FUNDAMENTALS OF PROTEIN STRUCTURE AND FUNCTION

By E. CAZIS

CONTENTS PART I PROTEIN STRUCTURE 1 AMINO ACIDS 3 1 1 BASIC STRUCTURE OF AMINO ACIDS 3 1 2 THE ISOELECTRIC POINT 3 1 3 THE ONE LETTER CODE 7 1 4 BIOLOGICAL FUNCTION OF AMINO ACID VARIETY 8 2 PROTEIN STRUCTURE 13 2 1 PRIMARY STRUCTURE 13 2 2 SECONDARY STRUCTURE 16 2 2 1 HOW DO WE DETERMINE SECONDARY STRUCTURE 19 2 3 TERTIARY STRUCTURE 23 2 4 QUATERNARY STRUCTURE 27 2 4 1 PROTEIN STRUCTURE AND THE DEVELOPMENT OF PHARMACEUTICALS 27 2 4 2 PROTEIN DENATURATION 29 2 4 3 PROTEIN FOLDING 29 2 5 POSTTRANSLATIONAL MODI CATIONS OF PROTEINS 31 3 PURI CATION AND CHARACTERISATION OF PROTEINS 39 3 1 HOMOGENISATION AND FRACTIONISATION OF CELLS AND TISSUES 39 3 2 PRECIPITATION METHODS 40 3 2 1 SALTS 40 3 2 2 SOLVENTS 41 3 2 3 HEAT 41 3 3 CHROMATOGRAPHY 41 3 4 ELECTROPHORESIS 45 3 4 1 NATIVE ELECTROPHORESIS 45 3 4 2 DENATURING ELECTROPHORESIS 45 3 4 3 ISOELECTRIC FOCUSING AND 2D ELECTROPHORESIS 46 3 5 MEMBRANE PROTEINS 47 4 PROTEIN SEQUENCING 53 4 0 1 PHYLOGENETIC TREES 54 PART II ENZYMES 5 ENZYMES ARE BIOCATALYSTS 59 5 1 THE NATURE OF CATALYSIS 59 5 1 1 A BRIEF HISTORY OF ENZYMOLOGY 60 5 2 ENZYME CLASSI CATION AND EC CODE 63 6 ENZYME KINETICS 67 6 1 THE HENRI MICHAELIS MENTEN HMM EQUATION 67 6 2 A MORE GENERAL FORM OF THE HMM EQUATION 69 6 2 1 EXPERIMENTAL PITFALLS 77 6 3 INHIBITION OF ENZYMES 80 6 3 1 COMPETITIVE INHIBITION 82 6 3 2 UNCOMPETITIVE INHIBITION 83 6 3 3 NON COMPETITIVE INHIBITION 86 6 3 4 PARTIALLY NON COMPETITIVE INHIBITION 86 6 4 INACTIVATION OF ENZYMES 89 6 5 ENZYMES WITH SEVERAL SUBSTRATES 92 6 5 1 NOMENCLATURE 93 6 5 2 HOW DO WE DETERMINE THE MECHANISM OF MULTI SUBSTRATE ENZYMES 94 6 6 ENZYME MECHANISM 95 6 6 1 ADVANCED MATERIAL MOLECULAR MECHANISM OF SERINE PROTEASES AND ESTERASES 97 6 7 ENZYME PRECURSORS AND THEIR ACTIVATION 97 6 8 USE OF ENZYMES FOR DIAGNOSTICS 99 6 8 1 THE COUPLED SPECTROPHOTOMETRIC ASSAY OF WARBURG 99 7 HAEMOGLOBIN AND MYOGLOBIN CO OPERATIVITY 105 7 1 STRUCTURE 105 7 2 OXYGEN BINDING AND CO OPERATIVITY 108 7 2 1 FUNCTIONAL SIGNI CANCE OF CO OPERATIVITY 109 7 2 2 MECHANISM OF CO OPERATIVITY 110 7 2 3 OTHER FACTORS INVOLVING OXYGEN A NITY OF HAEMOGLOBIN 112 7 3 HAEMOGLOBIN RELATED DISEASES 115 8 ENZYME KINETICS SPECIAL CASES 121 8 1 ACTIVATION CASCADES 121 8 2 FEEDBACK NETWORKS 124 8 2 1 ADVANCED MATERIAL SIMULATION OF FEED BACK SYSTEMS 125 8 3 MULTIPLE PHOSPHORYLATION 126 PART III SPECIAL PROTEINS 9 PRION PROTEINS AND PRION DISEASES 131 10 IMMUNOPROTEINS 137 10 1 OVERVIEW 137 10 1 1 CELLS OF THE IMMUNE SYSTEM 138 10 2 HUMORAL IMMUNITY IMMUNOGLOBULINS 139 10 2 1 STRUCTURE OF IMMUNOGLOBULINS 142 10 2 2 HOW IS THE LARGE NUMBER OF IG MOLECULES OBTAINED 145 10 2 3 TIME COURSE OF ANTIBODY RESPONSE 150 10 2 4 IMMUNISATION 152 10 2 5 MONOCLONAL ANTIBODIES 152 10 2 6 LABORATORY USES OF ANTIBODIES 153 10 3 DESTROYING INVADERS THE COMPLEMENT SYSTEM 155 10 3 1 HOW IS COMPLEMENT ACTIVATED 156 10 3 2 WHAT DOES COMPLEMENT DO 156 10 3 3 HOW IS COMPLEMENT DEGRADED 158 10 4 CELLULAR IMMUNITY 158 10 4 1 THE MAJOR HISTOCOMPATIBILITY COMPLEX 159 10 4 2 THE T CELL RECEPTOR 167 11 CELL SKELETON 175 11 1 THE MICRO LAMENT 175 11 1 1 BASIC ACTIN STRUCTURE 175 11 1 2 ACTIN NETWORKS 178 11 2 MICROTUBULES 178 11 2 1 MICROTUBULE STRUCTURE 179 11 3 INTERMEDIATE LAMENT 181 11 3 1 IF PROTEINS ARE CELL TYPE SPECI C 181 11 3 2 STRUCTURE OF INTERMEDIATE LAMENTS 183 11 3 3 INTERMEDIATE LAMENTS AND CELL CYCLE 183 11 3 4 OTHER PROTEINS ASSOCIATED WITH INTERMEDIATE LAMENTS 183 12 MOTOR PROTEINS AND MOVEMENT 185 12 1 MYOSIN MOVES ALONG ACTIN LAMENTS 185 12 1 1 MYOSIN STRUCTURE 185 12 1 2 MYOSIN II 187 12 1 3 MYOSIN I 190 12 1 4 MYOSIN V 190 12 2 KINESIN AND DYNEIN MOVE ALONG MICROTUBULES 190 12 2 1 KINESIN IS RESPONSIBLE FOR ANTEROGRADE TRANSPORT 191 12 2 2 DYNEIN IS RESPONSIBLE FOR RETROGRADE MOVEMENT 192 12 3 CILIA AND AGELLA 192 12 3 1 GENERIC STRUCTURE OF CILIA AND AGELLA 192 12 3 2 MECHANISM OF MOVEMENT 193 12 3 3 CILIA AND AGELLA START GROWING AT THE BASAL BODY 194 12 4 THE MITOTIC SPINDLE 194 13 CELL CELL INTERACTIONS 201 13 1 EXTRACELLULAR MATRIX 201 13 1 1 COLLAGEN 202 13 1 2 ELASTIN 205 13 2 CELL ADHESION MOLECULES 205 13 3 JUNCTIONS 208 PART I PROTEIN STRUCTURE 1