively charged residues, especially Asp. On a computer display, similar Asp-Lys interactions between enzyme and substrate can be modeled within the substrate specificity pocket but reversed compared with the wild-type enzyme. 

Mutations in the specificity pocket of trypsin, designed to change the substrate preference of the enzyme, also have drastic effects on the catalytic rate. These mutants demonstrate that the substrate specificity of an enzyme and its catalytic rate enhancement are tightly linked to each other because both are affected by the difference in binding strength between the transition state of the substrate and its normal state. 

Craik, C.S., et al. Redesigning trypsin alteration of substrate specificity. Science 228 291-297, 1985. 

Graf, L., et al. Selective alteration of substrate specificity by replacement of aspartic acid 189 with lysine in the binding pocket of trypsin. Biochemistry 26 ... 

Krieger, M., Kay, L.M., Stroud, R.M. Structure and specific binding of trypsin comparison of inhibited derivatives and a model for substrate binding. /. Mol. Biol. 83 209-230, 1974. 

FIGURE l.l Hydrophobic interaction and reversed-phase chromatography (HIC-RPC). Two-dimensional separation of proteins and alkylbenzenes in consecutive HIC and RPC modes. Column 100 X 8 mm i.d. HIC mobile phase, gradient decreasing from 1.7 to 0 mol/liter ammonium sulfate in 0.02 mol/liter phosphate buffer solution (pH 7) in 15 min. RPC mobile phase, 0.02 mol/liter phosphate buffer solution (pH 7) acetonitrile (65 35 vol/vol) flow rate, I ml/min UV detection 254 nm. Peaks (I) cytochrome c, (2) ribonuclease A, (3) conalbumin, (4) lysozyme, (5) soybean trypsin inhibitor, (6) benzene, (7) toluene, (8) ethylbenzene, (9) propylbenzene, (10) butylbenzene, and (II) amylbenzene. [Reprinted from J. M. J. Frechet (1996). Pore-size specific modification as an approach to a separation media for single-column, two-dimensional HPLC, Am. Lab. 28, 18, p. 31. Copyright 1996 by International Scientific Communications, Inc.. Shelton, CT.]... 

FIGURE 5.20 Trypsin is a proteolytic enzyme, or protease, that specifically cleaves only those peptide bonds in which arginine or lysine contributes the carbonyl function. The products of the reaction are a mixture of peptide fragments with C-terminal Arg or Lys residues and a single peptide derived from the polypeptide s C-terminal end. 

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