This book covers the latest findings of a wide variety of viral, prokaryotic and eukaryotic macromolecular protein complexes and builds upon the solid macromolecular foundations established by previous volumes of the Subcellular Biochemistry series. Thus, an almost encyclopaedic coverage of the broad field of protein complex structure and function has been established.
The 17 interesting chapters included in this book have been organised into four sections: Soluble Protein Complexes, Membrane Protein Complexes, Fibrous Protein Complexes and Viral Protein Complexes. Significant topics present here are: Fatty Acid Synthase, the Fork Protection Complex, Ribonucleotide Reductase, the Kinetochore, G proteins, the FtsEX Complex, the Kainate Receptor, the Photosystem I-antenna, the Mycobacterial Arabinofuranosyltransferases, the the Bacterial Flagellum, the Actomyosin Complex, Motile Cilia, SLS Collagen Polymorphic Structures, and the Reovirus Capsid and Polymerase. Up-dates/expansion of chapter topics present in earlier volumes are now included in chapters here, e.g., those on Ferritin-like proteins and the Multi-tRNA Synthetase.
The book is richly illustrated throughout, the result of an impressive integration of structural data from X-ray crystallography and cryo-electron microscopy. The functional aspects of protein-protein interactions are also given a high priority.
Author(s): J. Robin Harris, Jon Marles-Wright
Series: Subcellular Biochemistry, 99
Publisher: Springer
Year: 2022
Language: English
Pages: 547
City: Cham
Preface
Contents
Chapter 1: Fatty Acid Synthase: Structure, Function, and Regulation
The Importance of Fatty Acids and Fatty Acid Biosynthesis
Historical Background
Biochemical Steps in FA Biosynthesis
Type I and Type II FAS Architectures: Enzyme- and Enzymatic Domain Functions
Phylogeny of FAS Architectures
Regulation of FA Biosynthesis
Direct Regulation of ACP
Discovery of a Regulatory γ-Subunit of the Yeast FAS
Conclusions and Outlook
References
Chapter 2: ATP-Binding Cassette Transporters: Snap-on Complexes?
Introduction
Assembly of Protein Complexes
Molecular Recognition in ABC Transporter Complex Formation
Molecular Recognition and Subunit Assembly in ABC Transporters
Type I ABC Transporters
Type II ABC Transporters
Type III ABC Transporters or Energy Coupling Factor Transporters (ECF)
Interactions Between EcfA-A′ and EcfT
Interactions Between EcfS and EcfT Modules
Proposed Transport Mechanism of ECF Transporters
Genetic Organisation of the ECF Operons
Type IV ABC Transporters
Type V ABC Transporters
Type VI ABC Transporters
Type VII ABC Transporters (or ABC Mechanotransducers)
Thermodynamics of ABC Transporter Complex Formation
The Role of ATP in NBD Dimer Formation and Substrate Transport
Fused Subunits of Prokaryotic ABC Transporters and Assembly
AlphaFold Predictions of All E. coli K12 ABC Transporter Structures
Novel TMD Folds
Promiscuity in ABC Transporter Subunit Interactions and Assembly
Orphan/Multitask NBSs and Promiscuity of Complex Formation
Co-Translational Assembly of ABC Transporter Complexes
Operon Structure for ABC Transporter Complexes
Conclusions
References
Chapter 3: The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome
The Eukaryotic Replisome
Replication-Associated Processes
Replication-Associated Cohesion Establishment Factors
Functions of the Tof1-Csm3 Fork Protection Complex
Functional Domains of the Fork Protection Complex
The Solenoid Core
Anchoring onto the CMG Helicase
A dsDNA Grip Enables Fork Pausing and Replisome Progression
Interactions with the Checkpoint Mediator Mrc1
Mechanistic Conservation in Humans
The PARP1-Binding PAB Domain
DNA-binding Domains in Human Timeless
Tipin-RPA Interactions
Unresolved Interactions
Outlook
References
Chapter 4: Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes
Introduction: The Ferritin-Like Superfamily
Soluble Methane Monooxygenase
Chemical Mechanism of Methane Oxidation in sMMO
sMMOH Protein Structure and Function
sMMOH and MMOB Protein Complex
Enhancement of O2 Reactivity by MMOB Binding to sMMOH
Engendering Substrate Specificity for Methane
Dynamic Equilibrium of sMMOH, MMOB, and MMOR Protein Complexes
Class I Ribonucleotide Reductase
Ferritin-Like R2 Subunits in Class I RNR
The R2-NrdI Complex in Subclass Ib RNR
The R1-R2 Active-State Complex in Class I RNR
Aldehyde Deformylating Oxygenase
The Ferritin-Like ADO
ADO in Complex with AAR
Conclusion and Perspective
References
Chapter 5: Still no Rest for the Reductases: Ribonucleotide Reductase (RNR) Structure and Function: An Update
Introduction
RNR Chemistry
RNR Subunit Biochemistry
Allostery and Oligomerization, the Basis of RNR Activity Regulation
RNR-Targeting Drugs and Their Links to Allostery and Chemistry
Drug-Induced RNR-α Hexamers
RNR-Inhibited dNTP Pools and the Cell Cycle: Implications for Studies with RNR Inhibitors
Other dNTP Regulation Pathways
Regulation of RNR Activity in Cells
Subcellular Localization
RNR Binders That Regulate RNR Activity
Role of dNTPs in Health and Disease
RNR Activity During Cancer Development
RNR Activity in Cancer Treatment
RNR-β and p53R2 in Cancer
RNR-α: A Tumor Suppressor
Modes of RNR-α Tumor Suppression and Links to Approved Drug Mechanisms
Outlook
References
Chapter 6: Structure and Dynamics of the Human Multi-tRNA Synthetase Complex
Introduction
Mammalian MSC
Appended Domains in Human MSC
MSC Assembly Through the Appended Domains
Leucine Zipper-Mediated Assembly
GST-Like Domain-Mediated Assembly
UNE Domain-Mediated Assembly
Architecture of the Human MSC
Three Subcomplexes in MSC
Details of Interactions Within Subcomplexes
Symmetry of Subcomplexes in MSC
Spatial Arrangement of MSC Components
Molecular Root of MSC Dynamics
KARS1
MARS1
EPRS1
Flexibility of MSC Components via Linker Peptides
MSC Dynamics-Based Function Repertoire
KARS1
LARS1
EPRS1
AIMP2
AIMP3
Perspectives
References
Chapter 7: On the Regulation of Mitosis by the Kinetochore, a Macromolecular Complex and Organising Hub of Eukaryotic Organisms
Introduction
Kinetochore Structural Organisation
The KMN Network
Knl1
Mis12 Complex
Ndc80 Complex
Other Kinetochore-Associated Subcomplexes
The RZZ Complex
The CENP-O Class
The CCAN Complex
Kinetochore-Microtubule Attachments
Kinetochore-SAC Communication Often Involves Large Conformational Transitions
Regulation of Kinetochore-SAC Communication
The Kinetochore as a Potential Drug Target
Recent Technology-Driven Advances to Study the Kinetochore
What Lies Ahead?
References
Part I: Membrane Protein Complexes
Chapter 8: The Conformational Dynamics of Heterotrimeric G Proteins During GPCR-Mediated Activation
Introduction
GPCR-G Protein Complex Structures
Dynamic Conformational Changes in GDP Release
Conformational Dynamics Within Gα AHD
Perspectives
References
Chapter 9: Regulation of Lytic Machineries by the FtsEX Complex in the Bacterial Divisome
Introduction
FtsEX, a Type VII Member of the ABC Transporter Superfamily, Is Involved in the Regulation of Bacterial Cell Division
Role of Endopeptidases and Amidases in Bacterial Cell Division
Three-Dimensional Structures of Amidase AmiC from E. coli and Regulatory LytM Domains
The Three-Dimensional Structure of Pneumococcal Endopeptidase PcsB
Structural Information on the FtsX Membrane Protein
The Three-Dimensional Structure of Pneumococcal FtsE
Mechanotransmission Model for the Activation of PcsB by the FtsEX Complex
Conclusions and Future Perspectives
References
Chapter 10: Structure, Function, and Regulation of the Kainate Receptor
Introduction
Genomic Localization and Gene Expression Profiling of KARs
Spatial Expression of KARs
Pre- and Post-Translational Modifications of KARs
Post-Transcriptional Modifications
Alternative Splicing
RNA Editing
Post-Translational Modifications
N-Glycosylation
Phosphorylation
Protein Kinase C (PKC)-Mediated Phosphorylation of GluK2
CaMKII Phosphorylation of GluK5
SUMOylation
Palmitoylation
Ubiquitination
Trafficking/Retention Motifs
GluK1
GluK2
GluK3
GluK4
GluK5
Functional Characterization of KARs
Regulatory Partners of KARs
Identification of NETOs as a Kainate Receptor-Binding Protein
Synaptic Targeting and Functional Modulation
NETO Subunits and Synaptic Current Modulation
Structural Characterization of KARs
Crystal Structures of Amino-Terminal and Ligand-Binding Domains
Cryo-EM Structures of Full-Length KARs
KARS in Genetic Disorders
Future Perspectives
References
Chapter 11: Structure, Function, and Variations of the Photosystem I-Antenna Supercomplex from Different Photosynthetic Organi...
Introduction
Electron Transfer Chain of PSI
Structure of the Cyanobacterial PSI Core
Structure of the PSI Trimer
Structure of the PSI Tetramer
Structure of the PSI-IsiA Supercomplex
Structures of Eukaryotic PSI-LHCI Supercomplexes
Red Algal PSI-LHCI Supercomplexes
Diatom PSI-FCPI Supercomplexes
Green Algal PSI-LHCI Supercomplexes
Higher Plant PSI-LHCI Supercomplex
Concluding Marks and Perspectives
References
Chapter 12: Structure and Function of Mycobacterial Arabinofuranosyltransferases
Introduction
Overall Structure of the Mycobacterium Cell Envelope
Synthesis of the Cell Envelope by Arabinofuranosyltransferases
Structures and Function
Arabinofuranosyltransferase D (AftD)
Arabinofuranosyltransferase EmbA
Arabinofuranosyltransferase EmbB
Arabinofuranosyltransferase EmbC
Interacting Partners with Arabinofuranosyltransferases
Conclusions
References
Part II: Fibrous Protein Complexes
Chapter 13: Structure and Assembly of the Bacterial Flagellum
Introduction
Structure of the Bacterial Flagellum
The Motor, Stator, and Export Apparatus
The Basal Body
The Axial Components
Diversity of Flagellar Structure
Flagellar Assembly and Dynamics
Overall Assembly Pathway
Genetic Regulation
Mechanism and Regulation of Hook and Filament Assembly
Diverse Flagella: Species-Specific Assembly, Disassembly, and Regulation
Conclusion
References
Chapter 14: Actomyosin Complex
Introduction
General Structural Features of Actin and Myosin
Actin
Overview of the Actin Structure
Formation of the Actin Filament
Myosin
Overview of the Myosin Structure
Components of a Myosin-S1 Molecule
The Molecular Mechanisms of the Actomyosin Cross-Bridge Cycle
Overview of the Actomyosin Cross-Bridge Cycle
ATP-Induced Dissociation of Rigor Actomyosin
Recovery Stroke
Initial Actomyosin Association and Pi Release
ADP Release and Formation of Rigor Complex
The Structure of the Rigor Complex
Variations in the Actin-Binding Elements of Various Myosin Isoforms Tune Up Their Kinetic Parameters
Cellular and Physiological Contexts of Actomyosin Interaction
Muscle Contraction
Cargo Transport
Tension Sensing
Cytoskeletal Remodeling and Motility
Conclusion and Future Perspectives
References
Chapter 15: Structure of Motile Cilia
Motile and Nonmotile Cilia
What Are Cilia?
Functional Differences between Motile and Nonmotile Cilia
Axoneme/TZ/Basal Body
Motile Cilia Functioning in the Human Body and Ciliopathy
Model Organisms to Study Motile Cilia
Motile Cilia: Wave Form and Calcium Regulation
Overall Architecture of Cilia
``9 + 2´´/``9 + 0´´/Motile/Nonmotile
Structural Features of the Basal Body
IFT and BBSome: How Do Cilia Grow?
Detailed Structure of the 9 + 2 Axoneme from Motile Cilia
The Doublet Microtubule
Post-Translational Modification of DMT
Dynein
Outer and Inner Dynein Arms
Detailed Structure of ODA
Inner Dyneins and Associated Proteins
RS and CP
Nexin
Final Thoughts
Mechanics
Thought about Evolutionary Origins
References
Chapter 16: Segment-Long-Spacing (SLS) and the Polymorphic Structures of Fibrillar Collagen
Introduction
SLS: The Effective Molecular Tool for Collagen Research
The Molecular Packing of the Fibrils
The Fingerprints of Collagens
The Functions of Collagenase
SLS and the Structural Polymorphism of Fibrillar Collagen
The Formation of SLS under Different Buffer Conditions
SLS under Physiological Conditions and their Potential Involvement in Fibrillogenesis
The Other Structures of Fibrillar Collagen
The Determinant Factors for the Self-Assembly of Fibrillar Collagen
The Origin of the Structures Is in the Amino Acid Sequences
A Design Strategy Based on the Periodic Spacing of the Interacting Residues
The Recent Works on SLS and FLS in Tissues
Concluding Remarks
References
Part III: Virus Protein Complexes
Chapter 17: Viral Capsid and Polymerase in Reoviridae
Introduction
Icosahedral Capsid Structures of Reoviruses
Reoviruses in the Subfamily Spinareovirinae
Reoviruses in Sedoreovirinae
Reovirus RdRp
Structure of the RdRp Complex and Genome in a Nontranscribing Mature Virion
RdRp in Transcribing Reoviruses
Initiation
Elongation
Roles of the Shell Protein in the RdRp Transcription
Reovirus RNA Capping
Turreted Reovirus Capping
Nonturreted Reovirus Capping
Conclusions and Perspectives
References
