The authors’ objective has been to concentrate on amino acids and pep- tides without detailed discussions of proteins, although the book gives all the essential background chemistry, including sequence determination, synthesis and spectroscopic methods, to allow the reader to appreciate protein behaviour at the molecular level. The approach is intended to encourage the reader to cross classical boundaries, such as in the later chapter on the biological roles of amino acids and the design of peptide- based drugs. For example, there is a section on enzyme-catalysed synthesis of peptides, an area often neglected in texts describing peptide synthesis.
This modern text will be of value to advanced undergraduates, graduate students and research workers in the amino acid, peptide and protein field. Amino Acids and Peptides
G. C.IBARRETT D. T. ELMORE The Pitt Building, Trumpington Street, Cambridge, United Kingdom The Edinburgh Building, Cambridge CB2 2RU, UK 40 West 20th Street, New York, NY 10011-4211, USA 477 Williamstown Road, Port Melbourne, VIC 3207, Australia Ruiz de Alarcón 13, 28014 Madrid, Spain Dock House, The Waterfront, Cape Town 8001, South Africa http://www.cambridge.org
© Cambridge University Press 2004
First published in printed format 1998
ISBN 0-511-03952-2 eBook (netLibrary) ISBN 0-521-46292-4 hardback ISBN 0-521-46827-2 paperback Contents
Forewordpagexiii
1Introduction1 1.1Sources and roles of amino acids and peptides1 1.2Definitions1 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 polypeptides7 1.6 Post-translational processing: modification of amino-acid residues within polypeptides11 1.7 Post-translational processing: in vivo cleavages of the amide backbone of polypeptides11 1.8 ‘Non-protein amino acids’, alias ‘non-proteinogenic amino acids’ or ‘non-coded amino acids’11 1.9Coded amino acids, non-natural amino acids and peptides in nutrition and food science and in human physiology13 1.10The geological and extra-terrestrial distribution of amino acids15 1.11Amino acids in archaeology and in forensic science15 1.12Roles for amino acids in chemistry and in the life sciences16 1.12.1Amino acids in chemistry16 1.12.2Amino acids in the life sciences16 1.13 - and higher amino acids17 1.14References19
2Conformations ofamino acids and peptides20 2.1 Introduction: the main conformational features of amino acids and peptides20
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2.2Configurational isomerism within the peptide bond20 2.3Dipeptides26 2.4Cyclic oligopeptides26 2.5Acyclic oligopeptides27 2.6Longer oligopeptides: primary, secondary and tertiary structure27 2.7Polypeptides and proteins: quaternary structure and aggregation28 2.8 Examples of conformational behaviour; ordered and disordered states and transitions between them29 2.8.1The main categories of polypeptide conformation29 2.8.1.1One extreme situation29 2.8.1.2The other extreme situation29 2.8.1.3The general case29 2.9Conformational transitions for amino acids and peptides30 2.10References31
3Physicochemical properties ofamino acids and peptides32 3.1Acid–base properties32 3.2Metal-binding properties of amino acids and peptides34 3.3 An introduction to the routine aspects and the specialised aspects of the spectra of amino acids and peptides35 3.4Infrared (IR) spectrometry36 3.5 General aspects of ultraviolet (UV) spectrometry, circular dichroism (CD) and UVfluorescence spectrometry37 3.6Circular dichroism38 3.7Nuclear magnetic resonance (NMR) spectroscopy41 3.8 Examples of assignments of structures to peptides from NMR spectra and other data43 3.9References46
4Reactions and analytical methods for amino acids and peptides48 Part 1Reactions of amino acids and peptides48 4.1Introduction48 4.2General survey48 4.2.1Pyrolysis of amino acids and peptides49 4.2.2Reactions of the amino group49 4.2.3Reactions of the carboxy group49 4.2.4Reactions involving both amino and carboxy groups51 4.3A more detailed survey of reactions of the amino group51 4.3.1N-Acylation51 4.3.2Reactions with aldehydes52 4.3.3N-Alkylation53
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4.4A survey of reactions of the carboxy group53 4.4.1Esterification54 4.4.2Oxidative decarboxylation54 4.4.3Reduction54 4.4.4Halogenation55 4.4.5 Reactions involving amino and carboxy groups of -amino acids and their N-acyl derivatives55 4.4.6 Reactions at the -carbon atom and racemisation of -amino acids55 4.4.7Reactions of the amide group in acylamino acids and peptides57 4.5Derivatisation of amino acids for analysis58 4.5.1 Preparation of N-acylamino acid esters and similar derivatives for analysis58 4.6References60 Part 2 Mass spectrometry in amino-acid and peptide analysis and in peptide-sequence determination61 4.7General considerations61 4.7.1Mass spectra of free amino acids61 4.7.2Mass spectra of free peptides62 4.7.3Negative-ion mass spectrometry65 4.8Examples of mass spectra of peptides65 4.8.1 Electron-impact mass spectra (EIMS) of peptide derivatives65 4.8.2Finer details of mass spectra of peptides68 4.8.3Difficulties and ambiguities69 4.9 The general status of mass spectrometry in peptide analysis69 4.9.1 Specific advantages of mass spectrometry in peptide sequencing70 4.10Early methodology: peptide derivatisation71 4.10.1N-Terminal acylation and C-terminal esterification71 4.10.2N-Acylation and N-alkylation of the peptide bond72 4.10.3Reduction of peptides to ‘polyamino-polyalcohols’72 4.11 Current methodology: sequencing by partial acid hydrolysis, followed by direct MS analysis of peptide hydrolysates72 4.11.1Current methodology: instrumental variations74 4.12Conclusions77 4.13References77
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Part 3 Chromatographic and related methods for the separation of mixtures of amino acids, mixtures of peptides and mixtures of amino acids and peptides78 4.14Separation of amino-acid and peptide mixtures78 4.14.1Separation principles78 4.15Partition chromatography; HPLC and GLC80 4.16Molecular exclusion chromatography (gel chromatography)80 4.17Electrophoretic separation and ion-exchange chromatography82 4.17.1Capillary zone electrophoresis (CZE)83 4.18Detection of separated amino acids and peptides83 4.18.1 Detection of amino acids and peptides separated by HPLC and by other liquid-based techniques84 4.18.2Detection of amino acids and peptides separated by GLC85 4.19Thin-layer chromatography (planar chromatography; HPTLC)86 4.20Quantitative amino-acid analysis86 4.21References87 Part 4Immunoassays for peptides87 4.22Radioimmunoassays87 4.23Enzyme-linked immunosorbent assays (ELISAs)88 4.24References90 Part 5Enzyme-based methods for amino acids90 4.25Biosensors90 4.26References90
5Determination ofthe primary structure ofpeptides and proteins91 5.1Introduction91 5.2Strategy92 5.3Cleavage of disulphide bonds96 5.4Identification of the N-terminus and stepwise degradation97 5.5Enzymic methods for determining N-terminal sequences105 5.6Identification of C-terminal sequences106 5.7Enzymic determination of C-terminal sequences107 5.8Selective chemical methods for cleaving peptide bonds107 5.9Selective enzymic methods for cleaving peptide bonds109 5.10Determination of the positions of disulphide bonds112 5.11 Location of post-translational modifications and prosthetic groups114 5.12Determination of the sequence of DNA117 5.13References118
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6Synthesis ofamino acids120 6.1General120 6.2Commercial and research uses for amino acids120 6.3Biosynthesis: isolation of amino acids from natural sources121 6.3.1Isolation of amino acids from proteins121 6.3.2 Biotechnological and industrial synthesis of coded amino acids121 6.4 Synthesis of amino acids starting from coded amino acids other than glycine122 6.5 General methods of synthesis of amino acids starting with a glycine derivative123 6.6Other general methods of amino acid synthesis123 6.7Resolution of -amino acids125 6.8Asymmetric synthesis of amino acids127 6.9References129
7Methods for the synthesis ofpeptides130 7.1Basic principles of peptide synthesis and strategy130 7.2Chemical synthesis and genetic engineering132 7.3Protection of -amino groups134 7.4Protection of carboxy groups135 7.5Protection of functional side-chains138 7.5.1Protection of -amino groups138 7.5.2Protection of thiol groups139 7.5.3Protection of hydroxy groups140 7.5.4Protection of the guanidino group of arginine141 7.5.5Protection of the imidazole ring of histidine142 7.5.6Protection of amide groups145 7.5.7Protection of the thioether side-chain of methionine145 7.5.8Protection of the indole ring of tryptophan146 7.6Deprotection procedures146 7.7Enantiomerisation during peptide synthesis146 7.8Methods for forming peptide bonds149 7.8.1The acyl azide method150 7.8.2The use of acid chlorides and acid fluorides151 7.8.3The use of acid anhydrides151 7.8.4The use of carbodiimides153 7.8.5The use of reactive esters153 7.8.6The use of phosphonium and isouronium derivatives155 7.9Solid-phase peptide synthesis (SPPS)156 7.10Soluble-handle techniques163 7.11Enzyme-catalysed peptide synthesis and partial synthesis164
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7.12Cyclic peptides168 7.12.1Homodetic cyclic peptides168 7.12.2Heterodetic cyclic peptides170 7.13The formation of disulphide bonds170 7.14References172 7.14.1References cited in the text172 7.14.2References for background reading173
8Biological roles ofamino acids and peptides174 8.1Introduction174 8.2The role of amino acids in protein biosynthesis175 8.3Post-translational modification of protein structures178 8.4Conjugation of amino acids with other compounds182 8.5Other examples of synthetic uses of amino acids183 8.6Important products of amino-acid metabolism187 8.7Glutathione190 8.8The biosynthesis of penicillins and cephalosporins192 8.9References198 8.9.1References cited in the text198 8.9.2References for background reading199
9Some aspects ofamino-acid and peptide drug design200 9.1Amino-acid antimetabolites200 9.2Fundamental aspects of peptide drug design201 9.3The need for peptide-based drugs202 9.4The mechanism of action of proteinases and design of inhibitors204 9.5Some biologically active analogues of peptide hormones210 9.6The production of antibodies and vaccines213 9.7The combinatorial synthesis of peptides215 9.8The design of pro-drugs based on peptides216 9.9Peptide antibiotics217 9.10References218 9.10.1References cited in the text218 9.10.2References for background reading218
Subject index220
xii Foreword
This is an undergraduate and introductory postgraduate textbook that gives information on amino acids and peptides, and is intended to be self-sufficient in all the organic and analytical chemistry fundamentals. It is aimed at students of chem- istry, and allied areas. Suggestions for supplementary reading are provided, so that topic areas that are not covered in depth in this book may be followed up by readers with particular study interests. A particular objective has been to concentrate on amino acids and peptides, as the title of the book implies; the exclusion of detailed discussion of proteins is deliberate, but the book gives all the essential background chemistry so that protein behaviour at the molecular level can be appreciated. There is an emphasis on the uses of amino acids and peptides, and on their bio- logical roles and, while Chapter 8 concentrates on this, a scattering of items of information of this type will be found throughout the book. Important pharma- ceutical developments in recent years underline the continuing importance and potency of amino acids and peptides in medicine and the flavour of current research themes in this area can be gained from Chapter 9.
Supplementary reading (see also lists at the end of each Chapter)
Standard Student Texts Standard undergraduate Biochemistry textbooks relate the general field to the coverage of this book. Several such topic areas are covered in Zubay, G. (1993) Biochemistry, Third Edition, Wm. C. Brown Communications Inc, Dubuque, IA and Voet, D. and Voet, J. G. (1995) Biochemistry, Second edition, Wiley, New York
xiii Foreword
Typically, these topic areas as covered by Zubay are Chapter 3: ‘The building blocks of proteins: amino acids, peptides and proteins’ Chapter 4: ‘The three-dimensional structure of proteins’ Chapter 5: ‘Functional diversity of proteins’
Removed more towards biochemical themes, are Chapter 18: ‘Biosynthesis of amino acids’ Chapter 19: ‘The metabolic fate of amino acids’ Chapter 29: ‘Protein synthesis, targeting, and turnover’
Voet and Voet give similar coverage in Chapter 24: ‘Amino acid metabolism’ Chapter 30: ‘Translation’ (i.e. protein biosynthesis) Chapter 34: ‘Molecular physiology’ (of particular relevance to coverage in this book of blood clotting, peptide hormones and neurotransmitters)
Supplementary reading: suggestions for further reading
(a) Protein structure Branden, C., and Tooze, J. (1991) Introduction to Protein Structure, Garland Publishing Inc., New York
(b) Protein chemistry Hugli, T. E. (1989) Techniques of Protein Chemistry, Academic Press, San Diego, California Cherry, J. P. and Barford, R. A. (1988) Methods for Protein Analysis, American Oil Chemists’ Society, Champaign, Illinois
(c) Amino acids Barrett, G. C., Ed. (1985) Chemistry and Biochemistry of the Amino Acids, Chapman and Hall, London Barrett, G. C. (1993) in Second Supplements to the 2nd Edition of Rodd’s Chemistry of Carbon Compounds, Volume 1, Part D: Dihydric alcohols, their oxidation products and derivatives, Ed. Sainsbury, M., Elsevier, Amsterdam, pp. 117–66 Barrett, G. C. (1995) in Amino Acids, Peptides, and Proteins, A Specialist Periodical Report of The Royal Society of Chemistry, Vol. 26, Ed. Davies, J. S., Royal Society of Chemistry, London (preceding volumes cover the literature on amino acids, back to 1969 (Volume 1)) Coppola, G. M. and Schuster, H. F. (1987) Asymmetric Synthesis: Construction of Chiral Molecules using Amino Acids, Wiley, New York Dawson, R. M. C., Elliott, D. C., Elliott, W. H., and Jones, K. M. (1986) Data for Biochemical Research, Oxford University Press, Oxford
xiv Foreword
Greenstein, J. P., and Winitz, M. (1961) Chemistry of the Amino Acids, Wiley, New York (a facsimile version (1986) of this three-volume set has been made available by Robert E. Krieger Publishing Inc., Malabar, Florida) Williams, R. M. (1989) Synthesis of Optically Active -Amino Acids, Pergamon Press, Oxford
(d) Peptides Bailey, P. D. (1990) An Introduction to Peptide Chemistry, Wiley, Chichester Bodanszky, M. (1988) Peptide Chemistry: A Practical Handbook. Springer-Verlag, Berlin Bodanszky, M. (1993) Principles of Peptide Synthesis, Second Edition, Springer-Verlag, Heidelberg Elmore, D. T. (1993) in Second Supplements to the 2nd Edition of Rodd’s Chemistry of Carbon Compounds, Volume 1, Part D: Dihydric alcohols, their oxidation products and derivatives, Ed. Sainsbury, M., Elsevier, Amsterdam, pp. 167–211 Elmore, D. T. (1995) in Amino Acids, Peptides, and Proteins, A Specialist Periodical Report of The Royal Society of Chemistry, Vol. 26, Ed. Davies, J. S., Royal Society of Chemistry, London (preceding volumes cover the literature of peptide chemistry back to 1969 (Volume 1)) Jones, J. H. (1991) The Chemical Synthesis of Peptides, Clarendon Press, Oxford
xv
1 Introduction
1.1 Sources and roles of amino acids and peptides More than 700 amino acids have been discovered in Nature and most of them are -amino acids. Bacteria, fungi and algae and other plants provide nearly all these, which exist either in the free form or bound up into larger molecules (as constitu- ents of peptides and proteins and other types of amide, and of alkylated and ester- ified structures). The twenty amino acids (actually, nineteen -amino acids and one -imino acid) that are utilised in living cells for protein synthesis under the control of genes are in a special category since they are fundamental to all life forms as building blocks for peptides and proteins. However, the reasons why all the other natural amino acids are located where they are, are rarely known, although this is an area of much speculation. For example, some unusual amino acids are present in many seeds and are not needed by the mature plant. They deter predators through their toxic or oth- erwise unpleasant characteristics and in this way are thought to provide a defence strategy to improve the chances of survival for the seed and therefore help to ensure the survival of the plant species. Peptides and proteins play a wide variety of roles in living organisms and display a range of properties (from the potent hormonal activity of some small peptides to the structural support and protection for the organism shown by insoluble proteins). Some of these roles are illustrated in this book.
1.2 Definitions The term ‘amino acids’ is generally understood to refer to the aminoalkanoic acids, 1 2 H3N —(CR R )n—CO2 with n 1 for the series of -amino acids, n 2 for -amino acids, etc. The term ‘dehydro-amino acids’ specifically describes 2,3-unsaturated (or 1 2 ‘ -unsaturated’)-2-aminoalkanoic acids, H3N —(C CR R )—CO2 . However, the term ‘amino acids’ would include all structures carrying amine and acid functional groups, including simple aromatic compounds, e.g. anthranilic acid,
1
Figure 1.1. Peptides as condensation polymers of -amino acids.