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E-grāmata: Basics of Molecular Recognition

  • Formāts: 141 pages
  • Izdošanas datums: 05-Apr-2016
  • Izdevniecība: CRC Press Inc
  • ISBN-13: 9781482219692
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  • Formāts: 141 pages
  • Izdošanas datums: 05-Apr-2016
  • Izdevniecība: CRC Press Inc
  • ISBN-13: 9781482219692
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Basics of Molecular Recognition explores fundamental recognition principles between monomers or macromolecules that lead to diverse biological functions. Based on the authors longtime courses, the book helps readers understand the structural aspects of macromolecular recognition and stimulates further research on whether molecules similar to DNA or protein can be synthesized chemically.

The book begins with the types of bonds that participate in the recognition and the functional groups that are capable of forming these bonds. It then explains how smaller molecules select their partners in the overall recognition scheme, offering examples of specific recognition patterns involving molecules other than nucleic acids. The core of the book focuses on macromolecular recognitionthe central dogma of molecular biology. The author discusses various methods for studying molecular recognition. He also describes how molecules without biological functions can be arrayed or folded following certain rules and examines the nature of interactions among them.

Molecular recognition is a vast area encompassing every aspect of biology. This book highlights all aspects of non-covalent macromolecular recognition processes, including DNAprotein recognition and sugarprotein recognition.
Preface xi
Acknowledgments xiii
Author xv
Chapter 1 Features of Interacting Monomers with Different Functionalities: What Drives the Binding?
1(16)
1.1 FUNCTIONAL GROUPS IN RECOGNITION BETWEEN SMALL MOLECULES
2(2)
1.1.1 Functional Groups and Recognition Pattern
2(2)
1.2 MOLECULES WITH DIFFERENT FUNCTIONALITIES
4(7)
1.2.1 Sugars
4(1)
1.2.2 Nucleosides/Nucleotides/Purines/Pyrimidines
4(4)
1.2.3 Amino Acids
8(3)
1.3 CONFIGURATION AND CHIRALITY
11(1)
1.4 LOCK-AND-KEY AND INDUCED FIT MODEL
11(2)
1.4.1 Example of Lock-and-Key Model
13(1)
1.5 NONCOVALENT INTERACTIONS
13(4)
1.5.1 Hydrogen Bond
13(1)
1.5.2 Hydrophobic Interaction
14(1)
1.5.3 Van der Waals Interaction
15(1)
1.5.4 Stacking Interaction
15(1)
1.5.5 Ionic Interaction
15(1)
1.5.6 Interaction due to Spatial Match
15(2)
Chapter 2 Molecular Recognition among Various Monomers
17(14)
2.1 CROWN ETHER-METAL ION RECOGNITION
20(1)
2.2 PEPTIDE-ANTIBIOTIC RECOGNITION
20(1)
2.3 DRUG-RECEPTOR INTERACTION
21(2)
2.4 SUGAR-PROTEIN RECOGNITION
23(3)
2.5 CELL WALL COMPOSITION AND SUGARS
26(1)
2.6 CELL-CELL COMMUNICATION AND SMALL MOLECULE-RECEPTOR RECOGNITION
26(2)
2.7 LECTIN-SUGAR RECOGNITION
28(3)
Chapter 3 Macromolecular Recognition
31(50)
3.1 STATIC AND DYNAMIC MOLECULAR RECOGNITION
31(2)
3.2 DIFFERENCE BETWEEN CHEMICAL AND BIOLOGICAL MACROMOLECULES
33(1)
3.2.1 Ribonuclease
33(1)
3.3 BIOLOGICAL MACROMOLECULES
34(27)
3.3.1 Nucleosides, Nucleotides, and Nucleic Acids
35(3)
3.3.2 DNA Origami (Dynamic Molecular Recognition)
38(1)
3.3.3 What Are the Major Recognition Points in DNA/RNA Helices?
39(10)
3.3.4 Proteins That Bind Nucleic Acids
49(3)
3.3.5 Sequence-Specific Recognition between DNA and Proteins
52(3)
3.3.6 RNA-Protein Recognition
55(3)
3.3.7 Structural Basis for Protein-RNA Recognition
58(1)
3.3.8 tRNA-Aminoacyl tRNA Synthetase Interaction
59(1)
3.3.9 Recognition by miRNA (Micro RNA)
60(1)
3.4 POLYMERIZATION OF NUCLEIC ACIDS
61(5)
3.5 MOLECULAR RECOGNITION AT THE HEART OF THE CENTRAL DOGMA OF MOLECULAR BIOLOGY
66(2)
3.6 POLYMERIZATION OF BIOLOGICAL MONOMERS
68(2)
3.7 HORMONES AND RECEPTORS
70(2)
3.8 ANTIGEN-ANTIBODY RECOGNITION
72
3.8.1 Structure of Antibodies
73(1)
3.8.2 Constant Domain
74(1)
3.8.3 Variable Domain
74(1)
3.8.4 Antigen
75(1)
3.8.5 Antigen-Antibody Recognition
75
3.9 BLOOD GROUPING
71(10)
Chapter 4 Methods to Follow Molecular Recognition
81(18)
4.1 SIZE-EXCLUSION CHROMATOGRAPHY
82(2)
4.2 SURFACE PLASMON RESONANCE
84(1)
4.3 AFFINITY CHROMATOGRAPHY
85(1)
4.4 ION-EXCHANGE CHROMATOGRAPHY
86(1)
4.5 HYDROPHOBICITY
87(2)
4.6 SPECTROSCOPIC TOOLS THAT UTILIZE MOLECULAR RECOGNITION
89(7)
4.7 ISOTHERMAL TITRATION CALORIMETRY
96(3)
Chapter 5 Macromolecular Assembly and Recognition with Chemical Entities
99(16)
5.1 FOLDING AND MOLECULAR RECOGNITION
101(1)
5.1.1 Solvent-Induced Folding
101(1)
5.1.2 Folding due to Charge-Transfer Complex Formation
102(1)
5.1.3 Self-Organization due to Immiscibility
102(1)
5.2 HOST-GUEST RECOGNITION AND SUPRAMOLECULAR ASSEMBLY
102(4)
5.3 MOLECULAR INFORMATION PROCESSING AND SELF-ORGANIZATION
106(2)
5.4 RECOGNITION BETWEEN METAL IONS AND NUCLEIC ACIDS
108(7)
5.4.1 Stabilization of Nucleic Acids by Metal Ions
110(2)
5.4.2 Metal Ion Interaction with Nucleosides and Nucleotides
112(3)
Suggested Readings 115(6)
Index 121
Dipankar Chatterji is a professor in the Molecular Biophysics Unit at the Indian Institute of Science, Bangalore. Dr. Chatterji was the president of the Indian Academy of Sciences from 2013 to 2015. His major area of research focuses on the regulation of gene expression in bacteria under stress, including important pathways such as stringent response and quorum sensing.