Preface
Contents
Chapter 1: Structure and Function of the Stressosome Signalling Hub
1.1 Introduction
1.1.1 Environmental Sensing and Signalling in Bacteria
1.1.2 B. subtilis σB Partner Switching Cascade
1.1.3 RsbRST Module Distribution
1.1.4 Chapter Outline
1.2 Stressosome Components
1.2.1 Stressosome Composition
1.2.2 Structure of RsbS
1.2.3 Structure of RsbR
1.2.4 Structure of YtvA
1.2.5 Structure of RsbT
1.2.6 Structure of RsbX
1.3 Stressosome Complexes
1.4 Production of Recombinant B. subtilis Stressosomes for Structural Analysis
1.4.1 RsbR/RsbS Binary Complex
1.4.2 RsbR/S/T Ternary Complex
1.5 Cryo-EM Structure of the Bacillus subtilis Stressosome
1.5.1 RsbR/RsbS Core Structure
1.5.2 RsbR/RsbS Structure
1.5.3 RsbR/RsbS/RsbT Ternary Complex
1.5.4 Pseudo-atomic Model of the B. subtilis Stressosome
1.5.5 Other Stressosomes
1.6 Structure/Function Relationships in Stressosomes
1.6.1 Activation
1.6.2 Stressosome Signalling Response
1.6.3 Phosphorylation Dynamics of Stressosome
1.7 Evolution of the Stressosome Signalling Pathway
1.7.1 Structure and Conservation of the Stressosome Gene Cluster
1.7.2 Evolution of the Stressosome
1.7.3 Stressosome Function in Other Organisms
1.8 Conclusions
References
Chapter 2: The Canonical Inflammasome: A Macromolecular Complex Driving Inflammation
2.1 Introduction
2.2 The Major Constituents of the Inflammasome
2.2.1 The Receptors
2.2.1.1 NLRP Family Members
2.2.1.2 NAIP
2.2.1.3 AIM2
2.2.2 The Adaptors
2.2.2.1 ASC
2.2.2.2 NLRC4
2.2.3 The Effectors
2.2.3.1 Caspase-1
2.2.3.2 Caspase-8
2.3 The Initiation of Inflammasome Activation and Assembly
2.3.1 The NLRP1 Inflammasome
2.3.2 The NLRP3 Inflammasome
2.3.3 The NAIP/NLRC4 Inflammasome
2.3.4 The AIM2 Inflammasome
2.4 The Mechanism of Inflammasome Assembly
2.4.1 Formation of Helical Wheels
2.4.2 Assembly of Filament Fragments
2.4.3 When and Where Does the Inflammasome Assemble?
2.5 How Is the Inflammasome Regulated?
2.5.1 Receptor Auto-inhibition
2.5.2 Accessory Proteins
2.5.2.1 Pyrin Only Proteins
2.5.2.2 CARD Containing Proteins
2.5.3 Post-translational Modifications
2.5.3.1 Phosphorylation
2.5.3.2 Ubiquitination
2.5.4 NEK7
2.5.5 Chemical Regulation
2.6 Concluding Remarks
References
Chapter 3: The Ferritin Superfamily
3.1 Introduction
3.2 Structural Overview of Ferritins
3.2.1 Mechanism of Ferritin Self-Assembly
3.2.2 Structural Variety Amongst the Catalytic Ferroxidase Centers of Ferritins
3.2.2.1 The H-Chain-Type Ferroxidase Centers
3.2.2.2 Bacterial Ferritin Ferroxidase Centers
3.2.2.3 Bacterioferritin Ferroxidase Centers
3.2.3 Structural Variety in the Three and Fourfold Channel Amongst Ferritins (Possible Role of the B-Channel)
3.3 Mechanistic Variations in Mineralization Amongst Ferritins
3.3.1 Mechanism of Iron Release in Ferritin
3.4 Application of the 24-mer Ferritin
3.5 Concluding Remarks
References
Chapter 4: Antibody Recognition of Immunodominant Vaccinia Virus Envelope Proteins
4.1 Vaccinia Virus
4.2 IMV Antigen A27
4.2.1 Anti A27 MAbs
4.2.2 Crystal Structure of the A27peptide31–40 -1G6 Complex
4.2.3 Crystal Structure of the A27peptide101–110 -8E3 Complex
4.3 EEV Antigen A33
4.3.1 Anti A33 MAbs
4.3.2 Crystal Structure of the A33-A2C7 Complex
4.3.3 Crystal Structure of the A33-A20G2 Complex
4.3.4 Crystal Structure of the A33-A27D7 Complex
4.4 IMV Antigen D8
4.4.1 Anti D8 Antibodies
4.4.2 Crystal Structure of the D8-LA5 Complex
4.4.3 Possible Function of LA5
4.5 IMV Antigen L1
4.5.1 Anti L1 Antibodies
4.5.2 Crystal Structure of the L1-7D11 Complex
4.5.3 Crystal Structure of the L1-M12B9 Complex
4.5.4 7D11 Versus M12B9 Comparison
4.6 Concluding Remarks
References
Chapter 5: The Peroxiredoxin Family: An Unfolding Story
5.1 Peroxiredoxins and Their Classification
5.2 The Multifaceted Roles of Prxs
5.3 The Prx Active Site and Reactivity of the Peroxidatic Cysteine
5.4 Hyperoxidation of Prxs and Sulfiredoxin Mediated Reactivation
5.5 Role of Hyperoxidised Prxs in H2O2-Mediated Signalling
5.6 Alterations in Oligomeric State and Chaperone-Like Functions
5.7 Concluding Remarks
References
Chapter 6: α2-Macroglobulins: Structure and Function
6.1 Introduction
6.2 Evolutionary Origin
6.3 Structural Aspects of α2Ms
6.3.1 Primary Structure, Sequence Motifs and Post-translational Modifications
6.3.2 Secondary Structure Conservation and Domain Organization
6.3.3 Tertiary Structure and Conformational Changes During Induction
6.3.3.1 Early Studies
6.3.3.2 From Tetramers to Monomers and Vice-Versa
6.3.3.3 Conserved Multi-domain Structure
6.3.3.4 Apertures and Prey-Trapping Chambers
6.3.3.5 Mechanisms of Peptidase Entrapment
6.3.4 Bait Region and Bait-Region Domain
6.3.5 The Reactive β-Cysteinyl γ-Glutamyl Thioester Bond
6.3.6 Receptor Recognition and Endocytosis
6.4 Role of α2Ms in the Control of Proteolytic Activity
6.5 Other Physiological Functions
6.6 Conclusions
References
Chapter 7: The Structure and Function of the PRMT5:MEP50 Complex
7.1 Introduction
7.2 Diverse Functions of PRMT5
7.3 Role of MEP50
7.4 Structure of the Heterooctameric PRMT5:MEP50 Complex
7.5 Summary
References
Chapter 8: Symmetry-Directed Design of Protein Cages and Protein Lattices and Their Applications
8.1 Introduction
8.2 Natural Protein Assemblies
8.3 Applications of Natural Protein Assemblies
8.3.1 Functionalization of Protein Cages
8.3.2 Functionalization of S-Layer proteins
8.4 Design of de novo Protein Assemblies
8.4.1 Conceptual Approaches to Protein Assembly
8.4.2 Extended Assemblies – Designed Fibers and Lattices
8.4.3 Discrete Assemblies – Designed Protein Cages
8.5 Conclusions
References
Chapter 9: Structure and Function of RNA Polymerases and the Transcription Machineries
9.1 Multisubunit RNA Polymerases – Discovery of the Enzymes and Their Role Within the Central Dogma of Life
9.2 Multisubunit RNA Polymerases and Transcription Factors in the Three Domains of Life
9.2.1 Overall Subunit Composition and Architecture of RNA Polymerase in Bacteria, Eukaryotes and Archaea
9.2.2 Transcription Factors of RNA Polymerases in Bacteria, Eukaryotes and Archaea
9.2.2.1 Initiation Factors
9.2.2.2 Elongation Factors
9.3 Structural Dynamics of RNA Polymerase Throughout the Transcription Cycle
9.3.1 Overview
9.3.2 Initiation
9.3.2.1 Bacteria
9.3.2.2 Archaea
9.3.2.3 Eukaryotes
9.3.3 Elongation
9.3.3.1 Promoter Clearance
9.3.3.2 Overview of the RNA Polymerisation Reaction
9.3.3.3 The Nucleotide Addition Cycle
9.3.3.4 Dynamics of Elongation
9.3.3.5 Function of TFIIF-, Spt4/5- and TFIIS-Related Elongation Factors
9.3.4 Termination
References
Chapter 10: Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution
10.1 Background
10.1.1 Enzymes Are Often Oligomeric
10.1.2 Lysine Biosynthesis – A Model System for Quaternary Structure
10.2 Dihydrodipicolinate Synthase: Structure and Mechanism
10.2.1 Structure
10.2.2 Catalytic Mechanism
10.2.3 Mechanism of Allosteric Regulation
10.3 4-Hydroxy-2-oxoglutarate Aldolase – The New Kid on the Block
10.4 Evolution of Dihydrodipicolinate Synthase Quaternary Structure
10.5 Conclusion
References
Chapter 11: “Pyruvate Carboxylase, Structure and Function”
11.1 Introduction
11.2 Biotin-Dependent Carboxylases
11.3 Physiological Role of Pyruvate Carboxylase
11.3.1 Metabolic Activity of PC
11.3.2 PC and Human Disease
11.4 Enzymatic Reactions Catalyzed by PC
11.5 Atomic Structure
11.5.1 Structural Domains in PC Subunit
11.5.2 Quaternary Structures and the Allosteric (AL) Domain
11.5.3 Structural Insights of BCCP Domain Interaction with Active Sites
11.5.3.1 Interaction of Biotin-BCCP with the BC Active Site
11.5.3.2 Interaction of Biotin-BCCP with the CT Active Site
11.5.3.3 BCCP Domain Traveling Between Reaction Centers
11.6 Allosteric Control of PC
11.6.1 Communication Between BC Domains
11.6.2 Allosteric Activator Acetyl-CoA
11.7 Quaternary Structure of PC in Solution
11.7.1 CryoEM of SaPC
11.7.2 Observing SaPC by cryoEM During Catalysis
11.8 A Model for PC Enzyme Functioning
References
Chapter 12: Cullin-RING E3 Ubiquitin Ligases: Bridges to Destruction
12.1 Introduction: Overview and Function of CRLs
12.1.1 CRL1 Defines the Prototypical CRL
12.1.2 CRL2 and CRL5: The Same Adaptor, Different Substrate Receptors
12.1.3 CRL3: Integrating Adaptors and Substrate Receptors to Target One or Two Copies of a Substrate
12.1.4 CRL4: Propellers Drive Assembly
12.2 Regulation of CRLs
12.2.1 Neddylation Activates CRLs Through Conformational Change at the Cullin-RING Interface
12.2.2 CAND1 Acts as an Adaptor Protein Exchange Factor
12.2.3 Glomulin Sterically Blocks Rbx1-E2 Interactions
12.3 Viral Hijacking of CRLs: Turning the Cellular Machinery Against Itself
12.3.1 Paramyxoviruses and Hepatitus B Virus Utilizes CRL4 for Successfully Infection
12.3.2 SIVs Employ Vpx to Suppress SAMHD1 Via CRL4
12.3.3 HIV-1 Vif Downregulates the Immune Response by Targeting APOBEC3 Proteins to a CRL5
12.4 Therapeutic Targeting of CRL
12.4.1 Inactivation of Neddylation by MLN4924
12.4.2 Small-Molecule Subversion of CRL Targeting by PROTACs
12.5 Future Perspectives
References
Chapter 13: The Ccr4-Not Complex: Architecture and Structural Insights
13.1 Introduction
13.2 Composition of the Ccr4-Not Complex
13.3 Architecture of the Ccr4-Not Complex
13.4 The Ccr4-Not Complex Consists of Different Functional Modules
13.4.1 The Not2-Not5 Heterodimer
13.4.1.1 Physiological Relevance of the NOT Module
13.4.1.2 Molecular Mechanism of NOT Module Action
13.4.1.3 Structure of the Not Module
13.4.2 The Ubiquitylation Module
13.4.2.1 Pysiological Role of Not4
13.4.2.2 Molecular Mechanism of Not4 Action
13.4.2.3 Structure of the Ubiquitination Module
13.4.3 Caf40
13.4.3.1 Physiological Relevance of Caf40
13.4.3.2 Molecular Mechanism of Caf40 Action
13.4.3.3 Structure of the Caf40 Module
13.4.4 The Ccr4-Caf1 Nuclease Module
13.4.4.1 Physiological Roles of Ccr4 and Caf1
Ccr4
Caf1
13.4.4.2 Molecular Mechanism of Ccr4 and Caf1 Action
13.4.4.3 Structures of the Ccr4 and Caf1 Deadenylases
13.4.5 Non-conserved Ccr4-Not Subunits
13.5 Additional Structural Information
13.6 Perspectives
References
Chapter 14: Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes
14.1 Introduction
14.2 Functional and Genetic Organisation of TA Systems
14.3 Structural Hierarchy of the VapBC TA Systems
14.4 Overall TA Complex Architecture
14.5 The Stoichiometry of VapB Inhibition
14.6 Active Site Inhibition
14.7 DNA Binding by VapBC Complexes
14.8 Discussion
References
Chapter 15: D-Glyceraldehyde-3-Phosphate Dehydrogenase Structure and Function
15.1 Introduction
15.2 GAPDH Functional Diversity
15.2.1 Intermediary Metabolism
15.2.2 Membrane Fusion
15.2.2.1 Vesicle Fusion in Exocytosis
15.2.2.2 Vesicle Trafficking in Exocytosis
15.2.3 Interactions with Cytoskeletal Components
15.2.3.1 Interactions with Tubulin and Microtubules
15.2.3.2 Interactions with Actin and Microfilaments
15.2.4 GAPDH as a Redox Sensor
15.2.5 The Role of GAPDH in Cell Death
15.2.5.1 Apoptotic Pathway Involving GAPDH
Extrinsic Apoptotic Pathway
Intrinsic Apoptotic Pathway
15.2.5.2 Energy Depletion
15.2.5.3 GAPDH-Mediated Caspase-Independent Cell Death
15.2.6 Autophagy
15.2.7 Iron Homeostasis
15.2.8 Heme Metabolism
15.2.9 GAPDH Interactions Involving Nucleic Acids
15.2.9.1 DNA Binding Proteins
15.2.9.2 Cellular DNA
15.2.9.3 Cellular RNA
15.2.9.4 Viral Nucleic Acids
15.3 GAPDH Functional Regulation and Cellular Localization Diversity
15.3.1 Extracellular Localization
15.3.2 Membrane Localization
15.3.3 Cytosolic Localization
15.3.4 Mitochondrial Localization
15.3.5 Nuclear Localization
15.4 Structural Studies of GAPDH
15.4.1 Oligomerization and Interfaces
15.4.2 Cofactor Binding Site
15.4.3 Active Site and Mechanism
15.4.4 Positive Groove
15.4.5 The Central Channel
15.4.6 The Connection Between the Different Structural Determinants
15.4.7 Comparison of GAPDH from Different Domains of Life
15.5 Conclusions and Future Perspectives
References
Chapter 16: Protein Complexes in the Nucleus: The Control of Chromosome Segregation
16.1 Introduction
16.1.1 The SAC-KMN axis
16.1.2 Multidomain Protein Kinases Regulate the SAC
16.2 The Kinetochore Null Mutant 1 (KNL1)
16.3 The Ndc80 Complex
16.4 Mis12 Complex
16.5 Centromere-Associated Protein E (CENP-E)
16.6 The Centromeric Nucleosome-Associated Network (CCAN)
16.7 CLASP-1 and CLASP-2
16.8 Astrin and Kinastrin
16.9 KIF2B and Kif18A
16.10 SKAP
16.11 Disorder-to-Order Transitions in the KMN
16.12 The SAC-KMN Axis in Disease
16.13 Emerging Methods in Structural Biology
16.14 Closing Remarks
References
Chapter 17: GroEL and the GroEL-GroES Complex
17.1 Introduction
17.2 Molecular Structures
17.3 Various Structural Forms of the GroEL-GroES Complex
17.4 Function and Chaperonin Reaction ATPase Cycle
17.5 Applications as the Nanomolecular Machine
17.5.1 As a Carrier of the Artificial Substances
17.5.2 As an “AND” Logic Gate
17.5.3 As a GroEL Nanotube
17.6 Closing Remarks
References
Chapter 18: The Aminoacyl-tRNA Synthetase Complex
18.1 Introduction
18.2 Crystal Structure of Aminoacyl-tRNA Synthetase Components of the MSC
18.2.1 Class 2 AARS
18.2.2 WHEP Domains
18.2.3 Class 1 AARS
18.3 Crystal Structures of Auxiliary Components of the MSC
18.3.1 p18: Two Potential Protein-Binding Sites
18.3.2 p43: a Two-Domain Protein
18.4 Structural Organization of Subcomplexes
18.4.1 The Binary Complex LysRS:p38
18.4.2 The ArgRS:GlnRS:p43 Complex, the Subcomplex II of the MSC
18.4.3 Role of GST-Homology Domains in the Assembly of the MSC
18.5 Low-Resolution Structures of the Native MSC
References
Chapter 19: The Pyruvate Dehydrogenase Complex and Related Assemblies in Health and Disease
19.1 Introduction to Overall Complex Architecture, Macromolecular Organisation and the Reaction Cycle
19.1.1 E1, Pyruvate Dehydrogenase/Decarboxylase
19.1.2 E2, Dihydrolipoamide Acetyltransferase
19.1.3 E3, Dihydrolipoamide Dehydrogenase (E3)
19.1.4 The Interaction of E1 and E3 with the Core Complex
19.1.5 Core Complex Heterogeneity
19.2 Biosynthesis and Assembly of Mammalian PDC
19.3 Regulation of PDC by End-Product Inhibition and Phosphorylation
19.4 Clinical Consequences of PDC Deficiency
19.5 Genetic Defects in PDC Deficient Patients: In Vitro Evaluation Using Recombinant Human PDC
19.6 PDC and the Major Diseases
19.6.1 Primary Biliary Cirrhosis (PBC)
19.6.2 Malaria
19.6.3 Bacteria and Antimicrobials
19.7 Outlook
References
Chapter 20: Structure and Assembly of Clathrin Cages
20.1 Introduction
20.2 The Clathrin Triskelion
20.2.1 Trimerisation Domain
20.2.2 Light Chains
20.3 Formation of Clathrin Cages
20.4 Understanding the Structure of Clathrin Cages
20.5 Investigations of Clathrin Coated Vesicle Structure
20.6 Theoretical and Energetic Studies of Clathrin Cage Structure
20.7 Conclusions
References
Index