GAPDH: Biological Properties and Diversity (eBook)

1. Basic Biology of GAPDH1.1   The GAPDH Gene   1.1.1   Coding Region   1.1.2   Promoter Sequence      1.1.2.1   Hypoxia-Responsive Elements      1.1.2.2   Basal Level Expression      1.1.2.3   Glutamine-Responsive Elements   1.1.3   Testes-Specific Isoform   1.1.4   Pseudogenes1.2   Regulation of GAPDH Expression   1.2.1   Tissue Specificity   1.2.2   Electronic Databases   1.2.3   Cancer1.3   Cellular Levels of GAPDH1.4   Oxidoreductase Activity of GAPDH   1.4.1   Mechanism of Catalysis   1.4.2   Kinetic Parameters1.5   Protein Architecture of GAPDH    1.5.1   Asymmetric Homotetramer    1.5.2   Dinucleotide Binding Domain   1.5.3   Catalytic Domain 2. GAPDH and Intermediary Metabolism2.1   GAPDH, the Glycolytic Lynch-Pin   2.1.1   Metabolic Switch 2.1.2          Glycolytic Tissues   2.1.3   Anaerobic Glycolysis2.2   Determining GAPDH Activity   2.2.1   Chemical Inhibitors   2.2.2   Measurement of Glycolytic Flux   2.2.3   Oxidoreductase Activity of GAPDH      2.2.3.1   Conditions of Assay      2.2.3.2   Assay Protocol2.3   Role of GAPDH Metabolites   2.3.1   Counter-Catalytic Activity   2.3.2   Controlling NADH levels   2.3.3   Phosphocreatine, as a Competitive Inhibitor   2.3.4   Metabolic Parameters in the Brain2.4   Comparative Analysis   2.4.1   Structure-Function of NAD+-Binding   2.4.2   Sequence Homology3. Compartmentation of GAPDH3.1   Compartmentation of Glycolytic Energy   3.1.1   Microzones of Cellular ATP   3.1.2   Focal Regulation of NAD+/NADH Ratios   3.1.3   Channeling of Metabolites   3.1.4   Non-Glycolytic Compartmentation3.2   Binding to the Plasma Membrane   3.2.1   SLC4 Anion Exchanger      3.2.1.1   Band 3 in Erythrocytes      3.2.1.2   Kidney AE1 Isoform   3.2.2   Na+/K+-ATPase   3.2.3   ATP-sensitive K+-Channel   3.2.4   Glucose Transporters      3.2.4.1   GLUT1 Transporter in Erythrocytes      3.2.4.2   GLUT4 Transporter   3.2.5   GABA (type A) Receptor   3.2.6   GAPDH, as a Lactoferrin Receptor3.3   Translocation to the Nucleus3.4   Other Non-Cytosolic Destinations   3.4.1   Clathrin-Coated Vesicles    3.4.2   Golgi Apparatus and Endoplasmic Reticulum    3.4.3   Sarcoplasmic Reticulum   3.4.4   Mitochondria3.5   Dendrites, Axons and Synapses   3.5.1   Synaptic Vesicles      3.5.1.1   Glutamate Uptake into Vesicles   3.5.2   Post-Synaptic Density3.6   Specialized Compartment for Spermatogenic GAPDH 4. Functional Diversity4.1   Classical Example of Protein ‘Moonlighting’    4.1.1   Evolutionary Considerations   4.1.2   Molecular Mechanisms4.2   Structural Organization of the Cell   4.2.1   Cytoskeletal Components      4.2.1.1   Actin Filaments      4.2.1.2   Microtubules   4.2.2   Organelle Biogenesis      4.2.2.1   Triadic Junction      4.2.2.2   Nuclear Envelope      4.2.2.3   Vesicle Recycling/Membrane Fusion      4.2.2.4   Cell Polarization      4.2.2.5   Golgi and Endoplasmic Reticulum   4.2.3   Autophagy4.3   Transmission of Genetic Information   4.3.1   RNA      4.3.1.1   mRNA      4.3.1.2   Polyribosomes      4.3.1.3   tRNA      4.3.1.4   RNA viruses   4.3.2   Gene Expression   4.3.3   DNA Repair 4.4   Signal Transduction Networks   4.4.1   Nitric Oxide   4.4.2   Unfolded Protein Response   4.4.3   Peroxide Stress   4.4.4   PI3K/Akt/mTOR Signaling   4.4.5   Light and Dark Cycles5. GAPDH, as a Virulence Factor5.1   Surface-Localized GAPDH in Pathogenic Organisms   5.1.1   Streptococcal Microorganisms      5.1.1.1   Group A Streptococcus      5.1.1.2   Other b-Hemolytic Streptococci      5.1.1.3   a-Hemolytic Streptococci   5.1.2   Mycoplasmas   5.1.3   Candida albicans5.2   GAPDH, as a Pathogenic Secretory Protein5.3   Mining the Antigenic Properties of GAPDH   5.3.1   In Search of a Vaccine for Mycoplasma bovis   5.3.2   Tracking the Course of Candidiasis5.4    Pathogenic Mechanisms of Action   5.4.1   Molecular Mimicry and Immune Modulation   5.4.2   Virulence Maintenance   5.4.3   Phagocytic Strategy   5.4.4   Pathogenic Receptor for Host Plasminogen   5.4.5   Adhesive Functions in Pathogen-Host Interaction   5.4.6   Viral Mechanisms6. Target for Diverse Chemical Modifications6.1   Post-Translational Protein Modification    6.1.1   GAPDH Isozymes      6.1.1.1   Early Investigations      6.1.1.2   Current Observations      6.1.1.3   Organisms with GAPDH Isozymes   6.1.2   Auto-Catalytic Processes         6.1.3   Enzymatic Modifications of GAPDH 6.2   Susceptibility to Stochastic Chemical Modifications   6.2.1   Oxidation of Active Site Cysteine      6.2.1.1   Disulfide Bond Formation      6.2.1.2   Sulfhydryl to Sulfenic Acid   6.2.2   Succination of Active Site Cysteine   6.2.3   Nitration   6.2.4   Glycation   6.2.5   Lipid Peroxidative Byproducts   6.2.6   S-Sulfhydration6.3   Proposed Models for Cellular Decline   6.3.1   Blocking Cellular Chaperonins   6.3.2   Dehydration Model6.4   Proposed Models for Cell Survival   6.4.1   New and Old Perspectives      6.4.1.1   Continuity in Cell Funcion      6.4.1.2   Linkage to Energy Metabolism      6.4.1.3   Sensor of Chemical Stressors   6.4.2   S-Thiolation   6.4.3   ISGylation7. Dynamic Oligomeric Properties7.1   Factors affecting Stability   7.1.1   Cooperativity   7.1.2   Temperature      7.1.2.1   Testing Anti-Aggregation Agents      7.1.2.2   Folding Accessory Proteins   7.1.3   Chemical Denaturants7.2   Factors affecting Oligomerization   7.2.1   Storage (in vitro Aging)   7.2.2   Chemical Modification      7.2.2.1   Maleylation      7.2.2.2   Acetylation      7.2.2.3   Pyridoxal Phosphate      7.2.2.4   Carbamylation      7.2.2.5   Succinic Anhydride      7.2.2.6   Cross-Linking Agents   7.2.3   Substrates and Coenzymes   7.2.4   Chloride Ions   7.2.5   Adenine Nucleotides7.3   Comparative Analysis   7.3.1   Tetrameric Hybrids   7.3.2   Adenosine Binding Site7.4   Domain Exchange   7.2.1   Human Serum Albumin as a Model   7.3.2   Other Model Proteins   7.3.3   Proposed Oligomeric Dynamics of GAPDH8. Multiple Binding Partners8.1   The Interactome   8.1.1   Emerging Mechanisms    8.1.2   Role of Acidic Dipeptide Sequences   8.1.3   Criteria for Interactive Partner   8.1.4   Glycolytic Interactome8.2   Proteins associated with Neurodegenerative Diseases    8.2.1   Alzheimers Disease: Amyloid-b Peptide and Tau    8.2.2   Parkinsons Disease: a-Synuclein   8.2.3   Proteins with Tracts of Polyglutamine Repeats   8.2.4   Cataracts8.3   Multiple Catalytic Functions   8.3.1   Peroxidase Activity   8.3.2   S-Nitrosylase Activity   8.3.3   Kinase Activity   8.3.4   ADP-Ribosylase Activity9. GAPDH in Anesthesia9.1   Is Anesthesia Mediated by GAPDH?   9.1.1   GABAA Receptor   9.1.2   GAPDH Regulates GABAA Receptor   9.1.3   Proposed Mechanism of Action of Inhaled Anesthetics9.2   Binding of Inhaled Anesthetics   9.2.1   Anesthetic Binding Site   9.2.2   Human Serum Albumin as a Model Protein   9.2.3   Other Model Proteins   9.2.4   Adenine Metabolites9.3   GAPDH and Isoflurane Preconditioning   9.3.1   The Phenomenon of Anesthetic Preconditioning   9.3.2   Dehydration-Induced Protein Misfolding