Amino acids and peptides

1 Introduction 1 1.1 Sources and roles of amino acids and peptides 1 1.2 Definitions 1 1.3 ‘Protein amino acids’, alias ‘the coded amino acids’ 3 1.4 Nomenclature for ‘the protein amino acids’, alias ‘the coded amino acids’ 7 1.5 Abbreviations for names of amino acids and the use of these abbreviations to give names to polypeptides 7 1.6 Post-translational processing: modification of amino-acid residues within polypeptides 11 1.7 Post-translational processing: in vivo cleavages of the amide backbone of polypeptides 11 1.8 ‘Non-protein amino acids’, alias ‘non-proteinogenic amino acids’ or ‘non-coded amino acids’ 11 1.9 Coded amino acids, non-natural amino acids and peptides in nutrition and food science and in human physiology 13 1.10 The geological and extra-terrestrial distribution of amino acids 15 1.11 Amino acids in archaeology and in forensic science 15 1.12 Roles for amino acids in chemistry and in the life sciences 16 1.12.1 Amino acids in chemistry 16 1.12.2 Amino acids in the life sciences 16 1.13
- and higher amino acids 17 1.14 References 19 2 Conformations of amino acids and peptides 20 2.1 Introduction: the main conformational features of amino acids and peptides 20 2.2 Configurational isomerism within the peptide bond 20 2.3 Dipeptides 26 2.4 Cyclic oligopeptides 26 2.5 Acyclic oligopeptides 27 2.6 Longer oligopeptides: primary, secondary and tertiary structure 27 2.7 Polypeptides and proteins: quaternary structure and aggregation 28 2.8 Examples of conformational behaviour; ordered and disordered states and transitions between them 29 2.8.1 The main categories of polypeptide conformation 29 2.8.1.1 One extreme situation 29 2.8.1.2 The other extreme situation 29 2.8.1.3 The general case 29 2.9 Conformational transitions for amino acids and peptides 30 2.10 References 31 3 Physicochemical properties of amino acids and peptides 32 3.1 Acid–base properties 32 3.2 Metal-binding properties of amino acids and peptides 34 3.3 An introduction to the routine aspects and the specialised aspects of the spectra of amino acids and peptides 35 3.4 Infrared (IR) spectrometry 36 3.5 General aspects of ultraviolet (UV) spectrometry, circular dichroism (CD) and UV fluorescence spectrometry 37 3.6 Circular dichroism 38 3.7 Nuclear magnetic resonance (NMR) spectroscopy 41 3.8 Examples of assignments of structures to peptides from NMR spectra and other data 43 3.9 References 46 4 Reactions and analytical methods for amino acids and peptides 48 Part 1 Reactions of amino acids and peptides 48 4.1 Introduction 48 4.2 General survey 48 4.2.1 Pyrolysis of amino acids and peptides 49 4.2.2 Reactions of the amino group 49 4.2.3 Reactions of the carboxy group 49 4.2.4 Reactions involving both amino and carboxy groups 51 4.3 A more detailed survey of reactions of the amino group 51 4.3.1 N-Acylation 51 4.3.2 Reactions with aldehydes 52 4.3.3 N-Alkylation 53 Contents viii 4.4 A survey of reactions of the carboxy group 53 4.4.1 Esterification 54 4.4.2 Oxidative decarboxylation 54 4.4.3 Reduction 54 4.4.4 Halogenation 55 4.4.5 Reactions involving amino and carboxy groups of -amino acids and their N-acyl derivatives 55 4.4.6 Reactions at the -carbon atom and racemisation of -amino acids 55 4.4.7 Reactions of the amide group in acylamino acids and peptides 57 4.5 Derivatisation of amino acids for analysis 58 4.5.1 Preparation of N-acylamino acid esters and similar derivatives for analysis 58 4.6 References 60 Part 2 Mass spectrometry in amino-acid and peptide analysis and in peptide-sequence determination 61 4.7 General considerations 61 4.7.1 Mass spectra of free amino acids 61 4.7.2 Mass spectra of free peptides 62 4.7.3 Negative-ion mass spectrometry 65 4.8 Examples of mass spectra of peptides 65 4.8.1 Electron-impact mass spectra (EIMS) of peptide derivatives 65 4.8.2 Finer details of mass spectra of peptides 68 4.8.3 Difficulties and ambiguities 69 4.9 The general status of mass spectrometry in peptide analysis 69 4.9.1 Specific advantages of mass spectrometry in peptide sequencing 70 4.10 Early methodology: peptide derivatisation 71 4.10.1 N-Terminal acylation and C-terminal esterification 71 4.10.2 N-Acylation and N-alkylation of the peptide bond 72 4.10.3 Reduction of peptides to ‘polyamino-polyalcohols’ 72 4.11 Current methodology: sequencing by partial acid hydrolysis, followed by direct MS analysis of peptide hydrolysates 72 4.11.1 Current methodology: instrumental variations 74 4.12 Conclusions 77 4.13 References 77 Contents ix Part 3 Chromatographic and related methods for the separation of mixtures of amino acids, mixtures of peptides and mixtures of amino acids and peptides 78 4.14 Separation of amino-acid and peptide mixtures 78 4.14.1 Separation principles 78 4.15 Partition chromatography; HPLC and GLC 80 4.16 Molecular exclusion chromatography (gel chromatography) 80 4.17 Electrophoretic separation and ion-exchange chromatography 82 4.17.1 Capillary zone electrophoresis (CZE) 83 4.18 Detection of separated amino acids and peptides 83 4.18.1 Detection of amino acids and peptides separated by HPLC and by other liquid-based techniques 84 4.18.2 Detection of amino acids and peptides separated by GLC 85 4.19 Thin-layer chromatography (planar chromatography; HPTLC) 86 4.20 Quantitative amino-acid analysis 86 4.21 References 87 Part 4 Immunoassays for peptides 87 4.22 Radioimmunoassays 87 4.23 Enzyme-linked immunosorbent assays (ELISAs) 88 4.24 References 90 Part 5 Enzyme-based methods for amino acids 90 4.25 Biosensors 90 4.26 References 90 5 Determination of the primary structure of peptides and proteins 91 5.1 Introduction 91 5.2 Strategy 92 5.3 Cleavage of disulphide bonds 96 5.4 Identification of the N-terminus and stepwise degradation 97 5.5 Enzymic methods for determining N-terminal sequences 105 5.6 Identification of C-terminal sequences 106 5.7 Enzymic determination of C-terminal sequences 107 5.8 Selective chemical methods for cleaving peptide bonds 107 5.9 Selective enzymic methods for cleaving peptide bonds 109 5.10 Determination of the positions of disulphide bonds 112 5.11 Location of post-translational modifications and prosthetic groups 114 5.12 Determination of the sequence of DNA 117 5.13 References 118 Contents x 6Synthesis of amino acids 120 6.1 General 120 6.2 Commercial and research uses for amino acids 120 6.3 Biosynthesis: isolation of amino acids from natural sources 121 6.3.1 Isolation of amino acids from proteins 121 6.3.2 Biotechnological and industrial synthesis of coded amino acids 121 6.4 Synthesis of amino acids starting from coded amino acids other than glycine 122 6.5 General methods of synthesis of amino acids starting with a glycine derivative 123 6.6 Other general methods of amino acid synthesis 123 6.7 Resolution of -amino acids 125 6.8 Asymmetric synthesis of amino acids 127 6.9 References 129 7 Methods for the synthesis of peptides 130 7.1 Basic principles of peptide synthesis and strategy 130 7.2 Chemical synthesis and genetic engineering 132 7.3 Protection of -amino groups 134 7.4 Protection of carboxy groups 135 7.5 Protection of functional side-chains 138 7.5.1 Protection of -amino groups 138 7.5.2 Protection of thiol groups 139 7.5.3 Protection of hydroxy groups 140 7.5.4 Protection of the guanidino group of arginine 141 7.5.5 Protection of the imidazole ring of histidine 142 7.5.6 Protection of amide groups 145 7.5.7 Protection of the thioether side-chain of methionine 145 7.5.8 Protection of the indole ring of tryptophan 146 7.6 Deprotection procedures 146 7.7 Enantiomerisation during peptide synthesis 146 7.8 Methods for forming peptide bonds 149 7.8.1 The acyl azide method 150 7.8.2 The use of acid chlorides and acid fluorides 151 7.8.3 The use of acid anhydrides 151 7.8.4 The use of carbodiimides 153 7.8.5 The use of reactive esters 153 7.8.6 The use of phosphonium and isouronium derivatives 155 7.9 Solid-phase peptide synthesis (SPPS) 156 7.10 Soluble-handle techniques 163 7.11 Enzyme-catalysed peptide synthesis and partial synthesis 164 Contents xi 7.12 Cyclic peptides 168 7.12.1 Homodetic cyclic peptides 168 7.12.2 Heterodetic cyclic peptides 170 7.13 The formation of disulphide bonds 170 7.14 References 172 7.14.1 References cited in the text 172 7.14.2 References for background reading 173 8 Biological roles of amino acids and peptides 174 8.1 Introduction 174 8.2 The role of amino acids in protein biosynthesis 175 8.3 Post-translational modification of protein structures 178 8.4 Conjugation of amino acids with other compounds 182 8.5 Other examples of synthetic uses of amino acids 183 8.6 Important products of amino-acid metabolism 187 8.7 Glutathione 190 8.8 The biosynthesis of penicillins and cephalosporins 192 8.9 References 198 8.9.1 References cited in the text 198 8.9.2 References for background reading 199 9 Some aspects of amino-acid and peptide drug design 200 9.1 Amino-acid antimetabolites 200 9.2 Fundamental aspects of peptide drug design 201 9.3 The need for peptide-based drugs 202 9.4 The mechanism of action of proteinases and design of inhibitors 204 9.5 Some biologically active analogues of peptide hormones 210 9.6 The production of antibodies and vaccines 213 9.7 The combinatorial synthesis of peptides 215 9.8 The design of pro-drugs based on peptides 216 9.9 Peptide antibiotics 217 9.10 References 218 9.10.1 References cited in the text 218 9.10.2 References for background reading 218 Subject index