BIOMACROMOLECULES INTROUCTION TO STRUCTUREPDF电子书下载

CHAPTER 1 INTRODUCTION 1

1.1 Prelude 1

1.2 Covalent Bonds 4

1.3 Noncovalent Interactions 5

1.3.1 Electrostatic Interaction 6

1.3.2 Van der Waals Interaction 6

1.3.3 Hydrogen Bond 6

1.3.4 Hydrophobic Interaction 7

1.3.5 Steric Repulsion 8

1.4 Isomerism：Configuration versus Conformation 8

1.5 Trilogy 11

1.6 References 13

CHAPTER 2 MONOMER CONSTITUENTS OF BIOMACROMOLECULES 15

2.1 Nucleotides：Constituents of Nucleic Acids 15

2.2 α-Amino Acids：Constituents of Proteins 18

2.3 Monosaccharides：Constituents of Glycans 23

2.4 Addendum 28

2.5 References 30

CHAPTER 3 PURIFICATION AND CHARACTERIZATION 31

3.1 Purification：OvervieW 31

3.2 Purification：Chromatography 34

3.3 Purification：Electrophoresis 40

3.4 Characterization：General 44

3.4.1 Purity 44

3.4.2 Molecular Weight 44

3.4.3 Molecular Dimension 50

3.5 Characterization：Specific 51

3.5.1 Melting Temperature of DNA 51

3.5.2 Buoyant Density of Biomacromolecules 52

3.5.3 Isoelectric pH of Proteins 52

3.5.4 Removal of Glycosides from Glycoproteins 53

3.6 References 53

CHAPTER 4 BIOMACROMOLECULAR STRUCTURE：NUCLEIC ACIDS 55

4.1 Structural Organization 55

4.1.1 Structural Hierarchy 55

4.1.2 Representation of Structures of Nucleic Acids 56

4.2 Sequence Analysis of Nucleic Acids 57

4.2.1 General 57

4.2.2 Chemical Cleavage Method 59

4.2.3 Enzymatic Chain Term in ation/Dideoxy Method 60

4.2.4 Mass Spectrometric Analysis 61

4.2.5 Automated DNA Sequencing Technology 62

4.3 Secondary Structure and Structure Polymorphism of DNA 63

4.3.1 Key Structural Features of Nucleic Acids 63

4.3.2 DNA Polymorphism 66

4.3.3 Alternative Structures of DNA 69

4.4 Supercoiling and Tertiary Structure of DNA 77

4.4.1 DNA Topoisomers 77

4.4.2 Superhelical Density and Energetics of Supercoiling. 80

4.5 Classification and Structures of RNA 81

4.5.1 Structures of RNA 81

4.5.2 Transfer RNA 82

4.5.3 Ribosomal RNA 83

4.5.4 Messenger RNA 84

4.5.5 Other Classes of RNA 85

4.6 RNA Folds and Structure Motifs 86

4.6.1 RNA Folds 86

4.6.2 Structure Motifs of RNA 86

4.7 Energetics of Nucleic Acid Structure 89

4.8 Nucleic Acid Application 90

4.9 References 91

CHAPTER 5 BIOMACROMOLECULAR STRUCTURE：PROTEINS 94

5.1 Architecture of Protein Molecules 94

5.1.1 Introduction 94

5.1.2 Representation of Protein Structures 94

5.2 Primary Structure of Proteins：Chemical and Enzymatic Sequence Analysis 95

5.2.1 Amino Acid Composition 96

5.2.2 Peptide Cleavage，Separation and Analysis 97

5.2.3 Terminal and Sequence Determination 97

5.2.4 Peptide Ladder Sequencing 101

5.3 Primary Structure of Proteins：Sequence Analysis by Tandem Mass Spectrometry 101

5.3.1 An Application of Mass Spectrometry（MS）in Protein Chemistry 101

5.3.2 Application of Tandem Mass Spectrometry（MS-MS）in Protein Sequence Analysis 103

5.4 Conformational Map 108

5.5 Secondary Structures and Motifs of Proteins 110

5.5.1 α-Helical Structure 111

5.5.2 β-Sheet Structure 113

5.5.3 Nonrepetitive Structure：Connection （Loop）and Turn 115

5.5.4 Notes to Secondary Structures of Globular Proteins 116

5.5.5 Motifs：Supersecondary Structures 117

5.6 Domains and Tertiary Structures of Proteins 118

5.6.1 Domain Structures 119

5.6.2 Tertiary Structures and Protein Folds 121

5.6.3 Folds and Protein Binding 126

5.6.4 Membrane Proteins 128

5.6.5 Fibrous Proteins 128

5.6.6 Circular（Cyclic）Proteins 129

5.6.7 Representation of Protein Topology 130

5.6.8 Accessible Surface of Folded Structures 130

5.7 Classification of Protein Structures 133

5.7.1 α-Helical Proteins 133

5.7.2 β-Sheet Proteins 133

5.7.3 α＋β Proteins 135

5.7.4 α/β Proteins 135

5.7.5 Multidomain Structures 135

5.7.6 Membrane and Cell Surface Proteins 136

5.7.7 Irregular and Small Proteins 136

5.8 Quaternary（Subunit）Structures of Proteins 137

5.9 Quinteryary Structure Exemplified：Nucleoproteins 140

5.9.1 Chromosomes 140

5.9.2 Ribosomes 141

5.9.3 Spliceosome and Splicing Activities 142

5.10 Conformational Energetics 143

5.11 References 144

CHAPTER 6 BIOMACROMOLECULAR STRUCTURE：POLYSACCHARIDES 147

6.1 Propagation of Polysaccharide Chains 147

6.1.1 Introduction 147

6.1.2 Representation of Glycan Structures 148

6.1.3 Toward Linear Code for Glycans 148

6.2 Sequence Analysis of Polysaccharides：Primary Structure 153

6.2.1 Hydrolysis to Constituent Monosaccharides 154

6.2.2 Chemical Methods 154

6.2.3 Enzymatic Methods 155

6.2.4 Spectrometric Methods 157

6.3 Conformation：Secondary and Tertiary Structures of Polysaccharide Chains 161

6.4 Conformation：Description of Some Polysaccharide Structures 163

6.4.1 Starch 163

6.4.2 Glycogen 164

6.4.3 Pectins 165

6.4.4 Cellulose 165

6.4.5 Chitin 166

6.5 Glycobiology：Study of Glycoprotein-Associated Glycans 167

6.5.1 Glycoprotein and Glycoforms 167

6.5.2 Structure Diversity of Oligosaccharide Chains 168

6.5.3 Structural Analysis 174

6.6 Neoglycoproteins 177

6.7 Organizational Levels of Biomacromolecular Structures 177

6.8 References 181

CHAPTER 7 STUDIES OF BIOMACROMOLECULAR STRUCTURES：SPECTROSCOPIC ANALYSIS OF CONFORMATION 183

7.1 Biochemical Spectroscopy：Overview 183

7.2 Ultraviolet and Visible Absorption Spectroscopy 185

7.2.1 Basic Principles 185

7.2.2 Amino Acid Residues and Peptide Bonds 187

7.2.3 Purines，Pyrimidines and Nucleic Acids 188

7.2.4 Perturbation Difference Absorption Spectroscopy 189

7.3 Fluorescence Spectroscopy 190

7.4 Infrared Spectroscopy 193

7.4.1 Basic Principles 193

7.4.2 Biochemical Applications 195

7.5 Nuclear Magnetic Resonance Spectroscopy 197

7.5.1 Basic Principles 197

7.5.2 Two-Dimensional Fourier Transform NMR 202

7.5.3 NMR of Proteins 203

7.5.4 NMR of Nucleic Acids 206

7.5.5 NMR of Glycans 207

7.6 Optical Rotatory Dispersion and Circular Dichroism Spectroscopy 208

7.6.1 Basic Principles 208

7.6.2 ORD/CD Spectra and Protein Secondary Structures 209

7.6.3 Empirical Applications of ORD and CD 212

7.7 X-ray Diffraction Spectroscopy 214

7.7.1 Basic Principles 214

7.7.2 Crystallographic Study of Biomacromolecules 216

7.8 References 219

CHAPTER 8 STUDIES OF BIOMACROMOLECULAR STRUCTURES：CHEMICAL SYNTHESIS 220

8.1 Rationale 220

8.2 Synthetic Strategy：Conventional Approach 220

8.2.1 Protection and Deprotection of Common Functional Groups 221

8.2.2 Protection and Deprotection Specific to Peptide Synthesis 223

8.2.3 Coupling Reaction 225

8.3 Synthetic Strategy：Solid Phase Approach 225

8.3.1 General Concept 225

8.3.2 Solid-Phase Polymer Support 230

8.4 Practice of Solid Phase Synthesis and Its Application 232

8.4.1 Oligo- and Polypeptide Synthesis 232

8.4.2 Oligo- and Polynucleotide Synthesis 236

8.4.3 Oligo- and Polysaccharide Synthesis 237

8.5 Combinatorial Synthesis 241

8.5.1 Parallel Synthesis 241

8.5.2 Mixture Synthesis 242

8.6 Biochemical Polypeptide Chain Ligation 245

8.7 References 247

CHAPTER 9 STUDIES OF BIOMACROMOLECULAR STRUCTURES：COMPUTATION AND MODELING 249

9.1 Potential Energy and Molecular Thermodynamics 249

9.2 Molecular Modeling：Molecular Mechanical Approach 252

9.2.1 Introduction 252

9.2.2 Energy Calculation 254

9.2.3 Energy Minimization 256

9.2.4 Molecular Dynamics 258

9.2.5 Conformational Search 261

9.2.6 Remaining Issues 262

9.2.7 Computational Application of Molecular Modeling Packages 263

9.3 Statistical Thermodynamics 264

9.3.1 General Principles 264

9.3.2 Transitions of Regular Structures：Two-State Models 268

9.3.3 Random Structure：Random-Walk Problem 271

9.4 Structural Transition：Examples 273

9.4.1 Coil-Helix Transition in Polypeptides 273

9.4.2 Helical Transition in Nucleic Acids 274

9.4.3 Topological Transition of Closed Circular DNA Duplex 276

9.5 Structure Prediction from Sequence by Statistical Methods 276

9.5.1 Approaches 276

9.5.2 Secondary Structure of Proteins and Beyond 277

9.5.3 Functional Sites of Proteins 280

9.5.4 Nucleic Acid Fold 281

9.6 Molecular Docking：Prediction of Biomacromolecular Binding 282

9.7 References 286

CHAPTER 10 BIOMACROMOLECULAR INTERACTION 289

10.1 Biomacromolecules in Solution 289

10.2 Multiple Equilibria 291

10.2.1 Single-Site Binding 291

10.2.2 Multiple-Site Binding：General 292

10.2.3 Multiple-Site Binding：Equivalent Sites 293

10.2.4 Multiple-Site Binding：Nonequivalent Sites 294

10.3 Allosterism and Cooperativity 295

10.3.1 Models 295

10.3.2 Diagnostic Tests for Cooperativity 299

10.4 Specificity and Diversity of Antibody-Antigen Interactions 300

10.4.1 Structure of Antibody 300

10.4.2 Antibody-Antigen Complex 303

10.5 Complementarity in Nucleic Acid Interactions 305

10.5.1 DNA-Protein Interaction 305

10.5.2 Binding of Intercalation Agent to Supercoiled DNA 309

10.5.3 RNA-Protein Interaction 310

10.6 Molecular Recognition in Carbohydrate-Lectin Interaction 312

10.6.1 Classification and Structures of Lectins 312

10.6.2 Lectin-Carbohydrate Recognition：General 315

10.6.3 Lectin-Carbohydrate Recognition：Ligand Discrimination 318

10.7 References 320

CHAPTER 11 BIOMACROMOLECULAR CATALYSIS 322

11.1 Biocatalyst：Definition and Classification 322

11.2 Characteristics of Enzymes 325

11.2.1 Enzymes：Catalytic Proteins 325

11.2.2 Catalytic Efficiency 326

11.2.3 Enzyme Specificity 328

11.2.4 Active Site of Enzyme 330

11.2.5 Multienzyme Complex and Multifunctional Enzymes 331

11.3 Enzyme Kinetics 333

11.3.1 Fundamental of Enzyme Kinetics 333

11.3.2 Steady-State Kinetic Treatment of Enzyme Catalysis 336

11.3.3 Quasi-Equilibrium Treatment of Random Reactions 338

11.3.4 Cleland’s Approach 339

11.3.5 Nonlinear Kinetics 339

11.3.6 Environmental Effects 341

11.4 Enzyme Mechanisms 344

11.4.1 Essay on Enzyme Reaction Mechanism 344

11.4.2 Studies of Enzyme Mechanism：Active Site 349

11.4.3 Studies of Enzyme Mechanism：Transition State 356

11.4.4 Structure-Activity Relationship 357

11.4.5 X-ray Crystallographic Studies and Refinement 361

11.4.6 Case Studies of Enzyme Mechanisms 361

11.5 Enzyme Regulation 374

11.5.1 Elements of Enzyme Regulation 374

11.5.2 Covalent Modifications of Enzymes and Cascade Effect 374

11.5.3 Control of Enzyme Catalytic Activity by Effectors 377

11.5.4 Structure Basis of Allosteric Regulation：Glycogen Phosphorylase 381

11.6 Abzyme 383

11.7 Ribozyme 386

11.7.1 Characteristics of Catalytic RNA 386

11.7.2 Description of Ribozymes 388

11.7.3 Strategies for Ribozyme Catalysis 392

11.8 References 394

CHAPTER 12 SIGNAL TRANSDUCTION AND BIODEGRADATION 398

12.1 Chemical Transduction：Metabolism 398

12.2 Elements of Signal Transduction 400

12.2.1 First Messengers 400

12.2.2 Receptors 400

12.2.3 Second Messengers 403

12.2.4 Transducers：GTP-Binding Proteins 403

12.3 Effector Enzymes and Signal Transduction 406

12.3.1 Adenylyl Cyclase and Signal Transduction 406

12.3.2 Phospholipase C and Signal Transduction 408

12.4 Topics on Signal Transduction 410

12.4.1 Calcium Signaling 410

12.4.2 Phosphorylation and Dephosphorylation in Signaling 414

12.4.3 Signal Pathways Operated by Receptor Protein Tyrosine Kinase 417

12.4.4 Signaling Pathways Operated by Nonreceptor Proteins Tyrosine Kinase 419

12.5 Apoptosis 419

12.6 Hydrolysis versus Phosphorolysis of Glycans 422

12.7 Nucleolysis of Nucleic Acids 424

12.8 Proteolysis and Protein Degradation 426

12.8.1 Proteolytic Mechanism 426

12.8.2 Protein Degradation Pathway 427

12.9 References 433

CHAPTER 13 BIOSYNTHESIS AND GENETIC TRANSMISSION 436

13.1 Saccharide Biosynthesis and Glycobiology 436

13.1.1 Biosynthesis of Biopolymer：Distributive versus Processive 436

13.1.2 Biosynthesis of oligo- and poly-saccharide chains 436

13.1.3 Biosynthesis of Glycoproteins 437

13.2 Genetic Information and Transmission 442

13.3 DNA Replication and Repair 445

13.3.1 DNA Replication：Overview 445

13.3.2 DNA Replication：Enzymology 448

13.3.3 Reverse Transcription 455

13.3.4 Post-Replicational Modification 456

13.3.5 DNA Repair 458

13.4 Biosynthesis and Transcription of RNA 461

13.4.1 RNA Transcription：Prokaryotic System 461

13.4.2 RNA Transcription：Eukaryotic System 463

13.4.3 Regulation of RNA Transcription 466

13.4.4 Posttranscriptional Processing/Modification 469

13.5 Translation and Protein Biosynthesis 472

13.5.1 Protein Translation：Overview 472

13.5.2 Protein Translation：Processes 475

13.5.3 Decoding Mechanism 479

13.5.4 Recoding，Frameshifting and Expanded Genetic Code 481

13.5.5 Rescue System for Stalled Ribosomes 483

13.5.6 Posttranslational Modifications of Protein 484

13.5.7 Protein Translocation 488

13.6 Folding of Biomacromolecules 491

13.6.1 Overview 491

13.6.2 RNA Folding 491

13.6.3 In vitro Protein Folding Pathway 492

13.6.4 Molecular Chaperone in Cytosolic Protein Folding 494

13.7 Bioengineering of Biomacromolecules 494

13.7.1 Recombinant DNA Technology 494

13.7.2 RNA Engineering 500

13.7.3 Protein Engineering 501

13.7.4 Antibody Engineering 506

13.8 References 511

CHAPTER 14 BIOMACROMOLECULAR INFORMATICS 515

14.1 Overview 515

14.2 Biosequences 515

14.2.1 Sequencing Biomacromolecules 515

14.2.2 Sequence Similarity and Pair-Wise Alignment 517

14.2.3 Similarity Search and Multiple Sequence Alignment 522

14.2.4 Statistical Significance of Sequence Search/Alignments 524

14.3 Microarray：General Description 525

14.3.1 Introduction 525

14.3.2 Surface Preparation for Microarray 525

14.3.3 Microarray Targets 528

14.3.4 Microarray Probes 529

14.3.5 Biochemical Reaction of Microarray 530

14.3.6 Microarray Detection 530

14.3.7 Data analysis in microarray 531

14.4 Computer Technology 533

14.4.1 Machine：Computer 533

14.4.2 Tool：Program，Language and Programming 535

14.4.3 Molecular Graphics 537

14.4.4 Resource：Internet 540

14.3.5 Internet Resources of Biochemical Interest 546

14.5 Informatics 548

14.5.1 Introduction to Database 548

14.5.2 Biochemical Databases 549

14.5.3 Database Retrieval 551

14.6 Gene Ontology 553

14.7 References 555

CHAPTER 15 GENOMICS 558

15.1 Genome：Features and Organization 558

15.1.1 Genome Features 558

15.1.2 Gene Mapping 561

15.1.3 Information Content of Nucleotide Sequence 563

15.1.4 DNA Library 564

15.1.5 Alternative Splicing 566

15.1.6 Gene Variation：Single Nucleotide Polymorphism 567

15.2 Genome Informatics：Databases and Web Servers 568

15.2.1 Nucleic Acid Databases 568

15.2.2 Nucleic Acid Analysis Servers 571

15.3 Approaches to Gene Identification 571

15.3.1 Masking Repetitive DNA 575

15.3.2 Database Searches 576

15.3.3 Codon Bias Detection 576

15.3.4 Detecting Functional Sites in the DNA 577

15.4 Gene Expression 578

15.4.1 Expression Profiling：DNA Chips 578

15.4.2 Gene Expression：mRNA Quantification and Transcriptome Analysis 583

15.5 Genome Project 587

15.6 References 590

CHAPTER 16 PROTEOMICS 594

16.1 Proteome：Features and Properties 594

16.1.1 Proteome Features 594

16.1.2 Protein Identity Based on Composition and Properties 595

16.1.3 Physicochemical Properties Based on Sequence 596

16.2 Proteome Informatics：Sequence Databases and Servers 598

16.2.1 Amino Acid Sequence 598

16.2.2 Primary Sequence Database 599

16.2.3 Secondary Sequence Database 602

16.2.4 Boutique Databases 605

16.3 Proteome Informatics：Structure Databases and Servers 605

16.3.1 Structure Database：Primary Archive 605

16.3.2 Structure Databases：Substructures and Structure Classification 608

16.4 Proteome Informatics：Proteomic Servers 610

16.4.1 Proteome Analysis and Annotation 610

16.4.2 Integrated Databases 613

16.4.3 Post-Translational Modifications and Functional Sites 614

16.5 Protein Structure Analysis Using Bioinformatics 616

16.5.1 Secondary Structure Predictions 617

16.5.2 Three-Dimensional Structure Modeling 618

16.5.3 Sequence Similarity and Alignment 619

16.5.4 Structure Similarity and Overlap 620

16.5.5 Fold Recognition and Threading 623

16.5.6 Homology Modeling 623

16.5.7 Ab initio Prediction of Protein Structure 624

16.5.8 Solvation 625

16.5.9 On-line Protein Structure Prediction 626

16.5.10 Protein-Protein Interaction 628

16.6 Investigation of Proteome Expression and Function 629

16.6.1 Two-Dimensional Gel Electrophoresis 629

16.6.2 Proteome Analysis by Mass Spectrometry 631

16.6.3 Analysis of Posttranslational Modification by Mass Spectrometry 634

16.6.4 High Throughput Protein Crystallography 635

16.6.5 Protein-Protein Interactions by Two-Hybrid Assay 636

16.6.6 Protein Chip 638

16.6.7 Activity-Based Probe 640

16.6.8 Nonsense Suppression Mutagenesis 643

16.7 Metabolome 647

16.8 References 650

CHAPTER 17 GLYCOMICS 655

17.1 Features of Glycomics 655

17.1.1 Glycobiology：Nomenclature and Representation of Glycans 655

17.1.2 Glycobiology：Glycoforms 657

17.1.3 Glycomics：Response to Post-Genomic Era 659

17.2 Glycomic Databases and Servers 661

17.2.1 Glycan Structure 661

17.2.2 Glycan Analysis 663

17.2.3 Glycosylation of Proteins 665

17.3 Glycomics：Genetic Approaches 666

17.4 Glycomics：Proteoglycomic Approaches 668

17.4.1 Characterization of Glycosylation Sites 668

17.4.2 Lectin and Glycoenzyme-Based Proteoglycomics 670

17.4.3 Metabolic Oligosaccharide Engineering 672

17.4.4 Recombinant Glycoproteins 673

17.5 Glycomics：Chemoglycomic Approaches 674

17.5.1 Structural Analysis of Glycans 674

17.5.2 Glycoprotein Syntheses in Glycomics 674

17.5.3 Glycochip 675

17.6 References 678

CHAPTER 18 BIOMACROMOLECULAR EVOLUTION 680

18.1 Variation in Biomacromolecular Sequences 680

18.1.1 Mutation as Driving Force of Evolution 680

18.1.2 Evolutionary Rate and Role of Selection 682

18.2 Element of Molecular Phylogeny 685

18.3 Phylogenetic Analysis of Biosequences 687

18.3.1 General Consideration 687

18.3.2 Sequence Data 687

18.3.3 Phylogenetic Method：Distance-Based Approaches 690

18.3.4 Phylogenetic Method：Character-Based Approaches 691

18.3.5 Construction of Phylogenetic Tree 692

18.3.6 Assessment 692

18.4 Application of Sequence Analyses in Phylogenetic Inference 693

18.4.1 Phylogenetic Analysis Software 693

18.4.2 Phylogenetic Analysis with PHYLIP 693

18.4.3 Phylogenetic Analysis Online 697

18.5 Evolution of Biosequences 697

18.5.1 Evolution of Nucleic Acid Sequence 697

18.5.2 Regulation of Evolutionary Change 699

18.6 Evolution of Protein Structure and Function 701

18.6.1 Evolution of Protein Complexity：General 702

18.6.2 Evolution of Protein Complexity：Domain Duplication 703

18.6.3 Evolution of Protein Structure：Fold Change 704

18.6.4 Evolution of Protein Function：Catalytic Site Convergence versus Divergence 706

18.7 References 708

INDEX 710