Lorsch Laboratory Methods in Enzymology: Protein Part C

1. Auflage 2014
ISBN: 978-0-12-420178-1
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 541, 296 Seiten

Reihe: Methods in Enzymology

In this volume we have brought together a number of core protocols concentrating on Protein, carefully written and edited by experts. - Indispensable tool for the researcher - Carefully written and edited by experts to contain step-by-step protocols - In this volume we have brought together a number of core protocols concentrating on Protein

Autoren/Hrsg.

Lorsch, Jon

Inhaltsverzeichnis

1;Front Cover;1
2;Laboratory Methods in Enzymology: Protein Part C;4
3;Copyright;5
4;Contents;6
5;Contributors;14
6;Miscellaneous;16
7;Preface;18
8;Section I: Protein Protocols/Protein Precipitation;20
8.1;Chapter One: TCA Precipitation;22
8.1.1;1. Theory;23
8.1.2;2. Equipment;23
8.1.3;3. Materials;23
8.1.3.1;3.1. Solutions and buffers;24
8.1.4;4. Protocol;25
8.1.4.1;4.1. Preparation;25
8.1.4.2;4.2. Duration;25
8.1.4.3;4.3. Caution;25
8.1.5;5. Step 1A Trichloroacetic Acid Precipitation;25
8.1.5.1;5.1. Overview;25
8.1.5.2;5.2. Duration;25
8.1.5.3;5.3. Tip;26
8.1.5.4;5.4. Tip;26
8.1.5.5;5.5. Tip;26
8.1.6;6. Step 1B Deoxycholate-Trichloroacetic Acid Precipitation;26
8.1.6.1;6.1. Overview;26
8.1.6.2;6.2. Duration;26
8.1.6.3;6.3. Tip;27
8.1.6.4;6.4. Tip;28
8.1.6.5;6.5. Tip;28
8.1.7;References;29
8.1.7.1;Referenced Protocols in Methods Navigator;29
9;Section II: Protein Protocols/Protein Pull-Down Methods;30
9.1;Chapter Two: Coimmunoprecipitation of Proteins from Yeast;32
9.1.1;1. Theory;33
9.1.2;2. Equipment;34
9.1.3;3. Materials;34
9.1.3.1;3.1. Solutions and buffers;35
9.1.4;4. Protocol;36
9.1.4.1;4.1. Duration;36
9.1.4.2;4.2. Preparation;36
9.1.5;5. Step 1 Preparation of Whole Cell Lysates;37
9.1.5.1;5.1. Overview;37
9.1.5.2;5.2. Duration;37
9.1.6;6. Step 2 Normalization of Cell Lysates;39
9.1.6.1;6.1. Overview;39
9.1.6.2;6.2. Duration;39
9.1.6.3;6.3. Tip;39
9.1.7;7. Step 3 Coimmunoprecipitation;39
9.1.7.1;7.1. Overview;39
9.1.7.2;7.2. Duration;40
9.1.7.3;7.3. Tip;41
9.1.7.4;7.4. Tip;41
9.1.7.5;7.5. Tip;41
9.1.7.6;7.6. Tip;41
9.1.7.7;7.7. Tip;41
9.1.7.8;7.8. Tip;41
9.1.7.9;7.9. Note;41
9.1.8;8. Step 4 Wash and Elute the Immunoprecipitates;42
9.1.8.1;8.1. Overview;42
9.1.8.2;8.2. Duration;42
9.1.8.3;8.3. Tip;43
9.1.8.4;8.4. Tip;43
9.1.9;9. Step 5 Analysis of Immunoprecipitations;43
9.1.9.1;9.1. Overview;43
9.1.9.2;9.2. Duration;44
9.1.10;References;45
9.1.10.1;Referenced Literature;45
9.1.10.2;Related Literature;45
9.1.10.3;Referenced Protocols in Methods Navigator;45
9.2;Chapter Three: Coupling Antibody to Cyanogen Bromide-Activated Sepharose;46
9.2.1;1. Theory;47
9.2.2;2. Equipment;47
9.2.3;3. Materials;47
9.2.3.1;3.1. Solutions and buffers;47
9.2.4;4. Protocol;49
9.2.4.1;4.1. Duration;49
9.2.4.2;4.2. Preparation;49
9.2.5;5. Step 1 Preparation of Antibody and Resin;49
9.2.5.1;5.1. Overview;49
9.2.5.2;5.2. Duration;49
9.2.5.3;5.3. Tip;50
9.2.5.4;5.4. Tip;50
9.2.5.5;5.5. Tip;50
9.2.5.6;5.6. Tip;50
9.2.6;6. Step 2 Coupling the Antibody to the Resin;51
9.2.6.1;6.1. Overview;51
9.2.6.2;6.2. Duration;51
9.2.6.3;6.3. Tip;51
9.2.7;7. Step 3 Quench the Reaction;51
9.2.7.1;7.1. Overview;51
9.2.7.2;7.2. Duration;51
9.2.7.3;7.3. Tip;52
9.2.8;8. Step 4 Wash the Resin;52
9.2.8.1;8.1. Overview;52
9.2.8.2;8.2. Duration;53
9.2.9;References;53
9.2.9.1;Referenced Protocols in Methods Navigator;53
9.3;Chapter Four: Analysis of Protein-Protein Interactions by Coimmunoprecipitation;54
9.3.1;1. Theory;55
9.3.2;2. Equipment;57
9.3.3;3. Materials;58
9.3.3.1;3.1. Solutions and buffers;59
9.3.4;4. Protocol;61
9.3.4.1;4.1. Preparation;61
9.3.4.2;4.2. Duration;61
9.3.5;5. Step 1 Isolation of the Protein of Interest by Immunoprecipitation;61
9.3.5.1;5.1. Overview;61
9.3.5.2;5.2. Duration;62
9.3.5.3;5.3. Tip;62
9.3.5.4;5.4. Tip;62
9.3.5.5;5.5. Tip;62
9.3.6;6. Step 2 Detection of the Binding Partner by Immunoblotting;63
9.3.6.1;6.1. Overview;63
9.3.6.2;6.2. Duration;63
9.3.6.3;6.3. Tip;64
9.3.6.4;6.4. Tip;64
9.3.7;References;65
9.3.7.1;Referenced Literature;65
9.3.7.2;Referenced Protocols in Methods Navigator;66
10;Section III: Protein Protocols/Protein Purification;68
10.1;Chapter Five: Use and Application of Hydrophobic Interaction Chromatography for Protein Purification;70
10.1.1;1. Theory;71
10.1.1.1;1.1. Latest technology in HIC adsorbents;73
10.1.1.2;1.2. Advantages and disadvantages of using HIC;74
10.1.2;2. Equipment;75
10.1.3;3. Materials;75
10.1.3.1;3.1. Solutions and buffers;76
10.1.3.2;3.2. Preparation;76
10.1.4;4. Protocol;77
10.1.4.1;4.1. Preparation;77
10.1.4.2;4.2. Duration;77
10.1.5;5. Step 1 Column Equilibration;78
10.1.5.1;5.1. Overview;78
10.1.5.2;5.2. Duration;79
10.1.6;6. Step 2 Column Loading;79
10.1.6.1;6.1. Overview;79
10.1.6.2;6.2. Duration;79
10.1.7;7. Step 3 Product Elution;80
10.1.7.1;7.1. Overview;80
10.1.7.2;7.2. Duration;80
10.1.7.3;7.3. Gradient elution;81
10.1.7.4;7.4. Stepwise (isocratic) elution;82
10.1.8;8. Step 4 Adsorbent Regeneration and Sanitization;82
10.1.8.1;8.1. Overview;82
10.1.8.2;8.2. Duration;82
10.1.9;References;83
10.1.9.1;Referenced Literature;83
10.1.10;Source References;84
10.1.10.1;Referenced Protocols in Methods Navigator;84
10.2;Chapter Six: Hydroxyapatite Chromatography: Purification Strategies for Recombinant Proteins;86
10.2.1;1. Theory;87
10.2.2;2. Equipment;88
10.2.3;3. Materials;88
10.2.3.1;3.1. Solutions and buffers;89
10.2.4;4. Protocol;91
10.2.4.1;4.1. Duration;91
10.2.4.2;4.2. Preparation;91
10.2.4.2.1;4.2.1. BioLogic DuoFlow/Maximizer 10ml;91
10.2.4.2.2;4.2.2. BioLogic DuoFlow Maximizer 80 System;92
10.2.4.2.3;4.2.3. Column 1.1 cm x 22 cm packed bed (Steps 1 and 2);92
10.2.4.2.4;4.2.4. Column 3.2 cm x 22 cm packed bed (Step 3);93
10.2.4.3;4.3. Tip;94
10.2.5;5. Step 1 Purification Protocol Screening by Linear Salt Gradient;94
10.2.5.1;5.1. Overview;94
10.2.5.2;5.2. Duration;94
10.2.6;6. Step 2 Purification Protocol using a Step Gradient;96
10.2.6.1;6.1. Overview;96
10.2.6.2;6.2. Duration;96
10.2.7;7. Step 3 Purification Protocol using a Step Gradient and Simplified Analytics;98
10.2.7.1;7.1. Overview;98
10.2.7.2;7.2. Duration;98
10.2.8;8. Step 4 Offline pH Measurement and Calcium ion Analysis;99
10.2.8.1;8.1. Overview;99
10.2.8.2;8.2. Duration;99
10.2.9;9. Step 5SEC Profile for the Collected mAb Fraction and Regeneration Fraction;100
10.2.9.1;9.1. Overview;100
10.2.9.2;9.2. Duration;100
10.2.10;References;102
10.2.10.1;Referenced Literature;102
10.3;Chapter Seven: Salting out of Proteins Using Ammonium Sulfate Precipitation;104
10.3.1;1. Theory;105
10.3.2;2. Equipment;106
10.3.3;3. Materials;107
10.3.3.1;3.1. Solutions and buffers;107
10.3.4;4. Protocol;107
10.3.4.1;4.1. Preparation;107
10.3.4.2;4.2. Duration;107
10.3.5;5. Step 1 Removal of Proteins Marginally Soluble in (NH4)2SO4;108
10.3.5.1;5.1. Overview;108
10.3.5.2;5.2. Duration;108
10.3.5.3;5.3. Tip;108
10.3.6;6. Step 2 Precipitation of the Protein of Interest;108
10.3.6.1;6.1. Overview;108
10.3.6.2;6.2. Duration;111
10.3.6.3;6.3. Tip;112
10.3.6.4;6.4. Tip;112
10.3.6.5;6.5. Tip;112
10.3.6.6;6.6. Tip;112
10.3.6.7;6.7. Tip;112
10.3.7;References;113
10.3.7.1;Referenced Literature;113
10.3.7.2;Referenced Protocols in Methods Navigator;113
10.4;Chapter Eight: Using Ion Exchange Chromatography to Purify a Recombinantly Expressed Protein;114
10.4.1;1. Theory;115
10.4.2;2. Equipment;117
10.4.3;3. Materials;117
10.4.3.1;3.1. Solutions and buffers;117
10.4.4;4. Protocol;118
10.4.4.1;4.1. Duration;118
10.4.4.2;4.2. Preparation;118
10.4.5;5. Step 1 Equilibration of the Column;118
10.4.5.1;5.1. Overview;118
10.4.5.2;5.2. Duration;118
10.4.5.3;5.3. Tip;119
10.4.5.4;5.4. Tip;119
10.4.5.5;5.5. Tip;119
10.4.6;6. Step 2 Binding of the Protein Sample;120
10.4.6.1;6.1. Overview;120
10.4.6.2;6.2. Duration;120
10.4.6.3;6.3. Tip;120
10.4.6.4;6.4. Tip;120
10.4.7;7. Step 3 Removal of Unbound Proteins;120
10.4.7.1;7.1. Overview;120
10.4.7.2;7.2. Duration;120
10.4.8;8. Step 4 Elution of the Bound Protein;121
10.4.8.1;8.1. Overview;121
10.4.8.2;8.2. Duration;121
10.4.8.3;8.3. Tip;122
10.4.8.4;8.4. Tip;122
10.4.8.5;8.5. Tip;122
10.4.9;References;122
10.4.9.1;Referenced Literature;122
10.4.9.2;Referenced Protocols in Methods Navigator;122
10.5;Chapter Nine: Gel Filtration Chromatography (Size Exclusion Chromatography) of Proteins;124
10.5.1;1. Theory;125
10.5.2;2. Equipment;127
10.5.3;3. Materials;127
10.5.3.1;3.1. Solutions and buffers;128
10.5.4;4. Protocol;128
10.5.4.1;4.1. Preparation;128
10.5.4.2;4.2. Duration;129
10.5.5;5. Step 1 Standardization of the Gel Filtration Column;129
10.5.5.1;5.1. Overview;129
10.5.5.2;5.2. Duration;129
10.5.5.3;5.3. Tip;130
10.5.5.4;5.4. Tip;130
10.5.5.5;5.5. Tip;130
10.5.5.6;5.6. Tip;130
10.5.5.7;5.7. Tip;130
10.5.6;6. Step 2 Determination of the Sizes of Protein Species in a Sample;131
10.5.6.1;6.1. Overview;131
10.5.6.2;6.2. Duration;131
10.5.6.3;6.3. Tip;132
10.5.6.4;6.4. Tip;132
10.5.6.5;6.5. Tip;132
10.5.6.6;6.6. Tip;132
10.5.6.7;6.7. Tip;132
10.5.7;References;133
10.5.7.1;Referenced Literature;133
10.5.7.2;Referenced Protocols in Methods Navigator;133
11;Section IV: Protein Protocols/Purification of Membrane Proteins;134
11.1;Chapter Ten: Expression and Purification of Membrane Proteins;136
11.1.1;1. Theory;137
11.1.2;2. Equipment;140
11.1.3;3. Materials;140
11.1.3.1;3.1. Solutions and buffers;141
11.1.4;4. Protocol;143
11.1.4.1;4.1. Preparation;143
11.1.4.2;4.2. Duration;143
11.1.5;5. Step 1 Transformation of E. coli;145
11.1.5.1;5.1. Overview;145
11.1.5.2;5.2. Duration;145
11.1.5.3;5.3. Tip;145
11.1.6;6. Step 2 Cultivation of E. coli - Screening for the Optimal Expression Conditions;145
11.1.6.1;6.1. Overview;145
11.1.6.2;6.2. Duration;146
11.1.6.3;6.3. Tip;148
11.1.6.4;6.4. Tip;148
11.1.6.5;6.5. Tip;148
11.1.6.6;6.6. Tip;148
11.1.6.7;6.7. Tip;148
11.1.7;7. Step 3 Scale-Up Expression of a Membrane Protein Using the Optimal Expression Conditions;149
11.1.7.1;7.1. Overview;149
11.1.7.2;7.2. Duration;149
11.1.7.3;7.3. Tip;150
11.1.8;8. Step 4 Screening Detergents to Determine Optimal Solubilization of Membrane Protein;150
11.1.8.1;8.1. Overview;150
11.1.8.2;8.2. Duration;151
11.1.9;9. Step 5 Scale-up the Solubilization of the Membrane Protein;153
11.1.9.1;9.1. Overview;153
11.1.9.2;9.2. Duration;153
11.1.9.3;9.3. Tip;154
11.1.9.4;9.4. Tip;154
11.1.10;10. Step 6 Purification of Membrane Proteins Using Ni-NTA Superflow;155
11.1.10.1;10.1. Overview;155
11.1.10.2;10.2. Duration;155
11.1.10.3;10.3. Tip;157
11.1.11;References;159
11.1.11.1;Referenced Literature;159
11.1.11.2;Related Literature;159
11.1.11.3;Referenced Protocols in Methods Navigator;159
11.2;Chapter Eleven: Explanatory Chapter: Choosing the Right Detergent;160
11.2.1;1. Theory;161
11.2.2;2. Equipment;161
11.2.3;3. Materials;161
11.2.4;4. Protocol;163
11.2.4.1;4.1. Preparation;163
11.2.4.2;4.2. Tip;164
11.2.4.3;4.3. Caution;164
11.2.5;5. Using Detergents with Polyacrylamide Gel Electrophoresis;164
11.2.5.1;5.1. Tip;165
11.2.6;6. Using Detergents in Chromatograpy;165
11.2.6.1;6.1. Tip;165
11.2.6.2;6.2. Tip;165
11.2.7;7. Using Detergents with Optical Spectroscopy Techniques;166
11.2.7.1;7.1. Tip;166
11.2.8;8. Using Detergents with Mass Spectrometry Techniques;166
11.2.9;9. Using Detergents with Nuclear Magnetic Resonance (NMR);167
11.2.10;10. Using Detergents in Protein Crystallization;167
11.2.10.1;10.1. Tip;167
11.2.11;References;167
11.2.11.1;Referenced Literature;167
12;Section V: Protein Protocols/SDS PAGE;168
12.1;Chapter Twelve: One-dimensional SDS-Polyacrylamide Gel Electrophoresis (1D SDS-PAGE);170
12.1.1;1. Theory;171
12.1.2;2. Equipment;171
12.1.3;3. Materials;172
12.1.3.1;3.1. Solutions and buffers;172
12.1.4;4. Protocol;173
12.1.4.1;4.1. Duration;173
12.1.4.2;4.2. Preparation;173
12.1.5;5. Step 1 Casting an SDS-PAGE Gel: Resolving Gel;173
12.1.5.1;5.1. Overview;173
12.1.5.2;5.2. Duration;173
12.1.5.3;5.3. Tip;174
12.1.5.4;5.4. Tip;174
12.1.5.5;5.5. Caution;174
12.1.6;6. Step 2 Casting an SDS-PAGE Gel: Stacking Gel;174
12.1.6.1;6.1. Overview;174
12.1.6.2;6.2. Duration;175
12.1.7;7. Step 3 Running an SDS-PAGE Gel;176
12.1.7.1;7.1. Overview;176
12.1.7.2;7.2. Duration;176
12.1.7.3;7.3. Tip;178
12.1.8;References;178
12.1.8.1;Referenced Literature;178
12.1.8.2;Referenced Protocols in Methods Navigator;178
12.2;Chapter Thirteen: Coomassie Blue Staining;180
12.2.1;1. Theory;181
12.2.2;2. Equipment;181
12.2.3;3. Materials;181
12.2.3.1;3.1. Solutions and buffers;181
12.2.4;4. Protocol;182
12.2.4.1;4.1. Preparation;182
12.2.4.2;4.2. Duration;182
12.2.4.3;4.3. Tip;182
12.2.4.4;4.4. Caution;182
12.2.5;5. Step 1 Stain a Gel Using Coomassie Blue;182
12.2.5.1;5.1. Overview;182
12.2.5.2;5.2. Duration;183
12.2.5.3;5.3. Tip;183
12.2.5.4;5.4. Tip;183
12.2.5.5;5.5. Tip;183
12.2.5.6;5.6. Caution;183
12.2.6;6. Step 2 Destain the Gel to Reduce Background Staining;184
12.2.6.1;6.1. Overview;184
12.2.6.2;6.2. Duration;184
12.2.6.3;6.3. Tip;185
12.2.6.4;6.4. Tip;185
12.2.6.5;6.5. Caution;185
12.2.7;Source References;186
12.2.7.1;Referenced Protocols in Methods Navigator;186
12.3;Chapter Fourteen: Silver Staining of SDS-polyacrylamide Gel;188
12.3.1;1. Theory;189
12.3.2;2. Equipment;189
12.3.3;3. Materials;189
12.3.3.1;3.1. Solutions and buffers;189
12.3.4;4. Protocol;191
12.3.4.1;4.1. Duration;191
12.3.4.2;4.2. Preparation;191
12.3.4.3;4.3. Tip;191
12.3.4.4;4.4. Tip;191
12.3.4.5;4.5. Tip;191
12.3.4.6;4.6. Tip;191
12.3.5;5. Step 1 Fix the Gel;191
12.3.5.1;5.1. Overview;191
12.3.5.2;5.2. Duration;191
12.3.5.3;5.3. Tip;192
12.3.6;6. Step 2 Stain the Gel;192
12.3.6.1;6.1. Overview;192
12.3.6.2;6.2. Duration;192
12.3.7;7. Step 3 Preserve the Gel;194
12.3.7.1;7.1. Overview;194
12.3.7.2;7.2. Duration;194
12.3.8;References;195
12.3.8.1;Referenced Protocols in Methods Navigator;195
13;Section VI: Protein Protocols/Standard in vitro Assays for Protein-Nucleic Acid Interactions;196
13.1;Chapter Fifteen: Standard In Vitro Assays for Protein-Nucleic Acid Interactions - Gel Shift Assays for RNA and DNA Binding;198
13.1.1;1. Theory;199
13.1.2;2. Equipment;203
13.1.3;3. Materials;203
13.1.3.1;3.1. Solutions and buffers;204
13.1.4;4. Protocol;205
13.1.4.1;4.1. Preparation;205
13.1.4.2;4.2. Duration;205
13.1.4.3;4.3. Caution;205
13.1.5;5. Step 1 Radiolabeling the Nucleic Acid Probe;206
13.1.5.1;5.1. Overview;206
13.1.5.2;5.2. Duration;206
13.1.5.3;5.3. Tip;207
13.1.5.4;5.4. Tip;207
13.1.6;6. Step 2 Bind Protein and Nucleic Acid;207
13.1.6.1;6.1. Overview;207
13.1.6.2;6.2. Duration;207
13.1.6.3;6.3. Tip;208
13.1.6.4;6.4. Tip;209
13.1.6.5;6.5. Tip;209
13.1.7;7. Step 3 Preparation of Polyacrylamide Gel;209
13.1.7.1;7.1. Overview;209
13.1.7.2;7.2. Duration;209
13.1.7.3;7.3. Tip;210
13.1.7.4;7.4. Tip;210
13.1.7.5;7.5. Tip;210
13.1.7.6;7.6. Tip;210
13.1.8;8. Step 4 Loading and Running Gel;210
13.1.8.1;8.1. Overview;210
13.1.8.2;8.2. Duration;211
13.1.8.3;8.3. Tip;211
13.1.8.4;8.4. Tip;211
13.1.9;9. Step 5 Analysis of Gel;211
13.1.9.1;9.1. Overview;211
13.1.9.2;9.2. Duration;212
13.1.9.3;9.3. Tip;212
13.1.9.4;9.4. Tip;213
13.1.9.5;9.5. Tip;213
13.1.9.6;9.6. Tip;213
13.1.9.7;9.7. Tip;213
13.1.9.8;9.8. Tip;213
13.1.10;References;214
13.1.10.1;Referenced Literature;214
13.1.11;Source References;215
13.1.11.1;Referenced Protocols in Methods Navigator;215
13.2;Chapter Sixteen: Protein Filter Binding;216
13.2.1;1. Theory;217
13.2.2;2. Equipment;217
13.2.3;3. Materials;217
13.2.3.1;3.1. Solutions and buffers;218
13.2.4;4. Protocol;218
13.2.4.1;4.1. Preparation;218
13.2.4.2;4.2. Duration;219
13.2.4.3;4.3. Tip;219
13.2.4.4;4.4. Caution;219
13.2.5;5. Step 1 Assemble Binding Reactions;220
13.2.5.1;5.1. Overview;220
13.2.5.2;5.2. Duration;220
13.2.5.3;5.3. Tip;220
13.2.5.4;5.4. Tip;220
13.2.5.5;5.5. Tip;220
13.2.5.6;5.6. Tip;220
13.2.5.7;5.7. Tip;221
13.2.6;6. Step 2 Quantify Binding;221
13.2.6.1;6.1. Overview;221
13.2.6.2;6.2. Duration;221
13.2.6.3;6.3. Tip;222
13.2.6.4;6.4. Tip;222
13.2.6.5;6.5. Tip;222
13.2.7;7. Step 3 Process Binding Data;223
13.2.7.1;7.1. Overview;223
13.2.7.2;7.2. Duration;223
13.2.8;References;224
13.2.8.1;Referenced Literature;224
13.2.9;Source References;224
14;Section VII: Protein Protocols/Troubleshooting Protein Expression;226
14.1;Chapter Seventeen: Explanatory Chapter: Troubleshooting Recombinant Protein Expression: General;228
14.1.1;1. Theory;229
14.1.2;2. Equipment;232
14.1.3;3. Materials;232
14.1.3.1;3.1. Solutions and buffers;233
14.1.4;4. Protocol;233
14.1.4.1;4.1. Preparation;233
14.1.4.2;4.2. Duration;233
14.1.5;5. Step 1 Monitoring E. coli cell Growth Before Induction;233
14.1.5.1;5.1. Overview;233
14.1.5.2;5.2. Duration;234
14.1.5.3;5.3. Tip;234
14.1.5.4;5.4. Tip;234
14.1.5.5;5.5. Tip;235
14.1.6;6. Step 2 Induction of Expression;235
14.1.6.1;6.1. Overview;235
14.1.6.2;6.2. Duration;235
14.1.7;7. Step 3 Monitoring E. coli Cell Growth After Induction;236
14.1.7.1;7.1. Overview;236
14.1.7.2;7.2. Duration;236
14.1.7.3;7.3. Tip;237
14.1.7.4;7.4. Tip;237
14.1.8;8. Step 4 Measurement of Protein Production;237
14.1.8.1;8.1. Overview;237
14.1.8.2;8.2. Duration;237
14.1.8.3;8.3. Tip;237
14.1.8.4;8.4. Tip;238
14.1.9;9. Step 5 Further Troubleshooting in E. coli;238
14.1.9.1;9.1. Overview;238
14.1.9.2;9.2. Duration;238
14.1.10;10. Step 6 Eukaryotic Expression Systems;242
14.1.10.1;10.1. Overview;242
14.1.10.2;10.2. Duration;244
14.1.11;References;246
14.1.11.1;Referenced Literature;246
14.1.12;Source References;248
14.1.12.1;Referenced Protocols in Methods Navigator;248
14.2;Chapter Eighteen: Explanatory Chapter: Troubleshooting Protein Expression: What to do When the Protein is not Soluble;250
14.2.1;1. Theory;251
14.2.2;2. Equipment;251
14.2.3;3. Materials;252
14.2.3.1;3.1. Solutions and buffers;252
14.2.4;4. Protocol;253
14.2.4.1;4.1. Preparation;253
14.2.4.2;4.2. Duration;253
14.2.5;5. Step 1 Centrifuge the Culture;254
14.2.5.1;5.1. Overview;254
14.2.5.2;5.2. Duration;254
14.2.5.3;5.3. Tip;254
14.2.6;6. Step 2 Lyse the Cells;254
14.2.6.1;6.1. Overview;254
14.2.6.2;6.2. Duration;254
14.2.6.3;6.3. Tip;255
14.2.6.4;6.4. Tip;255
14.2.6.5;6.5. Tip;255
14.2.6.6;6.6. Tip;255
14.2.6.7;6.7. Tip;255
14.2.6.8;6.8. Tip;255
14.2.7;7. Step 3 Remove the Cell Debris;256
14.2.7.1;7.1. Overview;256
14.2.7.2;7.2. Duration;256
14.2.8;8. Step 4 Analyze Protein Expression by SDS-PAGE;256
14.2.8.1;8.1. Overview;256
14.2.8.2;8.2. Duration;257
14.2.8.3;8.3. Tip;257
14.2.8.4;8.4. Tip;257
14.2.8.5;8.5. Tip;257
14.2.9;9. Step 5 Troubleshooting the Lack of Soluble Protein Expressed;258
14.2.9.1;9.1. Overview;258
14.2.9.2;9.2. Duration;258
14.2.10;References;263
14.2.10.1;Referenced Literature;263
14.2.10.2;Referenced Protocols in Methods Navigator;266
15;Section VIII: Protein Protocols/Western Blotting;268
15.1;Chapter Nineteen: Western Blotting using Chemiluminescent Substrates;270
15.1.1;1. Theory;271
15.1.2;2. Equipment;271
15.1.3;3. Materials;271
15.1.3.1;3.1. Solutions and buffers;272
15.1.4;4. Protocol;272
15.1.4.1;4.1. Duration;272
15.1.4.2;4.2. Preparation;272
15.1.5;5. Step 1: Protein Transfer to a Membrane;273
15.1.5.1;5.1. Overview;273
15.1.5.2;5.2. Duration;273
15.1.5.3;5.3. Tip;274
15.1.5.4;5.4. Tip;275
15.1.6;6. Step 2: Western Blot Detection using a Chemiluminescent Substrate;275
15.1.6.1;6.1. Overview;275
15.1.6.2;6.2. Duration;275
15.1.6.3;6.3. Tip;276
15.1.6.4;6.4. Tip;277
15.1.6.5;6.5. Tip;277
15.1.7;References;277
15.1.7.1;Referenced Literature;277
15.1.8;Source References;278
15.1.8.1;Referenced Protocols in Methods Navigator;278
16;Author Index;280
17;Subject Index;286

Leseproben

Chapter One TCA Precipitation
Laura Koontz1,    Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA,    1Corresponding author: [e-mail] Abstract
Trichloroacetic acid (TCA) precipitation of proteins is commonly used to concentrate protein samples or remove contaminants, including salts and detergents, prior to downstream applications such as SDS-PAGE or 2D-gels. TCA precipitation denatures the protein, so it should not be used if the protein must remain in its folded state (e.g., if you want to measure a biochemical activity of the protein). Keywords
Bromophenol blue; Deoxycholate-trichloroacetic acid precipitation; Dithiothreitol (DTT); Glycerol; Sodium dodecyl sulfate (SDS); Sodium hydroxide (NaOH); Trichloroacetic acid (TCA); Tris base 1 Theory
TCA is an analog of acetic acid in which the three hydrogen atoms of the methyl carbon have been replaced with chlorine atoms. TCA is a relatively weak acid so it cannot hydrolyze the peptide bonds of proteins, but it does maintain an acidic pH in water. Addition of TCA to proteins in an aqueous solution disrupts the hydrogen-bonded water molecules (hydration sphere) surrounding a protein. These protein molecules no longer remain soluble and can be recovered by centrifugation. However, because TCA disrupts hydrogen bonding, the proteins will also lose their secondary structure and become denatured. TCA precipitation has several drawbacks: (1) TCA precipitation denatures proteins and cannot be used if the activity of the protein is to be retained; (2) the protein concentration of the starting solution must be fairly high (= 5 µg ml- 1); (3) TCA precipitation does not work for all proteins and can be somewhat finicky. If TCA precipitation does not work for your protein of interest, it is advisable to try variants of TCA precipitation (included in this protocol) or other methods of precipitation or concentration, such as acetone precipitation, salting out (see Salting out of proteins using ammonium sulfate precipitation), immunoprecipitation (you can extract a protocol from Analysis of Protein-Protein Interactions by Co-immunoprecipitation), or ultrafiltration. 2 Equipment
Microcentrifuge Vortex mixer Magnetic stir plate Aspirator Micropipettors Micropipettor tips Ice bucket Magnetic stir bars 1.5-ml microcentrifuge tubes 3 Materials
Trichloroacetic acid (TCA) Sodium hydroxide (NaOH) Deoxycholate (DOC, optional) Tris base Dithiothreitol (DTT) Sodium dodecyl sulfate (SDS) Bromophenol blue Glycerol Acetone (optional) 3.1 Solutions & buffers
100% TCA Dissolve 100 g of TCA in 85 ml deionized water. Bring the volume up to 100 ml after all the TCA is in solution Caution: TCA can cause chemical burns and is harmful if inhaled 0.1 N NaOH Dissolve 400 mg NaOH in 100 ml deionized water Caution: NaOH can cause chemical burns. Wear gloves and a lab coat 0.15% DOC Dissolve 150 mg DOC in 85 ml deionized water. Bring the volume up to 100 ml after the DOC is completely in solution 10% SDS Dissolve 10 g SDS in 85 ml deionized water. Bring the volume up to 100 ml after the SDS is completely in solution 10% SDS Caution: SDS and DOC are eye and lung irritants. Wear protective goggles and facemask 1 M Tris–HCl, pH 6.8 or pH 8.0 Add 121.14 g Tris base to 900 ml of deionized water. Adjust to final pH by adding 10 M or 1 M NaOH, dropwise. Adjust the volume to 1 l with deionized water 2× SDS loading buffer Tris–HCl, pH 6.8 100 mM 1 M 5 ml DTT 200 mM   1.5425 g SDS 4% 10% 20 ml Bromophenol blue 0.2%   < 0.1 g Glycerol 20% 100% 10 ml Water     15 ml Mix in a beaker with a stir bar until homogenous. Dispense into 1.5-ml microcentrifuge tubes as 1 ml aliquots 4 Protocol
4.1 Preparation
Prepare any of the chemicals and buffers listed above, if necessary. Prepare your protein solution to be concentrated. 4.2 Duration
Preparation About 2 h Protocol 1 h to 1 day 4.3 Caution
Many of the chemicals used in the following protocols are harmful. Gloves and a lab coat should be worn and caution should be taken with all chemicals. 5 Step 1A Trichloroacetic Acid Precipitation
5.1 Overview
Addition of TCA will concentrate a protein and result in its denaturation. The protein concentration must be at least 5 µg ml- 1 to use this method. 5.2 Duration
45 min 1A.1 Add 100 µl of 100% TCA to 1 ml of the protein sample. Vortex the sample. 1A.2 Allow the protein to precipitate on ice for 30 min. 1A.3 Centrifuge the samples at 10 000× g at 4 °C for 5–15 min. 1A.4 Quickly and carefully aspirate the supernatant, taking care not to disrupt the pellet. The pellet should be whitish and fluffy. 1A.5 (Optional) Wash the pellet several times with 500 µl ice-cold acetone to remove any residual TCA. Centrifuge at 10 000× g at 4 °C for an additional 5 min afterward and aspirate the supernatant. Allow the pellet to dry. 1A.6 Resuspend the sample in 50 µl of 2× SDS buffer. Heat the sample at 100 °C for 5 min and analyze by SDS-PAGE (see One-dimensional SDS-Polyacrylamide Gel Electrophoresis (1D SDS-PAGE)). 5.3 Tip
Keep all the reagents at 4 °C! 5.4 Tip
Precipitation can be carried out for 15 min at - 20 °C. 5.5 Tip
Bromophenol blue is a pH indicator, yellow below pH 4 and blue above that pH. Therefore, if the SDS sample buffer turns yellow, the solution is still slightly acidic due to remaining TCA. Just add a small amount of 1 M Tris pH 8.0, until the color returns to the usual blue (do not use NaOH because you could hydrolyze the protein!). See Fig. 1.1 for the flowchart of Step 1A.
Figure 1.1 Flowchart of Step 1A. 6 Step 1B Deoxycholate-Trichloroacetic Acid Precipitation
6.1 Overview
The addition of deoxycholate (DOC) to a regular TCA precipitation will aid in precipitating proteins less concentrated than 1 µg ml- 1. 6.2 Duration
45 min 1B.1 Add 100 µl of 0.15% DOC to 1 ml of the protein sample. Vortex the sample. 1B.2 Incubate at room temperature for 10 min. 1B.3 Add 50 µl of 100% TCA and vortex the sample. 1B.4 Allow the protein to precipitate on ice for 30 min. 1B.5 Centrifuge the samples at 10 000× g at 4 °C for 5–15 min. 1B.6 Quickly and carefully aspirate the supernatant, taking care not to disrupt the pellet. The pellet should be whitish and fluffy. 1B.7 (Optional) Wash the pellet several times in 500 µl ice-cold acetone to remove any left over TCA. Centrifuge at 10 000× g at 4 °C for an additional 5 min afterward and aspirate the supernatant. Allow the pellet to dry. 1B.8 Resuspend the sample in 50 µl of 2× SDS buffer. Heat the sample at 100 °C for 5 min and analyze by SDS-PAGE (see One-dimensional SDS-Polyacrylamide Gel Electrophoresis (1D SDS-PAGE)). 6.3 Tip
Keep all the reagents at 4 °C! 6.4 Tip
Precipitation can be carried out for 15 min at - 20 °C. 6.5 Tip
Bromophenol blue is a pH indicator, yellow below pH 4 and blue above that pH. Therefore, if the SDS sample buffer turns yellow, the solution is still slightly acidic due to remaining TCA. Just add a small amount of 1 M Tris pH 8.0, until the color returns to the usual blue (do not use NaOH because you could hydrolyze the...