Gapdh: Biological Properties and Diversity

ISBN-13: 9789402406290 / Angielski / Miękka / 2016 / 295 str.

Norbert W. Seidler

Recenzje

From the book reviews:

"The biochemical, physiological, and metabolic roles of GAPDH is discussed starting with the cell membrane and ionic mechanisms of glycolysis, energetics, and the TCA cycle. This is a book which should explore in greater detail the effects on blood brain barrier and CNS metabolism. I do however, highly recommend this book to physiologists and biochemists. Graduate students and postdocs will probably find this a very good discussion of GAPDH." (Joseph J. Grenier, Amazon.com, August, 2014)

Spis treści

1. Basic Biology of GAPDH
1.1   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   Pseudogenes
1.2   Regulation of GAPDH Expression
   1.2.1   Tissue Specificity
   1.2.2   Electronic Databases
   1.2.3   Cancer
1.3   Cellular Levels of GAPDH
1.4   Oxidoreductase Activity of GAPDH
   1.4.1   Mechanism of Catalysis
   1.4.2   Kinetic Parameters
1.5   Protein Architecture of GAPDH 
   1.5.1   Asymmetric Homotetramer 
   1.5.2   Dinucleotide Binding Domain
   1.5.3   Catalytic Domain

2. GAPDH and Intermediary Metabolism
2.1   GAPDH, the Glycolytic Lynch-Pin
   2.1.1   Metabolic Switch
2.1.2          Glycolytic Tissues
   2.1.3   Anaerobic Glycolysis
2.2   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 Protocol
2.3   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 Brain
2.4   Comparative Analysis
   2.4.1   Structure-Function of NAD⁺-Binding
   2.4.2   Sequence Homology

3. Compartmentation of GAPDH
3.1   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 Compartmentation
3.2   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 Receptor
3.3   Translocation to the Nucleus
3.4   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   Mitochondria
3.5   Dendrites, Axons and Synapses
   3.5.1   Synaptic Vesicles
      3.5.1.1   Glutamate Uptake into Vesicles
   3.5.2   Post-Synaptic Density
3.6   Specialized Compartment for Spermatogenic GAPDH

4. Functional Diversity
4.1   Classical Example of Protein ‘Moonlighting’ 
   4.1.1   Evolutionary Considerations
   4.1.2   Molecular Mechanisms
4.2   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   Autophagy
4.3   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 Cycles

5. GAPDH, as a Virulence Factor
5.1   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 albicans
5.2   GAPDH, as a Pathogenic Secretory Protein
5.3   Mining the Antigenic Properties of GAPDH
   5.3.1   In Search of a Vaccine for Mycoplasma bovis
   5.3.2   Tracking the Course of Candidiasis
5.4    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 Mechanisms

6. Target for Diverse Chemical Modifications
6.1   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-Sulfhydration
6.3   Proposed Models for Cellular Decline
   6.3.1   Blocking Cellular Chaperonins
   6.3.2   Dehydration Model
6.4   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   ISGylation

7. Dynamic Oligomeric Properties
7.1   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 Denaturants
7.2   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 Nucleotides
7.3   Comparative Analysis
   7.3.1   Tetrameric Hybrids
   7.3.2   Adenosine Binding Site
7.4   Domain Exchange
   7.2.1   Human Serum Albumin as a Model
   7.3.2   Other Model Proteins
   7.3.3   Proposed Oligomeric Dynamics of GAPDH

8. Multiple Binding Partners
8.1   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 Interactome
8.2   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   Cataracts
8.3   Multiple Catalytic Functions
   8.3.1   Peroxidase Activity
   8.3.2   S-Nitrosylase Activity
   8.3.3   Kinase Activity   8.3.4   ADP-Ribosylase Activity

9. GAPDH in Anesthesia
9.1   Is Anesthesia Mediated by GAPDH?
   9.1.1   GABA_A Receptor
   9.1.2   GAPDH Regulates GABA_A Receptor
   9.1.3   Proposed Mechanism of Action of Inhaled Anesthetics
9.2   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 Metabolites
9.3   GAPDH and Isoflurane Preconditioning
   9.3.1   The Phenomenon of Anesthetic Preconditioning
   9.3.2   Dehydration-Induced Protein Misfolding   

Blurb

GAPDH (glyceraldehyde 3-phosphate dehydrogenase) is more than just a glycolytic enzyme. An unprecedented amount of literature demonstrates that GAPDH has an astounding multiplicity of function. This diversity is not simply due to cell compartmentation (i.e. redistributing glycolytic energy to where it is needed), although this feature is undoubtedly important and discussed in the book. GAPDH integrates glycolysis with other cellular processes. This concept of integration cannot be understated. But, there is more.

GAPDH actively participates in numerous non-glycolytic cellular events that fall into very broad categories including the cell infrastructure and the transmission of genetic information. Some of GAPDH’s biological properties are completely non-intuitive given the current undergraduate textbook understanding of this glycolytic enzyme. For example, GAPDH binds to select phospholipids and catalyzes organelle biogenesis. It has fusogenic properties, enabling it to be actively involved in nuclear envelop reassembly, autophagy and membrane trafficking. Human macrophages exhibit surface-localized GAPDH with receptor function. As scientists, we are trained to consider GAPDH as a soluble cytosolic dehydrogenase enzyme. The literature observations - as described in this book - tell us something quite different. Besides oxidoreductase activity, GAPDH exhibits peroxidase, uracil DNA glycosylase, nitrosylase, mono-ADP-ribosylase, esterase and phosphotransferase activity. GAPDH binds membrane transport proteins, G-proteins, poly-nucleotides, adenines, specific lipids, select carbohydrates, cytoskeletal proteins, nuclear import and export proteins, diverse ATPases, molecular chaperones and other molecules.