1 Chemical Modification and Cleavage of Proteins and Chemical Strategy in Immunochemical Studies of Proteins M. Z. Atass.- I. Introduction.- A: Chemical Modification Reactions.- II. Usefulness and Limitations.- III. Choice of Reaction and Evaluation of Results.- IV. Modification Reactions of Various Side Chains.- A. Reactions for Amino Groups.- B. Reactions for Aliphatic Hydroxyls.- C. Reactions for Arginine.- D. Reactions for Carboxyl Groups.- E. Reactions for Histidine.- F. Reactions for Methionine.- G. Reactions for Sulfhydryl (Thiol) Groups.- H. Reactions for Disulfide Bonds.- I. Reactions for Tryptophan.- J. Reactions for Tyrosine.- K. Cross-Linking Reagents.- L. Affinity-Labeling (Active-Site-Directed) Reagents.- B: Chemical Cleavage Reactions.- V. Usefulness, Limitations, and Evaluation of the Results.- VI. Choice of Reaction.- VII. Cleavage Reactions.- A. N-Terminal Removal.- B. Cleavage at Carboxyl and Carboxamide Groups.- C. Cleavage at Cysteine Peptide Bonds.- D. Cleavage at Cystine Peptide Bonds.- E. Cleavage at Histidine Peptide Bonds.- F. Cleavage at Aliphatic Hydroxy 1 Groups.- G. Cleavage of Methionine Peptide Bonds.- H. Cleavage of Proline Peptide Bonds.- I. Cleavage of Tryptophan Peptide Bonds.- J. Cleavage at Tyrosine Peptide Bonds.- K. Miscellaneous Addition and Cleavage Reactions.- L. Modified Enzymatic Cleavage.- VII. References.- 2 Influence of Conformation on Immunochemical Properties of Proteins.- I. Introduction.- II. Factors Responsible for Protein Folding.- A. Factors Intrinsic to the Protein Molecule.- B. Dependence of Protein Conformation on Environment.- III. Dependence of Conformation on the Whole Amino Acid Sequence: Conformation of Unique Protein Fragments.- IV. Use of Immunochemical Methods as a Conformational Probe.- A. Influence of Evolutionary Amino Acid Replacements on Conformation.- B. Conformational Equilibrium in Protein Fragments.- V. Influence of Conformational Changes on Immunochemical Behavior.- A. Conformational Changes Induced by Modification of Nonimmunogenic Prosthetic Groups.- B. Conformational Changes Induced by Controlled Modification of Amino Acid Residues.- VI. Conclusion.- VII. References.- 3 Investigation of Immunochemical Reactions by Fluorescence Polarization.- I. Introduction.- II. Symbols.- III. Equations Relating Fluorescence Polarization and Intensity to Concentration.- IV. Equilibrium Equations.- A. Classical Mass Law, Uniformly Binding Sites, No Site-Site Interactions.- B. Nonuniformly Binding Sites Characterized by a Sips Distribution of Binding Affinities.- V. Kinetic Equations.- A. Reaction Order.- B. Evaluation of Rate Constants.- C. Dissociation of Complexes.- VI. Relaxation Methods.- VII. Results Obtained on Immunochemical Reactions by Means of Fluorescence Polarization and Intensity Measurements.- A. Determination of Binding Affinities and Site Concentration from Equilibrium Titrations.- B. Immunoassay.- C. Determination of Reaction Order.- D. Determination of the Forward- and Back-Reaction Rate Constants.- E. Activation Parameters.- VIII. What Has Been Learned from Fluorescence Polarization Measurements on Antigen-Antibody and Hapten-Antibody Reactions?.- A. Antibody Binding Affinity and Specificity.- B. Antibody “Maturation” during the Immune Response....- C. Effects of Fluorescent Labeling upon Immunochemical Reactivity.- D. Why Does Antifluorescein Quench the Fluorescence of Fluorescein?.- E. The Mechanism of Antigen-Antibody and Hapten- Antibody Reactions.- F. Specific Ionic Effects on Reaction Rates and Activation Parameters.- G. Manipulation of the Binding Affinity of Antibody by Changing Either the Forward- or Backward-Rate Constants of the Binding Reaction.- IX. References.- 4 In Vitro Immune Responses of Lymphoid Cell Populations to Proteins and Peptides.- I. Introduction.- A. Scope.- B. Historical.- II. In Vitro Consequences of the Reaction of Proteins or Peptides with Lymphoid Cell Populations.- A. Cellular Events, Requirements, and Kinetics of Responses to Proteins.- B. In Vitro Immunological Responses to Peptides.- C. Roles of Persisting Immunogen and Accessory and Thymus-Derived Cells in the Maintenance of the Antibody Response.- D. Regulation of the Antibody Response.- III. Induction and Regulation of in Vitro Immune Responses by Soluble Factors.- A. Production of Soluble Factors from T Cells.- B. Soluble Factors with Helper and/or Regulatory Activity Generated by or Prepared from T Lymphocytes.- IV. Discussion.- A. Antigen-Binding Receptors on Lymphocytes.- B. Cellular and Molecular Aspects of Induction.- C. Maintenance of the Antibody Response.- D. Nonspecific Induction and Regulation of the Antibody Response.- E. Future Outlook.- V. References.- 5 Immunochemistry of Encephalitogenic Protein.- I. Introduction.- A. Characteristics of Experimental Allergic Encephalomyelitis.- B. The Autoimmune Component(s).- II. Nature and Properties of Encephalitogenic Protein.- A. Localization and Biochemical Characteristics.- B. General Immunological Aspects.- III. Antigenic Determinants with Disease-Inducing Properties.- A. The Tryptophan-Containing Region.- B. Region 46–91.- C. The N-Terminal Region.- D. The C-Terminal Region.- IV. Antigenic Determinants Connected with Protection against Disease.- V. Antigenic Determinants Connected with Cell-Mediated Immunity.- A. Delayed-Type Hypersensitivity in Vivo.- B. Tests in Vitro.- VI. Antigenic Determinants for the Humoral Immune Response...- VII. Concluding Remarks.- VIII. References.- 6 Immunochemistry of Collagen.- I. Chemical and Structural Considerations of Collagen.- II. Immunochemistry of Collagen.- A. Rat Collagen.- B. Calf Collagen.- C. Human Collagen.- D. Guinea Pig Skin Collagen.- E. Fish Collagen.- F. Invertebrate Collagens.- G. Collagens of Types II, III, and IV.- H. Modified Collagens and Collagenlike Synthetic Peptides….- I. General Considerations.- III. Cell-Mediated Immunity to Collagen.- IV. Genetic Control of the Immune Response to Collagen.- V. Antibodies to Procollagen.- VI. Applications of Collagen Immunochemistry to Medical Research.- VII. References.- 7 Histocompatibility Antigens.- I. The HL-A System of Man.- II. Alloantigens of the Mouse.- A. H-2 Complex of the Mouse.- B. Other Antigen-Determining Loci of the Mouse H-.- Complex.- C. Ia Antigens and Ir Genes.- III. Purification Methods for H-2 and HL-A Alloantigens.- A. Cell Disruption.- B. Papain Solubilization.- C. Lectin Affinity Column.- D. Detergent Solubilization.- E. Solubilization by Sonication.- F. 3 M KC1 Extraction.- G. Molecular Sizes Encountered in Isolation.- IV. Chemical Nature of H-2 and HL-A Antigens.- A. Protein Nature.- B. Carbohydrate Content.- C. ?2-Microglobulin.- V. Conclusion.- VI. References.- Author Index.