Specificity of Proteolysis

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(ArgLys).- 5.1.3 Lys in P1 (LysArg).- 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 (GluAsp).- 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

Detailed information about the specificity of more than 280 protein cleaving enzymes - important tools for protein analysis - are presented in the book.