Frontiers in Physicochemical Biology

List of Contributors

Preface

Part I The Physical Chemistry of Fundamental Biomolecules


1 Current Progress and Future Prospects of the Research on Nucleic Acids

I. Introduction

II. Nuclear Magnetic Resonance Studies

III. Experimental Evaluation of Electrostatic Interaction and Studies on Nonionic Oligonucleotide Analogues

IV. Future Prospects

References


2 The Structure of Transfer RNA Molecules in Solution

I. Introduction

II. Tertiary Structure of tRNA in Solution

III. Ring-Current Shift Theory Analysis of Low-Field nmr Spectra

IV. Hydrogen Binding of the Ribose 2'-OH Group in RNA

V. Summary

References


3 The Chemistry of Membrane-Active Peptides and Proteins

Text

References


4 Conformational Analysis of Polypeptides: Application to Homologous Proteins

I. Introduction

II. Standard Geometry

III. Computation Procedures

IV. Approaches to the Multiple-Minimum Problem

V. Computation of Models for the Three-Dimensional Structures of Three Snake Venom Inhibitors

VI. Concluding Remarks

References


5 Aspects of Biomolecules in Their Surroundings: Hydration and Cation Binding

I. Introduction

II. Hydration

III. Cation Binding

IV. The Triple System: Substrate-Water-Cation or the Problem of the Through-Water Cation Binding

References

Part II Physicochemical Aspects of the Mechanisms of Genetic Expression


6 Site-Directed Mutagenesis as a Tool in Genetics

I. Phage Qβ and Its Replication

II. Site-Directed Mutations in Qβ RNA

III. Perspectives for Site-Directed Mutagenesis

References


7 Gene Control by the λ Phage Repressor

I. Operator Structure

II. Promoter Structure

III. λ Repressor

IV. Repressor Control of Ν and cro

V. Self-Regulation of cl

VI. Translational Control of cI

VII. Summary

References


8 Nuclear Magnetic Resonance Studies of Protein-Nucleotide Interactions

I. Ternary Enzyme-Metal Nucleotide Complexes

II. Higher Enzyme-Substrate Complexes

III. Working Enzymes

IV. Conclusions

References


9 The Role of RNA's in the Structure and Function of Ribosomes

I. A Rapid Survey of Present Knowledge on the Structure of E. coli Ribosomal RNA's

II. RNA-RNA Interactions

III. Interactions between Ribosomal RNA's and Proteins

References


10 Mechanism of Initiation of Protein Synthesis

I. Initiation Sequence: Characterization of Factors

II. Selection of Initiation Signals

III. Secondary Structure of mRNA as Negative Control

IV. Part Played by Ribosomal Proteins and Initiation Factors

V. Specific Mutants Affecting Initiation

VI. Conclusion

References

Part III Biochemistry of Oxygen and Hemoglobin


11 Molecular Oxygen and Superoxide Dismutase: Environmental Threat and Biological Defense

I. Induction of Superoxide Dismutase in Escherichia coli K12

II. Induction of Superoxide Dismutase in E. coli, at Constant Oxygenation, in Response to Changes in Metabolism

III. A Convenient New Assay for Superoxide Dismutase

References


12 Indoleamine 2,3-Dioxygenase: A Superoxide-Utilizing Enzyme

I. Introduction

II. Biological Function

III. Purification and Molecular Properties

IV. Role of Superoxide Anion

V. Experiments with KO2

VI. Interaction of Enzyme with KO2

VII. Experiments with 18O2-

VIII. Interaction of Enzyme with Substrate

IX. Is O2- a Substrate in Vivo?

X. Conclusion

References


13 Reaction Intermediates of D-Amino Acid Oxidase

I. Introduction

II. Occurrence of Two Types of Oxidoreduction Intermediates

III. Lifetime of the Purple Intermediate

IV Effect of Hydrogen Bonding on the Formation of the Intermediate

V. Role of Protein in the Formation of the Intermediates

VI. Reactivity of the Intermediates with Molecular Oxygen

References


14 Biological Aspects of Superoxide Dismutase

I. Introduction

II. Production of O2-

III. Superoxide Dismutases

IV. Variation in SOD Levels during Development of Ceratitis capitata

V. Erythrocyte SOD, Catalase, and Glutathione Peroxidase Levels in Different Animals

VI. Biological Utility of O2-

VII. Toxicity of Superoxide Radicals

VIII. Ionizing Irradiations

IX. Chemiluminescence of O2-

X. Clinical Aspects of SOD Levels in Humans

XI. General Conclusion

References


15 Recent Developments on the Active-Site Structure and Mechanism of Bovine Copper- and Zinc-Containing Superoxide Dismutase

I. Chemical Structure of the Metal Binding Sites and General Reaction Mechanism of the Enzyme

II. Anionic Inhibitors of the Enzyme

III. Spectral Studies of Co2+-Substituted Superoxide Dismutase

IV. Catalytic Protonation and Deprotonation of the Bridging Imidazole

References


16 Binding of Oxygen to Hemoglobin A in the T-State

I. Models

II. The Value of L and Properties of R- and T-State Hemoglobins

III. Effects of Temperature on the Oxygen-Hemoglobin Reaction

IV. Effect of pH and Effectors

V. Conclusions and Problems

References

Part IV Study of Organized Systems


17 The Structure and Assembly of the Membrane of Semliki Forest Virus

I. Semliki Forest Virus

II. Composition of SFV

III. Growth Cycle of SFV

IV. Structure of the Virus Membrane Glycoproteins

V. The Final Event in Virus Maturation: The Budding

Process

References


18 Oscillations: A Property of Organized Systems

I. General Mechanistics of Dynamic Organization

II. Nonequilibrium Dynamics

III. Experimental Observation of Oscillations

IV. General Remarks

References


19 Cation-Induced Regulatory Mechanism of Enzyme Reactions

I. Introduction

II. Catalytic Implications of the Polyelectrolyte Theory: An Oversimplified Treatment

III. Membrane-Bound Enzymes

IV. Gene Expression Systems

V General Conclusion

References


20 The Proton Pumps of Photosynthesis

I. Introduction

II. Protolytic Reactions in Green Plant Photosynthesis

III. The Proton Pumps of Bacterial Photosynthesis

IV. Photochemical Reaction Centers

References


21 The Photosynthetic Intramembrane Electric Field

I. Formation of the Membrane Potential in Algae

II. Relaxation of the Membrane Potential

References

Subject Index