Ebook: Chemical Recognition in Biology

Studies of chemical recognition in biology were initiated about half a century ago with the flrst kinetic data obtained on enzyme catalysis and inhibition. They led to a rather static representation of the recognition process illustrated by the lock and key model that still continues to influence our overall image of recognition and its specificity. In several cases, crystallographic studies of enzyme-substrate complexes have supported this model. Indeed, in a crystallized ligand-enzyme complex, a close fltting is observed between the active center of the enzyme and the functional groups of the ligand. How­ ever, this does not necessarily result from a direct recognition process between rigid structures, but may result from a progressive adaptation during which the initial struc­ tures of the enzyme and the ligand are modified (induced-flt mechanism). Recently, a great deal of work has been devoted to the study of recognition in more complex systems such as the replication or the translation machin~ries; clearly, the extraordinary precision of such systems cannot be explained solely in terms of physical matching between enzymes and their substrates. This has led to a noticeable change of perspective in these areas. As a result of the new kinetic viewpoint, one rather focuses on the time-course of the processes, on the kinetic balance between steps of the reaction, on the energy-accuracy relationships and on the strategies which permit the achievement of high precision using relatively error-prone components in an appropriate dynamic interplay.

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Content:
Front Matter....Pages I-XI
Front Matter....Pages 1-1
What Everyone Wanted to Know About Tight Binding and Enzyme Catalysis, but Never Thought of Asking....Pages 3-25
The Cytochromes C: Paradigms for Chemical Recognition....Pages 26-37
Recognition of Ligands by Haem Proteins....Pages 38-42
Influences of Solvent Water on the Transition State Affinity of Enzymes, Protein Folding, and the Composition of the Genetic Code....Pages 43-61
Suicide Substrates: Mechanism-Based Inactivators of Specific Target Enzymes....Pages 62-77
Recognition: the Kinetic Concepts....Pages 78-85
Coupled Oscillator Theory of Enzyme Action....Pages 86-96
Stereochemical Aspects of Chain Lengthening and Cyclization Processes in Terpenoid Biosynthesis....Pages 97-110
Front Matter....Pages 111-111
Three Multifunctional Protein Kinase Systems in Transmembrane Control....Pages 113-135
Effect of Catabolite Repression on Chemotaxis in Salmonella Typhimurium....Pages 136-143
Subunit Interaction of Adenylylated Glutamine Synthetase....Pages 144-156
Dynamic Compartmentation....Pages 157-164
The Genes for and Regulation of the Enzyme Activities of two Multifunctional Proteins Required for the De Novo Pathway for UMP Biosynthesis in Mammals....Pages 165-182
Regulation of Muscle Contraction by Ca Ion....Pages 183-194
Why is Phosphate so Useful?....Pages 195-196
ppGpp, a Signal Molecule....Pages 197-204
Gramicidin S-Synthetase: On the Structure of a Polyenzyme Template in Polypeptide Synthesis....Pages 205-216
A Molecular Approach to Immunity and Pathogenicity in an Insect-Bacterial System....Pages 217-228
Front Matter....Pages 229-229
Structure of the Gene 5 DNA Binding Protein from Bacteriophage fd and its DNA Binding Cleft....Pages 231-240
Recognition of Nucleic Acids and Chemically-Damaged DNA by Peptides and Protein....Pages 241-249
Front Matter....Pages 229-229
Specific Interaction of Base-Specific Nucleases with Nucleosides and Nucleotides....Pages 250-277
Structural and Dynamic Aspects of Recognition Between tRNAs and Aminoacyl-tRNA Synthetases....Pages 278-300
Recognition of Promoter Sequences by RNA Polymerases from Different Sources....Pages 301-307
DNA as a Target for a Protein Antibiotic: Molecular Basis of Action....Pages 308-322
Site-Specific Mutagenesis in the Analysis of a Viral Replicon....Pages 323-330
Front Matter....Pages 331-331
Molecular Mechanism of Protein Biosynthesis and an Approach to the Mechanism of Energy Transduction....Pages 333-346
On Codon-Anticodon Interactions....Pages 347-367
Fluorescent tRNA Derivatives and Ribosome Recognition....Pages 368-375
Structure and Evolution of Ribosomes....Pages 376-397
Front Matter....Pages 399-399
Molecular Biology, Culture, and Society....Pages 401-414
Personal Recollections on Fritz Lipmann During the Early Years of Coenzyme a Research....Pages 415-430
Back Matter....Pages 431-432

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Content:
Front Matter....Pages I-XI
Front Matter....Pages 1-1
What Everyone Wanted to Know About Tight Binding and Enzyme Catalysis, but Never Thought of Asking....Pages 3-25
The Cytochromes C: Paradigms for Chemical Recognition....Pages 26-37
Recognition of Ligands by Haem Proteins....Pages 38-42
Influences of Solvent Water on the Transition State Affinity of Enzymes, Protein Folding, and the Composition of the Genetic Code....Pages 43-61
Suicide Substrates: Mechanism-Based Inactivators of Specific Target Enzymes....Pages 62-77
Recognition: the Kinetic Concepts....Pages 78-85
Coupled Oscillator Theory of Enzyme Action....Pages 86-96
Stereochemical Aspects of Chain Lengthening and Cyclization Processes in Terpenoid Biosynthesis....Pages 97-110
Front Matter....Pages 111-111
Three Multifunctional Protein Kinase Systems in Transmembrane Control....Pages 113-135
Effect of Catabolite Repression on Chemotaxis in Salmonella Typhimurium....Pages 136-143
Subunit Interaction of Adenylylated Glutamine Synthetase....Pages 144-156
Dynamic Compartmentation....Pages 157-164
The Genes for and Regulation of the Enzyme Activities of two Multifunctional Proteins Required for the De Novo Pathway for UMP Biosynthesis in Mammals....Pages 165-182
Regulation of Muscle Contraction by Ca Ion....Pages 183-194
Why is Phosphate so Useful?....Pages 195-196
ppGpp, a Signal Molecule....Pages 197-204
Gramicidin S-Synthetase: On the Structure of a Polyenzyme Template in Polypeptide Synthesis....Pages 205-216
A Molecular Approach to Immunity and Pathogenicity in an Insect-Bacterial System....Pages 217-228
Front Matter....Pages 229-229
Structure of the Gene 5 DNA Binding Protein from Bacteriophage fd and its DNA Binding Cleft....Pages 231-240
Recognition of Nucleic Acids and Chemically-Damaged DNA by Peptides and Protein....Pages 241-249
Front Matter....Pages 229-229
Specific Interaction of Base-Specific Nucleases with Nucleosides and Nucleotides....Pages 250-277
Structural and Dynamic Aspects of Recognition Between tRNAs and Aminoacyl-tRNA Synthetases....Pages 278-300
Recognition of Promoter Sequences by RNA Polymerases from Different Sources....Pages 301-307
DNA as a Target for a Protein Antibiotic: Molecular Basis of Action....Pages 308-322
Site-Specific Mutagenesis in the Analysis of a Viral Replicon....Pages 323-330
Front Matter....Pages 331-331
Molecular Mechanism of Protein Biosynthesis and an Approach to the Mechanism of Energy Transduction....Pages 333-346
On Codon-Anticodon Interactions....Pages 347-367
Fluorescent tRNA Derivatives and Ribosome Recognition....Pages 368-375
Structure and Evolution of Ribosomes....Pages 376-397
Front Matter....Pages 399-399
Molecular Biology, Culture, and Society....Pages 401-414
Personal Recollections on Fritz Lipmann During the Early Years of Coenzyme a Research....Pages 415-430
Back Matter....Pages 431-432
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