From Metabolite, to Metabolism, to Metabolon

Paul A. Srere

Section I. The Cytomatrix And Enzyme Organization

Cellular Infrastructure and Metabolic Organization

I. Introduction

II. What Is the Cytosol?

III. The Nature of the Cytomatrix: An Unresolved Issue

IV. Protein Synthesis in Permeabilized Cells

V. On the Ontogeny and Evolutionary Origin of the Cytomatrix

References

Association of Glycolytic Enzymes with the Cytoskeleton

I. Introduction

II. Dynamic Involvement of the Cytoskeleton in Intracellular Structure and Organization, Transportation, and Cellular Contraction

III. Association of Glycolytic Enzymes with the Cytoskeleton

IV. Summary

References

Interactions of Glycolytic Enzymes with Cellular Membranes

I. Introduction

II. Hexokinase

III. Phosphofructokinase

IV. Fructose- 1,6-Bisphosphate Aldolase

V. Glyceraldehyde-3-Phosphate Dehydrogenase

VI. Concluding Remarks

References

Section II. Membrane-Associated Processes

How Carbohydrates Cross the Lipid Membrane of Bacterial Cells

I. Introduction

II. Binding Protein-Dependent Systems

III. Cation Symport Systems

IV. Phosphoenolpyruvate-Dependent Phosphotransferase System

References

Platelet-Activating Factor: A Novel Lipid Agonist

I. Introduction

II. Characterization of Platelet-Activating Factor Receptor(s) by Use of Antagonists

III. Biological and Chemical Characteristics of Platelet-Activating Factor

IV. Endogenous Modulators of Platelet-Activating Factor Activity

V. Concluding Remarks

References

Section III. Macromolecular Processes

Protein-Protein Interaction in the α-Complementation System of ß-Galactosidase

I. Introduction

II. Converting Full-Length Chimeric lacZ Genes to Chimeric lacZα Genes

III. Demonstrating the Interaction of Chimeric α-Peptides with α-Acceptor via TrpR Phenotypes

IV. Summary and Future Prospects in α-Complementation Research

References

Calmodulin and Dynamics of Interactions of Cytosolic Enzymes

I. Introduction: Relationship of Filament Systems and Calmodulin

II. Interactions in Muscle Protein Systems

III. Interactions in Brain Protein Systems

IV. Concluding Remarks

Note Added in Proof

References

Chaperones and Matchmakers: Inhibitors and Stimulators of Protein Phosphorylation

I. Introduction

II. Model for the Action of Chaperones and Matchmakers

III. Temperature Dependence of the Action of Chaperones

IV. Role of Chaperones and Matchmakers as Substrate Modulators in Phosphorylation-Dephosphorylation Reactions

References

Organization of RNA Splicing in the Cell Nucleus

I. Split Genes and Mammalian mRNA Processing

II. Molecular Dissection of a Subnuclear RNA Splicing Domain

III. Concluding Remarks

References

Section IV. Citric Acid Cycle

Structural Aspects of Citrate Biochemistry

I. Introduction

II. Structure of Citrates

III. Conclusion

References

Citrate: Its Relation to Free Magnesium Ion Concentration and Cellular Energy

I. Introduction

II. The Aconitase Reaction

III. Adjustment of Keq for Variations in Temperature, Ionic Strength, and Free [Mg2+]

IV. Determination of Free [Mg2+] from the Variation of the [Σ Citrate]/[Σ Isocitrate] Ratio

V. Effects of Change of Free [Mg2+] on the Major Reactions of Energy Metabolism

VI. Effects of Variation of Free [Mg2+] on Other Citrate Enzymes

References

Structure and Mechanism of Citrate Synthase

I. Introduction

II. General Background

III. Enzyme-Substrate/Inhibitor Interactions

IV. Implications for Catalytic Activity

References

Complexes and Complexities of the Citric Acid Cycle in Escherichia coli

I. Introduction and Scope

II. Gene-Protein Relationships and Expression

III. Succinate Dehydrogenase, Fumarate Reductase, and Two Mechanisms of Oxygen-Regulated Gene Expression

IV. Multiple Forms of Fumarase

V. The 2-Oxo Acid Dehydrogenase Complexes

VI. Concluding Remarks

References

Regulatory Consequences of Organization of Citric Acid Cycle Enzymes

I. Introduction

II. Materials and Methods

III. Results

IV. Discussion

References

The Molecular Physiology of Citrate

I. Introduction

II. Citrate Chemistry

III. Citrate-Protein Interactions

IV. Supramolecular Complexes

V. Organellar and Higher Levels of Organization

VI. Apologia

References

Section V. Electron Transport Systems

The Protonmotive Force as an Intermediate in Electron Transport-Linked Phosphorylation: Problems and Prospects

I. Introduction and Overview

II. Principles of the Chemiosmotic Coupling Hypothesis

III. Phosphorylation Driven by an Artificial Protonmotive Force

IV. Values of the Protonmotive Force Obtained When Measured Directly

V. Redox-Linked Proton Translocation

VI. Coreconstituted Systems

VII. Protoneural Proteins as Targets for Inhibitory Drugs

VIII. Double-Inhibitor Titrations

IX. What Types of Mechanism Are Therefore Possible?

X. Nonlinear Dielectric Spectroscopy: A Novel Approach to the Study of Membrane Energy-Coupling Systems

References

Substrate Channeling of NADH in Mitochondrial Redox Processes

I. Introduction

II. NADH Channeling to Complex I

Note Added in Proof

References

Interactions Between Mitochondria and Cytoplasm in Isolated Hepatocytes

I. Introduction

II. Materials

III. Methods

IV. Results and Discussion

References

Section VI. Nucleotide Biosynthesis

Orotidylate Decarboxylase of Yeast and Man

I. Introduction

II. UMP Synthase, a Bifunctional Animal Protein Having Orotate Phosphoribosyltransferase and Orotidylate Decarboxylase Activities

III. Mechanism of Reaction Catalyzed by Orotidylate Decarboxylase

IV. Summary

References

Nucleoside Diphosphokinase: A Functional Link Between Intermediary Metabolism and Nucleic Acid Synthesis

I. Metabolic Roles of Nucleoside Diphosphokinase

II. Purification and Properties of Nucleoside Diphosphokinase from Escherichia coli

III. Progress Toward Cloning and High-Level Expression of the Escherichia coli ndk Gene

IV. Future Directions

Note Added in Proof

References

Section VII. Theoretical Analysis Of Metabolism In Organized States

Enzyme Organization and the Direction of Metabolic Flow: Physicochemical Considerations

I. Enzyme Organization and Cellular Microenvironments

II. Homogeneous Versus Heterogeneous Catalysis

III. Diffusional Transit and Channeling

IV. Free-Energy Transduction in Organized Enzyme Systems

V. Quantification of Metabolic Control in Vivo

VI. Concluding Remarks

References

Mechanisms of Metabolite Transfer Between Enzymes: Diffusional Versus Direct Transfer

I. Introduction

II. Dehydrogenases: Diffusional Versus Direct Transfer

III. Two- and Three-Enzyme Pathways

IV. Concluding Remarks

References

Section VIII. Bioengineering Applications

Molecular Studies on Trypanothione Reductase: An Antiparasitic Target Enzyme

I. Introduction: A Parasitic Analog of Glutathione

II. Mechanistic Studies on Trypanothione Reductase

III. Concluding Remarks

References

"Designer Membranes": Construction of a Cell Containing Multiple Membrane-Bound Cytochromes P450

I. Introduction

II. Cytochromes P450 and Their Role in Steroidogenesis

III. Expression of Cytochromes P450 in COS Cells

IV. Concluding Remarks

References

Index