Specificity of Proteolysis

Specificity of Proteolysis presents a survey and conclusions on the action or proteinases - enzymes which are cleaving proteins or peptides. The specificity of proteinases which is determined as the sequence of amino acids at the cleavage site of a substrate, is an important criteria to choose an enzyme as tool in protein research. Whenever one is looking for an enzyme to act at a defined site or to give defined cleavage products one will find comprehensive information in this work. Comprehensive information about more than 280 endopeptidases which are based on the database LYSIS including a calculation program to determine cleavage sites, is given in the book.

1 Introduction.- 2 Nomenclature and Conventions.- 2.1 EC Numbers.- 2.2 Enzyme Names.- 2.3 Enzyme and Substrate Codes.- 2.4 Subsite Nomenclature.- 2.5 Bibliography.- 3 Data Treatment.- 3.1 Data Bank LYSIS.- 3.2 Statistical Approach to Specificity.- 3.2.1 Calculations.- 3.2.2 Sources of Errors and Limits.- 3.2.3 Influence of Subsites on Chymotryptic Cleavages.- 3.2.4 Roles of Subsites P4-P3’ in Cleavages by Pepsin.- 3.2.5 Fixation Preference of Chymotrypsin and Pepsin.- 3.2.6 Predictions of Cleavage Probability.- 3.2.7 Comparison with Kinetic Study.- 4 Standard Polypeptide Substrates.- 4.1 Choice of Standard Polypeptides.- 4.2 Available Data on Cleavages of Insulin Chains and Glucagon.- 4.3 Repartition of Cleavage-Susceptible Bonds.- 4.4 Binding Sites — Proposal for Fixation Site Types.- 4.5 Influence of Subsites.- 5 Essential Substrate Residues for Action of Endopeptidases.- 5.1 Basic Residue.- 5.1.1 Arg in P1.- 5.1.2 Arg or Lys in P1(Arg>Lys).- 5.1.3 Lys in P1 (Lys>Arg).- 5.1.4 Lys in P1’.- 5.1.5 Arg in P2 and Gly in P1.- 5.1.6 A Pair of Basic Residues.- 5.1.7 Basic or Aromatic Residue in P1.- 5.2 Acidic Residue.- 5.2.1 Glu in P1 (Glu>Asp).- 5.2.2 Asp in P1 or P1’.- 5.3 Neutral Residue.- 5.3.1 Leu or Val in P1.- 5.3.2 Aromatic or Hydrophobic Residue in P1.- 5.3.3 Aromatic or Hydrophobic Residue in P1 (Acidic pH).- 5.3.4 Aromatic or Hydrophobie Residue in P1 and P1’.- 5.3.5 Hydrophobie Residue in P2.- 5.3.6 Hydrophobie Residue in P1’.- 5.3.7 Hydrophobie Residue in P3’.- 5.3.8 Small Neutral Residue in P1.- 5.3.9 Miscellaneous Neutral Residues in P1.- 5.3.10 Neutral Residues in Both P1 and P1’.- 5.4 Proline Residue.- 5.4.1 Pro in P1.- 5.4.2 Pro in P2’.- 5.5 Alpha-Epsilon Peptide Bond.- 5.6 Peptidases with Occasional Endopeptidase Activity.- 5.7 Vague or Insufficient Information on Specificity.- 5.8 No Information on Bond Specificity.- 6 Comments.- 6.1 Frequently Used Proteinases and Restriction Proteinases.- 6.2 Group of Microbial Proteinases.- References.- Appendices.- A Tabular Index of LYSIS Enzyme Codes.- B Tabular Index of LYSIS Protein Codes.