Amino Acids, Peptides and Proteins (SPR Amino Acids, Peptides, and Proteins (RSC)) (vol. 5) PDF
Preview Amino Acids, Peptides and Proteins (SPR Amino Acids, Peptides, and Proteins (RSC)) (vol. 5)
Reporters P. M. Bayley, Nafional Institute of Medical Research, Mill Hill, London T. L. Blundell, Universify of Sussex J. Bridgen, MRC Laboratory of Molecular Biology, Cambridge B. W. Bycroft, University of Noffingham R. D. Gillard, University ofKent P. M. Hardy, University of Exefer R. W. Hay, University of Stirling C. E. Johnson, University of Liverpool J. H. Jones, Universify of Oxford G. L. Kellett, Universify of York P. Knowles, Universify of Leeds G. L. E. Koch, MRC Laboratory of Molecular Biology, Cambridge S. H. Laurie, Leicester Polytechnic H. D. Law, Glasgow College of Technology R. H. Pain, University of Newcastle upon Tyne G. R. Penrer, University of York H. W. E. Rattle, Portsmouth Polytechnic B. Ridge, Universify of Exefer B. Robson, University of Newcastle upon Tyne R. D. Ryder, University of Newcastle upon Tyne R. M. Stephens, Portsmouth Polytechnic Organic formulae composed by Wright’s Symbolset method Printed in Great Britain by John Wright and Sons Ltd. at The Stonebridge Press, Bristol BS4 5NU Preface This fifth Report reviews papers relevant to the chemistry of amino-acids, peptides, and proteins published in the main journals during 1972. The subject matter of Chapter 5 (Chemical Structure and Biological Activity) has not been covered in this series since Volume 1, and therefore this article also includes some references from the 1971 and earlier literature. Chapter 6 (Metal Derivatives of Amino-acids, Peptides, and Proteins) is a biennial survey and covers papers appearing during 1971 and 1972. In all, some 2700 references are cited. As in some previous volumes, we have taken the opportunity of reprinting (in Chapter 7) new and revised recommendations of the 1.U.P.A.C.-I.U.B. Commission on Biochemical Nomenclature. This year we reproduce revised versions of two previously published recommendations, uiz. ‘Definitive Rules for Naming Synthetic Modifications of Natural Peptides’ and ‘Abbreviated Nomenclature of Synthetic Polypeptides (Polymerised Amino-acids)’. Also included are definitive rules for ‘A One-letter Notation for Amino-acid Sequences’ not previously published in this series. Chapter 2 includes two examples of the use of this one-letter notation for the presentation of large amounts of data in a relatively compact and, to the experienced eye, a reasonably easily assimilated form. In general, however, the conventional three-letter symbols are preferred throughout these Reports. All who have in the past found these Reports a useful guide to the current literature will wish to thank my predecessor, Dr. G. T. Young, for establishing this series in its present format. My personal thanks are also due to the many contributors to the present volume for their time and effort willingly devoted to its preparation. R. C. SHEPPARD A Specialist Periodical Report Amino-acids, Peptides, and Proteins Volume 5 A Review of the Literature Published during 1972 Senior Reporter R. C. Sheppard, MRC Laborafory of Molecular Biology, Cambridge ISBN : 0 85186 044 3 Library of Congress Catalog Card No. 72-92548 @ Copyright 1974 The Chemical Society Burlington House, London, WIV OBN vi Cont ents 5 Analytical Methods 34 Gas-Liquid Chromatography 34 Ion-exchange Chromatography 35 Thin-layer Chromatography 36 Other Methods 37 Determination of Specific Amino-acids 37 Chapter 2 Structural Investigation of Peptides and Proteins I: Primary Structure and Chemical Modification By J. Bridgen and G. L. E. Koch 1 Introduction 40 2 Methods 40 Polyacrylamide Gel Electrophoresis 41 Protein Determination 42 Amino-acid Analysis 43 Separation Techniques 43 Cleavage of Peptide Bonds 45 Sequence Determination 46 3 Enzymes 51 Glycolytic Enzymes 51 Proteolytic Enzymes 57 Serine Proteases 57 Tr ypsin 59 Subtilisin 61 Carboxypep tidases 62 Carboxypeptidase A 62 Carboxypeptidase B 63 Procarboxypeptidases 64 Other Pro teases 65 Thermol y sin 65 Pepsin 65 Papain 67 Proteinase Inhibitors 69 Soybean trypsin inhibitor (Kunitz) 69 Bowman-Birk soybean proteinase inhibitor 70 Pancreatic trypsin inhibitor 72 Aminoacyl-tR NA Syn thetases 73 Subunit Structures of Synthetases 74 Proteolytic Fragmentation of Synthetases 76 Other Enzymes 77 Contents vii 4 Structural Proteins 81 Collagen 81 Actin 85 Myosin 86 The Troponin-Tropomyosin System 87 Protein Kinases in Muscle 88 Other Structural Proteins 90 Myogen 90 Tubulin 90 Flagellar Proteins 91 Viral Proteins 91 5 Immunoglobulins 92 Complete Sequences 92 Partial Sequences 93 Disulphide Bridges 96 Partial Fragment ati on 97 Chemical Modification 99 Concanavalin A 101 6 Membrane Proteins 103 Solubilization and Fractionation 103 Receptor Proteins 105 7 Peptides and Hormones 107 Pituitary Hormones 108 Pancreatic Hormones 109 Growth Factors 111 Miscellaneous 114 8 Toxins 116 Snake Toxins 117 Other Toxins 121 9 Chromosomal Proteins 122 Histones 122 Acidic Nuclear Proteins 124 Pro tamines 125 10 Ribosomal Proteins 126 11 Proteins of the Nervous System 130 Myelin 131 Brain Proteins 132 viii Conteizts 12 Chemical Modification 135 Contributed by G. Allen Alkylating Reagents 136 Arylat ing Reagents 139 Acylating Reagents 1 40 Oxidizing Reagents 142 Other Reagents 144 /I: X-Ray Studies By T. L. Blundell 1 Introduction 145 2 Amino-acids and Peptides 146 3 Methods of Protein Structure Analysis 150 4 Globular Proteins 152 General Features 152 Proteases 153 Nucleases 158 Glycoside Hydrolases 159 Carbonic Anhydrases 159 Enzymes of the Glycolytic Pathway 159 Dehydrogenases 161 Regulatory Enzymes 164 Redox Proteins 166 Haemoglobins 170 Agglutinan ts 172 Toxins 174 Protein Hormones 174 Calcium Binding Protein 175 Immunoglobulins 175 Other Globular Proteins 177 5 Fibrous Proteins 177 Collagens and Synthetic Analogues 177 Fibrinogen 177 Synthetic Polyamino-acid Structures 178 Muscle 179 ill: Conformation and Interaction of Pepfides and Proteins in Solution Edited by R. H. Pain 1 Introduction 179 By-R. H. Pain Contents ix 2 Theoretical Aspects of Protein Structure 180 Contributed by B. Robson The Analytic Approach 181 The Theoretical Background to the Use of Con- formational Energy Calculations 181 Quantum-mechanical Calculations 183 Empirical Energy Calculations 183 Assignment of Parameters to Empirical Functions 184 Hard Variables 185 Solvent Effects 186 General Conclusions 187 3 Folding Mechanisms in Globular Proteins 187 Contributed by R. D. Ryder Introduction 187 Staphylococcal Nuclease 189 Lysozyme and Cytochrome c : Mathematical Analysis 189 Ri bonuclease 191 Chymotrypsinogen 192 Myoglobin 193 Ovalb umin 193 Carbonic Anhydrase 194 Multimeric Proteins 194 Aldolase 195 Lactate Dehydrogenase 195 RNA Polymerase 195 4 Spin Labels 196 Contributed by P. Knowles Haemoglobin 197 Enzyme-binding Studies 197 Carbonic Anhydrase 197 Lysozyme 197 Phosphorylase 198 Chymotrypsin and other Active-site Serine Enzymes 199 Phosphofructokinase 199 Dehydrogenases 200 /?-Galactosidase and /?-Galactoside. Permease 200 New Spin Labels 200 Membranes 201 Lateral-diffusion Studies 201 Membrane Fluidity 202 Hydrocarbon Chain Mobility 202 Contents X 5 Fluorescence 203 Contributed by G. R. Penzer Theory 203 Measurements and their Interpretation 204 Fluorescence Probes 207 Structure Mapping 209 Aggregation and Shape Changes 21 1 Interactions with Small Ligands 213 6 Mossbauer Spectroscopy 21 5 Confribufed by C. 15. Johnson Introduction 215 Haem Proteins 216 Iron-Sulphur Proteins 217 0t her Molecules 217 7 Nuclear Magnetic Resonance 218 Contributed by H. W. E. Rattle New Techniques 218 Amino-acids and Small Synthetic Peptides 219 Synthetic Polypeptides 219 Small Natural Peptides 220 Iron-containing Proteins 220 Other Proteins 221 Water in Biological Systems 223 8 Infrared and Raman Spectroscopy 223 Confributed by R. M. Stephens Model Compounds 223 Polypeptide Conformat ion 223 Hydration 224 Conformation 225 Raman Spectra 226 9 Dissociation and Association of Proteins 227 Confributed by G. L. Kelleff Analytical Ultracentrifugation Techniques 227 Interferometry 227 Theory 229 Binding St oicheiometry 229 Gel Chromatography 230 Kinetic Studies 232 Electron Microscopy 235 Subunit Structure of Proteins 236 SDS-Gel Electrophoresis 236 Associating-Dissociating Systems 237 Contents xi 10 Circular Dichroism and Optical Rotatory Dispersion 237 Contributed by P. M. Bayley Introduction 237 General 238 Reviews 238 Theory 238 Analysis 241 Instrument a1 242 Magnetic Circular Dichroism 242 Small Molecules, Model Compounds, and Synthetic Polymers 243 Amino-acids and Derivatives 243 Dipep tides and Oligopept ides 244 Polypeptides 245 Proteins 248 Model Aromatic and Disulphide Chromophores 248 Aromatic and Disulphide Chromophores in Proteins 250 Peptide Antibiotics, Hormones, etc. 25 1 Antibiotics and Ionophores 25 1 Hormones 253 Other Peptides and Non-enzymic Systems 254 Membranes 255 Artifacts 255 Membranes and Membrane Proteins 255 Lipoproteins 257 Chapter 3 Peptide Synthesis By J. H. Jones and B. Ridge 1 Introduction 258 2 Methods 258 Protective Groups 258 Established Methods of Amino-group Protection 258 New Methods of Amino-group Protection 26 1 Protection of Carboxy-groups 274 Protection of Thiol Groups and the Synthesis of Cystine Peptides 277 Protection of Primary Amide Groups and the Syn- thesis of Pyroglutamyl Peptides 283 Miscellaneous Matters relating to Protective Groups and Functional Side-chains 284 Formation of the Peptide Bond 286 Activated Esters 286
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