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The chemical biology of phosphorus / Christopher T. Walsh. -- Cambridge : Royal Society of Chemistry, 2021. – (54.4152/W223) |
Contents
Section I Introduction to Phosphorus and Inorganic Phosphates
Chapter I Introduction to Phosphorus Chemical Biology
1.1 The Element: Discovery, Abundance, Valence States
1.2 Chemical Biology of Phosphorus
1.3 Inorganic Pyrophosphate
1.4 Phosphoric Anhydride Side Chains in ATP, NTPs, and 2’deoxyNTPs
1.5 Families of Thermodynamically Activated Phosphoryl Derivatives
1.6 Phosphomonoesters: Alcohols as Nucleophiles in Phosphoryl Transfers
1.7 Phosphodiesters: Alcohols as Nucleophiles in Nucleotidyl Transfers
1.8 Phosphonates, Phosphoramidates, and Phosphorothioates
1.9 Phosphoproteomics
1.10 Phosphoryl Groups: Kinetic vs. Thermodynamic Stability
1.11 The Structure of This Book
References
Chapter 2 Inorganic Phosphate, Pyrophosphate, and Polyphosphate
2.1 Inorganic Phosphate Bodily Levels
2.2 Inorganic Phosphate Transport
2.3 Hydroxyapatite Formation and Deposition by Osteoblasts During Bone Formation
2.4 Inorganic Pyrophosphate: The Simplest Inorganic Phosphoric Anhydride
2.5 Thermodynamic Activation Balanced by Useful Kinetic Stability
2.6 Thermodynamically Favored Enzymatic Hydrolysis Drives Otherwise Unfavorable Cellular Equilibria
2.7 From Triphosphates to Long Inorganic Polyphosphates
2.8 Organic Pyrophosphate Scaffolds. Monosubstituted Organic Pyrophosphate Metabolites: Incorporation of Inorganic Phosphate and Pyrophosphate Groups into Organic Scaffolds Enables a Wide Range of Chemistries in Energy Metabolism
2.9 Overview
2.10 Disubstituted Organic Pyrophosphate Linkages
References
Section II ATP and Nucleoside Triphosphate Congeners: Substrates for Phosphoryl-, Pyrophosphoryl-, and Nucleotidyl Transferases
Chapter 3 ATP as the Premier Biological Phosphoryl Transfer Reagent
3.1 Phosphoryl Group Transfers under Enzymatic Control
3.2 Timing and Mechanism of Phosphoryl Group Transfers
3.3 Phosphoryl Group Transfers from Mg-ATP: Electrophilic γ-P032- in Flight
3.4 ATP: Daily Human Consumption Equal to Total Body Weight
3.5 Phosphoryl Transfers from ATP: Logic and Mechanisms
3.6 ATPases and Coupled Equilibria
3.7 Transmembrane ATPases
3.8 AAA Proteins: A Plethora of ATPase Domains Coupled to Diverse Functions
3.9 Beyond ATPases: GTPases as Conditional Hydrolases Coupled to Multiple Forms of Cellular Work
3.10 Mg-ATP Bidentate Coordination Complexes are the Immediate Forms of ATP, GTP, and other NTP Substrates
References
Chapter 4 Nucleotidyl Transfers (ATP and NTP's)
4.1 Adenylyl and Nucleotidyl Transfers
4.2 Aminoacyl tRNA Synthetases
4.3 Nucleotidyl Transfers in Each Step of RNA Chain Elongation
4.4 Equivalent 2’dXMP Transfers in Every Chain Elongation Step of DNA Polymerization
4.5 DNA Ligases
4.6 RNA Splicing
4.7 Cyclic Nucleotides: Intramolecular and Intermolecular Nucleotidyl Transfers
4.8 Isoamide Anions as Nucleophiles in Nucleotidyl Transfers
4.9 Tandem Phosphoryl and Nucleotidyl Transfers
4.10 Summary
References
Chapter 5 Pyrophosphoryl and Adenosyl Transfers from Mg-ATP
5.1 Pyrophosphoryl Transfers
5.2 Tandem Phosphorylations as An Alternative Strategy to Pyrophosphorylation
5.3 Adenosyl Transfers
References
Chapter 6 Activated Phosphoryl Groups and Biosynthetic Paths to ATP
6.1 The Spectrum of Biologically Activated Phosphoryl Groups
6.2 Three Ways to Make ATP: Acyl Phosphates, Enol Phosphates, and Coupled Proton Gradients
References
Chapter 7 phosphomonoesters: Enzymatic Formation and Decomposition
7.1 Phosphomonoesters: Formation, Function, Hydrolysis
7.2 Phosphoglucomutase: Connecting Glycolysis to Hexose Oligomerizations
7.3 PEP Activated for P-O or C-O Bond Cleavage
7.4 Phosphorylated Lipids
7.5 Phosphatases: Hydrolysis of Phosphate Monoesters
References
Section III Types of Phosphorylated Metabolites and Metabolic Logic
Chapter 8 Phosphodiesters and Phosphotriesters
8.1 Phosphodiesterases as Nucleases
8.2 Phosphodiesterase/Nuclease Cleavage Regiospecificity
8.3 Ribonucleases
8.4 Polynucleotide Phosphorylase: A Two-way Enzyme
8.5 Sequence-specific DNA Restriction Endonucleases Make Double Strand Cuts
8.6 CRISPR-CAS9: Another Bacterial Defense Strategy Involving Specific Double Strand Cuts of Foreign DNA
8.7 Type II Topoisomerases
8.8 Cyclic Nucleotide Phosphodiesterases
8.9 Cyclic Dinucleotide Phosphodiesterases
8.10 Phospholipases C and D
8.11 Phosphotriesters and Phosphotriesterases
References
Chapter 9 Phosphorylases: Inorganic Phosphate as Oxygen Nucleophile
9.1 Phosphate Anion as Oxygen Nucleophile
9.2 Equilibrating Acyl Thioesters and Acyl Phosphates
9.3 Polynucleotide Phosphorylase
9.4 Phosphorylase Summary
References
Chapter 10 N-P Bond Chemical Biology
10.1 N-Phosphoryl Proteinogenic Amino Acids
10.2 phosphagens and Phosphoramidates
10.3 Phosphoramidate Nomenclature
10.4 N-phospho-asparaginyl Residue in Microcin C7 Maturation
10.5 N-Phospho-glutamine and Tailoring of C. jejuni Capsular Polysaccharide
10.6 Nucleotide Phosphoramidates: Transfer of a Phosphoramidinyl Group
10.7 Talopeptin/Phosphoramidon: α-Aminokinase Action
10.8 Phosphoramidites in Synthetic Oligonucleotide Chemistry
References
Chapter 11 C-P Bonds in Biology: Phosphonates and phosphinates
11.1 C-P Bonds: Naturally Occurring Phosphonates
11.2 PEP Mutase: The Singular Route to C-P Bonds
11.3 Phosphonate Metabolism I
11.4 Phosphonate Metabolism II: A Route to Phosphinates in Phosphinothricin Biosynthesis: Phosphinates as Carboxylate Isosteres
11.5 Cleaving C-P Bonds
References
Chapter 12 P-S Bonds: Phosphorothioates
12.1 Phosphorothioates/Thiophosphates
12.2 Inorganic Thiophosphate: Not a Known Metabolite
12.3 Phosphorothioate Monoesters and Diesters
12.4 Stereochemical Inversion at Phosphorus in Enzymatic Nucleotidyl Transfers
12.5 Stereochemical Inversion at Phosphorus in Phosphoryl Transfers
12.6 Naturally Occurring DNA-based Phosphorothioates
12.7 Oxygenative Conversion of Parathion to Paraoxon
12.8 Synthetic Phosphorothioate Oligonucleotides and the Problem of Chirality Control
12.9 Thiophosphoryl Enzyme Intermediates
References
Section IV Phosphoproteomics
Chapter 13 Scope and Roles of Posttranslational Protein Phosphorylations
13.1 Proteomics
13.2 Phosphoproteomics: Version 1.0
13.3 How do Phosphate Groups Have Their Effects in Proteins
13.4 Nine of Twenty Protein Residues Can Be Phosphorylated
13.5 Criteria for Phosphoproteomics 2.0
References
Chapter 14 Noncanonical Phosphoproteomes
14.1 Types of Phosphate Scaffolds in Biology
14.2 The N-phosphoproteomes: Phosphohistidine Residues
14.3 Arginine Phosphoramidates in Proteins
14.4 N-phospho-lysine Protein Residues
14.5 S-phosphocysteinyl Proteomes
14.6 Acyl Phosphates in Phosphoproteomes
References
Chapter 15 Canonical Phosphoproteomics: Phosphoserine, Phosphothreonine, and Phosphotyrosine
15.1 Scope of the Canonical Phosphoproteome
15.2 Phosphoserine, Phosphothreonine and Phosphotyrosine are Chemically Stable Phosphomonoesters
15.3 Consequences of Phosphate Monoester Chemical Stability
15.4 The Human Kinome
15.5 "Cascades" of Protein Kinase Activation from Outside In: Cell Surface to Cytoplasm and Nucleus
15.6 Phosphoserine and Phosphotyrosine Binding Domains
15.7 Visualization of Binding Pockets for p-Thr, P-Ser, and P-Tyr in Protein Partner Domains
15.8 FDA-approved Protein Kinase Inhibitors
15.9 Phosphoprotein Phosphatases: Two Limiting Strategies for Specificity
References
Chapter 16 Noncanonical Phosphoproteomics - II
16.1 Noncanonical Adducts in a Broadened View of Phosphoproteomics
16.2 Cryptic Phosphoserines in Lanthipeptide Formation
16.3 Nucleotidyl Transfers to Thr and Tyr Side Chains: Protein AMPylations
16.4 Transfers of Phosphorylcholine to Proteins
16.5 Covalent Tethering of Atg8 to Autophagosomal Membranes
16.6 NAD+ as a Donor of Electrophilic Fragments to Protein Side Chains: Proteomic Roles
References
Chapter 17 Broad Biological Arcs from Only Four Types of Phosphate Molecules
17.1 The Simplicity of Phosphate Chemistry in Biological Systems: Inorganic Phosphate, Phosphoric Anhydrides, Phosphate Monoesters, Phosphate Diesters
17.2 Phosphate Involvement by Metabolite Category
17.3 Glucokinase Regiochemistry Connected to Directionality of RNA and DNA Polymerase Replication and Transcription
Subject Index
