Amino Acids, Peptides and Proteins in Organic Chemistry, Volume 5: Analysis and Function of Amino Acids and Peptides (Hardcover)

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