Amino Acids, Peptides and Proteins in Organic Chemistry, Analysis and Function of Amino Acids and Peptides : Analysis and Function of Amino Acids and Peptides

Amino Acids, Peptides and Proteins in Organic Chemistry:Volume 5 - Analysis and Function of Amino Acids and Peptides......Page 1
Contents......Page 7
List of Contributors......Page 17
1.1.1 Mass Terminology......Page 21
1.1.2 Components of a Mass Spectrometer......Page 24
1.1.3 Resolution and Mass Accuracy......Page 26
1.1.4 Accurate Analysis of ESI Multiply Charged Ions......Page 30
1.1.5 Fragment Ions......Page 31
1.2.2 In Vivo Protein Modi.cations......Page 41
1.2.3 Ex Vivo Protein Modi.cations......Page 46
1.3.2 Shotgun Versus Targeted Proteomics......Page 48
1.3.3 Enzymatic Digestion for Bottom-Up Proteomics......Page 49
1.3.4 Liquid Chromatography and Capillary Electrophoresis for Mixtures in Bottom-Up......Page 50
1.4.1 Identi.cation of Proteins from MS/MS Spectra of Peptides......Page 52
1.4.2 De Novo Sequencing......Page 55
1.5 MS of Protein Structure, Folding, and Interactions......Page 56
1.5.1 Methods to Mass-Tag Structural Features......Page 57
References......Page 60
2.1.1 Light Microscopy......Page 71
2.1.2 X-Rays and Crystallography at the Start......Page 72
2.1.3 X-Ray Crystallography Today......Page 73
2.1.4 Limitations of X-Ray Crystallography......Page 74
2.2.2 Basic Methods of Growing Protein Crystals......Page 75
2.2.4 Preliminary Crystal Analysis......Page 79
2.2.5 Mounting Crystals for X-Ray Analysis......Page 81
2.3.1 Crystals and the Unit Cell......Page 82
2.3.2 Point Groups......Page 85
2.3.3 Space Groups......Page 86
2.4.1 X-Rays and Mathematical Representation of Waves......Page 87
2.4.2 Interaction of X-Rays with Matter......Page 90
2.4.3 Crystal Lattice, Miller Indices, and the Reciprocal Space......Page 93
2.4.4 X-Ray Diffraction from a Crystal: Bragg.s Law......Page 95
2.4.5 Bragg.s Law in Reciprocal Space......Page 97
2.4.6 Fourier Transform Equation from a Lattice......Page 99
2.4.7 Friedel' s Law and the Electron Density Equation......Page 100
2.5.1 Data Collection Strategy......Page 102
2.6.1 Molecular Replacement......Page 103
2.6.2 Isomorphous Replacement......Page 105
2.6.3 MAD......Page 108
2.7.1 Electron Density Interpretation and Model Building......Page 110
2.7.2 Protein Structure Refinement......Page 111
2.7.3 Protein Structure Validation......Page 113
References......Page 114
3.1 Introduction......Page 117
3.1.2 Energy Levels and Spin States......Page 118
3.1.3.1 Chemical Shift......Page 119
3.1.3.3 NOE......Page 120
3.2.2 Amino Acids Structure......Page 121
3.2.3 Random Coil Chemical Shift......Page 122
3.2.4 Spin Systems......Page 125
3.2.5 Labile Protons......Page 130
3.2.6 Contemporary Relevance: Metabolomics......Page 132
3.3.1 Historical Significance......Page 133
3.3.2 Oligopeptides as Models for Conformational Transitions in Proteins......Page 134
3.3.3 Bioactive Peptides......Page 136
3.3.4 Choice of the Solvent......Page 137
3.3.4.1 Transport Fluids......Page 138
3.3.4.2 Membranes......Page 140
3.3.4.3 Receptor Cavities......Page 142
3.3.6.1 Aspartame......Page 145
3.3.6.2 Opioids......Page 146
3.3.6.3 Transmembrane Helices......Page 147
3.3.6.4 Cyclopeptides......Page 148
3.4.2 Protein Spectra......Page 149
3.4.3 Wüthrich.s Protocol......Page 150
3.4.3.3 Sequential Assignment......Page 151
3.4.3.4 Conformational Constraints......Page 152
3.4.4 Recent Developments......Page 154
3.4.5 Selected Structures......Page 156
3.4.5.2 Malate Synthase G......Page 157
3.4.5.3 Interactions......Page 158
3.5 Conclusions......Page 165
References......Page 166
4.1 Introduction......Page 175
4.2 Conformational Effects of N-Methylation......Page 177
4.3.2 Cyclic Peptides......Page 179
4.3.3 Somatostatin Analogs......Page 180
4.3.4 Antimalarial Peptide......Page 181
4.4 Concluding Remarks......Page 182
References......Page 183
5.1 Introduction......Page 187
5.2 Basic Terms and Concepts in Chromatography......Page 189
5.3.1 Biophysical Properties of Peptides and Proteins......Page 193
5.3.3 Optical Properties of Peptides and Proteins......Page 196
5.4 HPLC Separation Modes in Peptide and Protein Analysis......Page 197
5.4.1 SEC......Page 198
5.4.2 RPC......Page 199
5.4.4 HILIC......Page 201
5.4.5 ANPC......Page 203
5.4.6 HIC......Page 204
5.4.7 IEX......Page 207
5.4.8 AC......Page 208
5.5 Method Development from Analytical to Preparative Scale Illustrated for HP-RPC......Page 209
5.5.1 Development of an Analytical Method......Page 210
5.5.2 Scaling Up to Preparative Chromatography......Page 216
5.6 Multidimensional HPLC......Page 218
5.6.1 Puri.cation of Peptides and Proteins by MD-HPLC Methods......Page 220
5.6.3.1 Off-line Coupling Mode for MD-HPLC Methods......Page 222
5.6.4.1 Orthogonality of Chromatographic Modes......Page 223
5.6.4.2 Compatibility Matrix of Chromatographic Modes......Page 225
5.7 Conclusions......Page 226
References......Page 227
6.1.1 LSPR and Micro Total Analysis Systems......Page 231
6.1.2 Microfluidic LSPR Chip Fabrication and LSPR Measurement......Page 232
6.1.3 Detection of the Insulin–Anti-Insulin Antibody Reaction on a Chip......Page 233
6.2.2 Fabrication of E-LSPR Substrate and Formation of the Hybrid Bilayer Membrane......Page 235
6.2.3 Measurements of Membrane-Based Sensors for Peptide Toxin......Page 237
6.3.1 Alzheimer.s Ab Aggregation and Electrochemical Detection Method......Page 238
6.3.2 Label-Free Electrochemical Detection of Ab Aggregation......Page 239
References......Page 241
7.2 SPR-Based Optical Biosensors......Page 245
7.3 Principle of Operation of SPR Biosensors......Page 246
7.4.1 Sensor Surface......Page 248
7.4.2 Flow System......Page 249
7.5 Application of SPR in Immunosensor Design......Page 250
7.5.1.1 Immobilization of the Analyte to a Speci.c Chip Surface......Page 252
7.5.1.2 Assay Design......Page 253
7.6 Application of SPR in Membrane Interactions......Page 254
7.6.1.2 Formation of Bilayer Systems......Page 256
7.6.1.3 Analyte Binding to the Membrane System......Page 257
7.6.1.4 Membrane Binding of Antimicrobial Peptides by SPR......Page 258
7.7.1 Linearization Analysis......Page 260
7.7.2 Numerical Integration Analysis......Page 261
7.7.3 Steady-State Approximations......Page 262
7.8 Conclusions......Page 263
References......Page 264
8.1 Foreword......Page 269
8.2.1 Principle and Basic Modes of Operation......Page 270
8.2.2 How Does a Tip Tap?......Page 271
8.3.1 Protein Oligomerization, Aggregation, and Fibers......Page 273
8.3.2 Membrane Binding and Lysis......Page 275
8.3.3 Ion Channel Activity......Page 277
8.4 Issues......Page 281
8.4.1 Resolution......Page 282
8.4.2 Imaging Force......Page 283
8.4.3 Repetitive Stress......Page 284
8.4.4 Artifacts Related to too Low Free Amplitude......Page 285
8.4.6 Accuracy of Surface Tracking......Page 286
8.4.7 Step Artifacts......Page 288
8.6 Liquid Imaging......Page 289
8.7.1 Adhesion......Page 292
8.7.2 Physical Entrapment......Page 293
8.8 Outlook......Page 294
References......Page 295
9.1 Introduction......Page 297
9.2.1 Research......Page 300
9.2.2 Precipitation......Page 307
9.2.3 Chromatography......Page 308
9.2.4 Protein Refolding......Page 316
9.2.5 Formulation......Page 317
9.3 Solvent Application for Viruses......Page 320
9.3.1 Isolation and Puri.cation of Viruses......Page 321
9.3.2 Stabilization and Formulation of Viruses......Page 322
9.3.3 Inactivation of Viruses......Page 329
9.4.1 Isolation and Puri.cation of DNA......Page 330
9.4.2 Stability of DNA in a Cosolvent System......Page 332
9.5 Mechanism......Page 334
9.5.1.1 Hydration......Page 335
9.5.1.2 Excluded Volume......Page 338
9.5.2.1 Group Interaction: Model Compound Solubility......Page 342
9.5.3 Preferential Interaction......Page 348
9.6.1 Frozen Systems......Page 362
9.6.2 Freeze-Dried System......Page 365
9.7 Conclusions......Page 368
References......Page 369
10.1 Sulfur: A Redox Chameleon with Many Faces......Page 381
10.2 Three Faces of Thiols: Nucleophilicity, Redox Activity, and Metal Binding......Page 385
10.3 Towards a Dynamic Picture of Disulfide Bonds......Page 391
10.4 Chemical Protection and Regulation via S-Thiolation......Page 394
10.5 ‘‘Dormant’’ Catalytic Sites......Page 398
10.6 Peroxiredoxin/Sulfiredoxin Catalysis and Control Pathway......Page 399
10.7 Higher Sulfur Oxidation States: From the Shadows to the Heart of Biological Sulfur Chemistry......Page 404
10.8 Cysteine as a Target for Oxidants, Metal Ions, and Drug Molecules......Page 408
10.9 Conclusions and Outlook......Page 410
References......Page 411
11.1 Introduction......Page 415
11.3 Contribution of Disulfide Bonds to Protein Stability......Page 416
11.4 Role of Disulfide Bonds in Protein Folding......Page 417
11.5 Role of Individual Disulfide Bonds in Protein Structure......Page 419
11.6 Disulfide Bonds in Protein Dynamics......Page 421
11.7.1 Conservation and Evolution of Disulfide Bonding Patterns......Page 423
11.7.3 Cysteine Framework and Disulfide Connectivity......Page 424
11.7.4 Non-Native Disulfide Connectivities......Page 427
11.8 Applications......Page 428
11.9 Conclusions......Page 429
References......Page 430
12.1 Introduction......Page 439
12.2 Quantification in Biological MS......Page 440
12.2.1 Label-Free Approaches in Quantitative MS Proteomics......Page 443
12.2.2 SIL in Quantitative Proteomics......Page 445
12.3 Identifying Proteins Interacting with Small Molecules with Quantitative Proteomics......Page 450
12.4 Conclusions......Page 453
References......Page 454
13.2 Aim of Protein Analysis and Development of 2-DE Techniques......Page 459
13.3 Current Status of 2-DE Techniques......Page 461
13.3.1.1 Principle......Page 462
13.3.1.2 Procedures......Page 464
13.3.2.1 Principle......Page 465
13.3.2.2 Procedures......Page 466
13.3.2.3 Specific Features......Page 467
13.3.3.2 Procedures......Page 468
13.3.4 Visualization of Proteins Separated on 2-DE Gels......Page 469
13.3.4.3 Silver Staining......Page 470
13.3.4.6 Quantitation......Page 471
13.4.1 Development of Protein Assignment Techniques......Page 472
13.4.2 MS-Based Assignment Techniques Utilizing Amino Acid Sequence Databases......Page 474
13.4.2.1 Sample Preparation for MS Analysis......Page 475
13.4.2.2 MALDI-TOF-MS and PMF......Page 476
13.4.2.3 MS/MS and Peptide Sequence Search......Page 479
References......Page 480
14.1 Introduction......Page 483
14.2 PTM Discovery with MS......Page 485
14.2.1 Detecting PTMs in MS and MS/MS Data......Page 486
14.2.2 Discovering PTMs in MS or MS/MS Data......Page 488
14.2.3.2 From Sequence Data......Page 489
14.3 Database Resources for PTM Analysis......Page 490
References......Page 493
Index......Page 497