Preface |
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xi | |
Acknowledgments |
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xiii | |
Author |
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xv | |
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Chapter 1 Features of Interacting Monomers with Different Functionalities: What Drives the Binding? |
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1 | (16) |
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1.1 FUNCTIONAL GROUPS IN RECOGNITION BETWEEN SMALL MOLECULES |
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2 | (2) |
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1.1.1 Functional Groups and Recognition Pattern |
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2 | (2) |
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1.2 MOLECULES WITH DIFFERENT FUNCTIONALITIES |
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4 | (7) |
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4 | (1) |
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1.2.2 Nucleosides/Nucleotides/Purines/Pyrimidines |
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4 | (4) |
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8 | (3) |
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1.3 CONFIGURATION AND CHIRALITY |
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11 | (1) |
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1.4 LOCK-AND-KEY AND INDUCED FIT MODEL |
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11 | (2) |
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1.4.1 Example of Lock-and-Key Model |
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13 | (1) |
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1.5 NONCOVALENT INTERACTIONS |
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13 | (4) |
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13 | (1) |
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1.5.2 Hydrophobic Interaction |
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14 | (1) |
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1.5.3 Van der Waals Interaction |
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15 | (1) |
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1.5.4 Stacking Interaction |
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15 | (1) |
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15 | (1) |
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1.5.6 Interaction due to Spatial Match |
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15 | (2) |
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Chapter 2 Molecular Recognition among Various Monomers |
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17 | (14) |
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2.1 CROWN ETHER-METAL ION RECOGNITION |
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20 | (1) |
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2.2 PEPTIDE-ANTIBIOTIC RECOGNITION |
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20 | (1) |
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2.3 DRUG-RECEPTOR INTERACTION |
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21 | (2) |
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2.4 SUGAR-PROTEIN RECOGNITION |
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23 | (3) |
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2.5 CELL WALL COMPOSITION AND SUGARS |
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26 | (1) |
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2.6 CELL-CELL COMMUNICATION AND SMALL MOLECULE-RECEPTOR RECOGNITION |
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26 | (2) |
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2.7 LECTIN-SUGAR RECOGNITION |
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28 | (3) |
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Chapter 3 Macromolecular Recognition |
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31 | (50) |
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3.1 STATIC AND DYNAMIC MOLECULAR RECOGNITION |
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31 | (2) |
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3.2 DIFFERENCE BETWEEN CHEMICAL AND BIOLOGICAL MACROMOLECULES |
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33 | (1) |
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33 | (1) |
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3.3 BIOLOGICAL MACROMOLECULES |
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34 | (27) |
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3.3.1 Nucleosides, Nucleotides, and Nucleic Acids |
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35 | (3) |
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3.3.2 DNA Origami (Dynamic Molecular Recognition) |
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38 | (1) |
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3.3.3 What Are the Major Recognition Points in DNA/RNA Helices? |
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39 | (10) |
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3.3.4 Proteins That Bind Nucleic Acids |
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49 | (3) |
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3.3.5 Sequence-Specific Recognition between DNA and Proteins |
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52 | (3) |
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3.3.6 RNA-Protein Recognition |
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55 | (3) |
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3.3.7 Structural Basis for Protein-RNA Recognition |
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58 | (1) |
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3.3.8 tRNA-Aminoacyl tRNA Synthetase Interaction |
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59 | (1) |
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3.3.9 Recognition by miRNA (Micro RNA) |
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60 | (1) |
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3.4 POLYMERIZATION OF NUCLEIC ACIDS |
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61 | (5) |
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3.5 MOLECULAR RECOGNITION AT THE HEART OF THE CENTRAL DOGMA OF MOLECULAR BIOLOGY |
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66 | (2) |
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3.6 POLYMERIZATION OF BIOLOGICAL MONOMERS |
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68 | (2) |
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3.7 HORMONES AND RECEPTORS |
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70 | (2) |
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3.8 ANTIGEN-ANTIBODY RECOGNITION |
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72 | |
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3.8.1 Structure of Antibodies |
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73 | (1) |
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74 | (1) |
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74 | (1) |
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75 | (1) |
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3.8.5 Antigen-Antibody Recognition |
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75 | |
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71 | (10) |
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Chapter 4 Methods to Follow Molecular Recognition |
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81 | (18) |
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4.1 SIZE-EXCLUSION CHROMATOGRAPHY |
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82 | (2) |
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4.2 SURFACE PLASMON RESONANCE |
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84 | (1) |
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4.3 AFFINITY CHROMATOGRAPHY |
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85 | (1) |
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4.4 ION-EXCHANGE CHROMATOGRAPHY |
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86 | (1) |
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87 | (2) |
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4.6 SPECTROSCOPIC TOOLS THAT UTILIZE MOLECULAR RECOGNITION |
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89 | (7) |
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4.7 ISOTHERMAL TITRATION CALORIMETRY |
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96 | (3) |
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Chapter 5 Macromolecular Assembly and Recognition with Chemical Entities |
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99 | (16) |
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5.1 FOLDING AND MOLECULAR RECOGNITION |
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101 | (1) |
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5.1.1 Solvent-Induced Folding |
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101 | (1) |
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5.1.2 Folding due to Charge-Transfer Complex Formation |
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102 | (1) |
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5.1.3 Self-Organization due to Immiscibility |
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102 | (1) |
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5.2 HOST-GUEST RECOGNITION AND SUPRAMOLECULAR ASSEMBLY |
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102 | (4) |
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5.3 MOLECULAR INFORMATION PROCESSING AND SELF-ORGANIZATION |
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106 | (2) |
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5.4 RECOGNITION BETWEEN METAL IONS AND NUCLEIC ACIDS |
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108 | (7) |
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5.4.1 Stabilization of Nucleic Acids by Metal Ions |
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110 | (2) |
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5.4.2 Metal Ion Interaction with Nucleosides and Nucleotides |
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112 | (3) |
Suggested Readings |
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115 | (6) |
Index |
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121 | |