List of Contributors XV
1 Mass Spectrometry of Amino Acids and Proteins 1
Simin D. Maleknia and Richard Johnson
1.1 Introduction 1
1.2 Basic Protein Chemistry and How it Relates to MS 21
1.3 Sample Preparation and Data Acquisition 28
1.4 Data Analysis of LC-MS/MS (or CE-MS/MS) of Mixtures 32
1.5 MS of Protein Structure, Folding, and Interactions 36
1.6 Conclusions and Perspectives 40
References 40
2 X-Ray Structure Determination of Proteins and Peptides 51
Andrew J. Fisher
2.1 Introduction 51
2.2 Growing Crystals 55
2.3 Symmetry and Space Groups 62
2.4 X-Ray Scattering and Diffraction 67
2.5 Collecting and Processing Diffraction Data 82
2.6 Solving the Structure (Determining Phases) 83
2.7 Analyzing and Refining the Structure 90
References 94
3 Nuclear Magnetic Resonance of Amino Acids, Peptides, and Proteins 97
Andrea Bernini and Pierandrea Temussi
3.1 Introduction 97
3.2 Amino Acids 101
3.3 Peptides 113
3.4 Proteins 129
3.5 Conclusions 145
References 146
4 Structure and Activity of N-Methylated Peptides 155
Raymond S. Norton
4.1 Introduction 155
4.2 Conformational Effects of N-Methylation 157
4.3 Effects of N-Methylation on Bioactive Peptides 159
4.4 Concluding Remarks 162
References 163
5 High-Performance Liquid Chromatography of Peptides and Proteins 167
Reinhard I. Boysen and Milton T.W. Hearn
5.1 Introduction 167
5.2 Basic Terms and Concepts in Chromatography 169
5.3 Chemical Structure of Peptides and Proteins 173
5.4 HPLC Separation Modes in Peptide and Protein Analysis 177
5.5 Method Development from Analytical to Preparative Scale Illustrated for HP-RPC 189
5.6 Multidimensional HPLC 198
5.7 Conclusions 206
References 207
6 Local Surface Plasmon Resonance and Electrochemical Biosensing Systems for Analyzing Functional Peptides 211
Masato Saito and Eiichi Tamiya
6.1 Localized Surface Plasmon Resonance (LSPR)-Based Microfluidics Biosensor for the Detection of Insulin Peptide Hormone 211
6.2 Electrochemical LSPR-Based Label-Free Detection of Melittin 215
6.3 Label-Free Electrochemical Monitoring of b-Amyloid (Ab) Peptide Aggregation 218
References 221
7 Surface Plasmon Resonance Spectroscopy in the Biosciences 225
Jing Yuan, Yinqiu Wu, and Marie-Isabel Aguilar
7.1 Introduction 225
7.2 SPR-Based Optical Biosensors 225
7.3 Principle of Operation of SPR Biosensors 226
7.4 Description of a SPR Instrument 228
7.5 Application of SPR in Immunosensor Design 230
7.6 Application of SPR in Membrane Interactions 234
7.7 Data Analysis 240
7.8 Conclusions 243
References 244
8 Atomic Force Microscopy of Proteins 249
Adam Mechler
8.1 Foreword 249
8.2 AFM 250
8.3 Bioimaging Highlights 253
8.4 Issues 261
8.5 Force Measurements 269
8.6 Liquid Imaging 269
8.7 Sample Preparation for Bioimaging 272
8.8 Outlook 274
References 275
9 Solvent Interactions with Proteins and Other Macromolecules 277
Satoshi Ohtake, Yoshiko Kita, Kouhei Tsumoto, and Tsutomu Arakawa
9.1 Introduction 277
9.2 Solvent Applications 280
9.3 Solvent Application for Viruses 300
9.4 Solvent Application for DNA 310
9.5 Mechanism 314
9.6 Protein–Solvent Interactions in Frozen and Freeze-Dried Systems 342
9.7 Conclusions 348
References 349
10 Role of Cysteine 361
Lalla A. Ba, Torsten Burkholz, Thomas Schneider, and Claus Jacob
10.1 Sulfur: A Redox Chameleon with Many Faces 361
10.2 Three Faces of Thiols: Nucleophilicity, Redox Activity, and Metal Binding 365
10.3 Towards a Dynamic Picture of Disulfide Bonds 371
10.4 Chemical Protection and Regulation via S-Thiolation 374
10.5 ‘‘Dormant’’ Catalytic Sites 378
10.6 Peroxiredoxin/Sulfiredoxin Catalysis and Control Pathway 379
10.7 Higher Sulfur Oxidation States: From the Shadows to the Heart of Biological Sulfur Chemistry 384
10.8 Cysteine as a Target for Oxidants, Metal Ions, and Drug Molecules 388
10.9 Conclusions and Outlook 390
References 391
11 Role of Disulfide Bonds in Peptide and Protein Conformation 395
Keith K. Khoo and Raymond S. Norton
11.1 Introduction 395
11.2 Probing the Role of Disulfide Bonds 396
11.3 Contribution of Disulfide Bonds to Protein Stability 396
11.4 Role of Disulfide Bonds in Protein Folding 397
11.5 Role of Individual Disulfide Bonds in Protein Structure 399
11.6 Disulfide Bonds in Protein Dynamics 401
11.7 Disulfide Bonding Patterns and Protein Topology 403
11.8 Applications 408
11.9 Conclusions 409
References 410
12 Quantitative Mass Spectrometry-Based Proteomics 419
Shao-En Ong
12.1 Introduction 419
12.2 Quantification in Biological MS 420
12.3 Identifying Proteins Interacting with Small Molecules with Quantitative Proteomics 430
12.4 Conclusions 433
References 434
13 Two-Dimensional Gel Electrophoresis and Protein/Polypeptide Assignment 439
Takashi Manabe and Ya Jin
13.1 Introduction 439
13.2 Aim of Protein Analysis and Development of 2-DE Techniques 439
13.3 Current Status of 2-DE Techniques 441
13.4 Development of Protein Assignment Techniques on 2-DE Gels and Current Status of Mass Spectrometric Techniques 452
13.5 Conclusions 460
References 460
14 Bioinformatics Tools for Detecting Post-Translational Modifications in Mass Spectrometry Data 463
Patricia M. Palagi, Erik Arhné, MarKus Müller, and Frédérique Lisacek
14.1 Introduction 463
14.2 PTM Discovery with MS 465
14.3 Database Resources for PTM Analysis 470
14.4 Conclusions 473
References 473
Index 477