Cover
Halftitle
Title
Copyright
Foreword by James Barber FRS
Preface
Contents
Chapter 1 Maquette Strategy for Creation of Light- and Redox-active Proteins
1. Introduction
2. Maquette protein strategy
2.1. Recognizing natural complexity
2.2. α-Helical scaffolds common in natural protein structures reveal the basics of how cofactors are ligated and positioned
2.3. First-principles of de novo designed protein structures outlined
2.4. Electron transfer in protein understood for engineering
3. Practical Strategies for Development of Functional Light- and Redox-active Proteins
3.1. Lessons learned from the first heme protein maquettes
3.2. Characterization of one maquette promotes development of others
3.2.1. Charge-activated conformational switch in a homodimeric four-α-helix heme B protein [Grosset et al., 2001]
3.2.2. Electron tunneling between monolayers of linked-homodimeric heme protein and gold electrodes [Chen et al., 1999; 2002]
3.2.3. Linked-homodimeric heme protein oxygen transporter [Koder et al., 2009]
4. Single-chain Four-α-Helix Maquettes
4.1. From disulfide linked homodimeric bundles to single-chain four-α-helix structures
4.2. Compatibility of single-chain four-α-helix maquettes with natural proteins
4.2.1. Single-chain four-α-helix heme B maquette interactions with natural cytochrome c
4.2.2. In vivo single-chain four-α-helix protein covalently linking heme C: a novel cytochrome c
5. Prospects and Previews
Acknowledgements
References
Chapter 2 Free, Stalled, and Controlled Rotation Single Molecule Experiments on F1-ATPase and their Relationships
1. Introduction
2. Description of Three Single-Molecule Experiments
2.1. Free rotation experiments: Stepping rotation and concerted kinetics
2.2. Stalling experiments
2.3. Controlled rotation experiments
3. Group Transfer Theory in Stalling and Controlled Rotation Experiments
3.1. Angle dependent rate constants and free energies
3.2. Application to ATP binding in the overlapping θ-range
3.3. Turnover, near symmetry and long binding events in the controlled rotation experiments
4. Application of the Theory to Free Rotation
4.1. Rate constant of a free rotation experiment
4.2. Relation between controlled and free rotation experiments
4.3. Use of the rate constant versus rotor angle data to predict the step size and dwell angles in free rotation
5. Concluding Remarks
Acknowledgements
Appendix
Evaluation of Eq. (8)
References
Chapter 3 The Role of the H-Channel in Cytochrome c Oxidase: A Commentary
1. Introduction
2. Conservation of the H-Channel Structure
3. The Linkage of Proton Pumping to Individual Steps of the Catalytic Cycle
4. The Proton Pump Cycle
5. Conclusions
Acknowledgements
References
Chapter 4 Cytochrome c Oxidase: Insight into Functions from Studies of the Yeast S. cerevisiae Homologue
1. Introduction: Catalysis, Coupling and Efficiency
2. Core Structural and Functional Variations in the HCO Superfamily
3. Yeast CcO — A Link Between Mammalian and A1 Bacterial CcOs
3.1. The H channel and its possible roles
3.2. Supernumerary and additional subunits
4. Concluding Remarks
Acknowledgements
References
Chapter 5 Femtosecond Infrared Crystallography of Photosystem II Core Complexes: Watching Exciton Dynamics and Charge Separation in Real Space and Time
1. Introduction
2. Femtosecond Infrared Crystallography
3. Summary of Theory for Exciton Dynamics and Trapping by Electron Transfer for the Crystallographic Case
4. Femtosecond Infrared Crystallography of Exciton Dynamics
5. Structural Measurement of the Charge Separated State P680+/Pheo−
5.1. Vibrational mode assignments of the P680+/P680 and Pheo−/Pheo spectra
5.2. Fitting the P680+/P680 and Pheo−/Pheo FTIR spectra
5.3. Fitting the 832 ps TR-IR crystallography spectra
6. Implications for Light Harvesting Function of PSII Core Complexes
References
Chapter 6 Bioenergetics, Water Splitting and Artificial Photosynthesis
1. Introduction
2. Photosystem II (PSII)
2.1. The catalytic centre
2.2. Synthetic cubane mimics
3. Mechanism of Water Splitting
3.1. Base-catalysed nucleophilic attack mechanism
3.2. Indirect support for the nucleophilic mechanism for O–O bond formation in PSII
3.3. Comparison with Fe–Ni carbon monoxide dehydrogenase (CODH)
3.4. Ligands to the Mn4Ca2+O5 cluster
4. Synthesized Chemical Model Systems
4.1. Mechanism of O2 production from organo-Ru complexes
4.2. Mechanism of O2 production from organo-Mn complexes
5. Alternative Mechanisms are Less Compelling
6. Artificial Photosynthesis
7. Conclusions
References
Chapter 7 A Quest for the Atomic Resolution of Plant Photosystem I
1. Introduction
2. The Structure of Plant PSI
3. The Light Harvesting Complex of Plant PSI
Acknowledgements
References
Chapter 8 Rubisco Activase: The Molecular Chiropractor of the World’s Most Abundant Protein
1. Introduction
2. The Most Abundant Protein on Earth is a Poor Catalyst
2.1. The structure and diversity of Rubisco
2.2. Reaction mechanism: co-factor binding and catalysis
2.3. Rubisco is prone to inhibition by sugar phosphates
3. Rubisco Activase, the Molecular Chiropractor
3.1. Rubisco activases are members of the AAA+ family of proteins
3.2. Oligomeric state and mechanism of the Rubisco activase
3.3. Regulation of Rubisco activase
3.4. The role of Rubisco activase in regulating photosynthesis at elevated temperatures
4. Outlook
References
Chapter 9 Adaptive Reorganisation of the Light Harvesting Antenna
1. Introduction
2. The Structure of LHCII Complex and the Landscapes of the Photosystems
3. Evidence for the Fast Dynamics of the Photosynthetic Membrane
4. LHCII Composition and Membrane Dynamics
5. State Transitions are Affected by PSII Antenna Composition
6. Zeaxanthin and Non-Photochemical Quenching Modulate LHCII Dynamics
6.1. LHCII clustering versus mobility
6.2. NPQ control by LHCII antenna hydrophobicity
7. Formation of the NPQ Quencher(s): Inner LHCII Complex Dynamics
8. Physiological Implications of the Dynamic Properties of LHCII
Acknowledgements
References
Chapter 10 Thylakoid Membrane Dynamics in Higher Plants
1. Introduction
2. Supramolecular Dynamics
2.1. Protein order and disorder in thylakoid membranes
2.1.1. Significance of mesoscopic dynamics for energy transformation and its regulation
2.1.2. Types of semi-crystalline protein arrays in grana thylakoids
2.2. Potential advantages and disadvantages of semi-crystalline protein arrays
2.2.1. PSII repair
2.2.2. Diffusion in the lipid matrix
2.3. Factors controlling mesoscopic protein arrangements
2.3.1. Lipids and fatty acids
2.3.2. Protein phosphorylation
2.4. The elusive mesoscopic level
3. Thylakoid Membrane Dynamics
3.1. Types of thylakoid lumen swelling and shrinkage
3.2. Factors controlling thylakoid membrane dynamics
3.2.1. Ion transporters
3.2.2. Protein kinases and phosphatases
3.2.3. Membrane curvature proteins
3.3. Controversies of observed thylakoid dynamics
Acknowledgements
References
Chapter 11 Oxygenic Photosynthesis — Light Reactions within the Frame of Thylakoid Architecture and Evolution
1. Introduction
2. Thylakoid Membrane Heterogeneity — From Cyanobacteria to Higher Plants
3. Key Regulatory Mechanisms of Thylakoid Electron Transfer Reactions
3.1. No clear model organism for regulation of light reactions
3.2. Evolution of key regulatory mechanisms of thylakoid electron transfer reactions
4. Factors Regulating the Thylakoid Architecture in Oxygenic Photosynthetic Organisms
5. Revealing the Dynamics of Thylakoid Architecture in Higher Plant Chloroplasts
5.1. Methods to study thylakoid heterogeneity — Dark acclimated plants
5.2. Thylakoid fractionation from light-acclimated plants demonstrates light-dependent, reduced stringency of lateral heterogeneity
5.3. Significance of thylakoid plasticity for photosynthetic light reactions and beyond
Acknowledgments
References
Chapter 12 Estimation of the Cyclic Electron Flux around Photosystem I in Leaf Discs
1. Introduction
2. Partitioning of Absorbed Light Between the Two Photosystems
3. Cyclic Electron Flux in Spinach Leaves
4. Cyclic Electron Flux in Arabidopsis Leaves
4.1. CEF in wild type Arabidopsis
4.2. CEF in the pgr5 mutant of Arabidopsis
4.3. CEF in the ndh mutant of Arabidopsis
4.4. The antimycin A-sensitive component of ETR1 in Arabidopsis
5. Concluding Remarks
Acknowledgements
References
Chapter 13 The Contribution of Electron Transfer after Photosystem I to Balancing Photosynthesis
1. Introduction
2. The Hierarchy of Electron Donation
3. Diversity Among Electron Carriers
4. Regulation of Sink Demand Beyond the First Acceptor
5. Flexible Adjustment of Target-Enzyme Activity According to Metabolic Demand
6. Signaling upon Redox-Imbalances for Long-Term Adaptation at the Transcriptional Level
References
Chapter 14 Cyclic Electron Flow in Cyanobacteria and Eukaryotic Algae
1. Introduction
2. In Vivo Evidence of Cyclic Photophosphorylation in Algae
2.1. Overview
2.2. Energetics of the assimilation of exogenous glucose and acetate powered by CEF and their mechanistic implications
3. Detailed Mechanism of Cyclic Electron Transport and ATP Formation in Oxygenic Photosynthetic Organisms
3.1. Overview
3.2. Non-cyclic (= linear) electron flow, cyclic electron flow, the Q cycle and ATP generation
3.3. Early evolution of NAD dehydrogenases — Bacteria, cyanobacteria, plastids and mitochondria.
3.4. Mechanisms for CEF in Cyanobacteria.
3.5. Detailed mechanism and inhibitors of the NDH system
3.6. Towards a better understanding of cyanobacterial CEF
4. Cyclic Electron Transport Complexes of Chlamydomonas and Other Green Algae
4.1. Introduction
4.2. PGR5/PGRL1 complexes in thylakoids
4.3. Reductases of thylakoid membranes and their role in CEF
5. Evidence for Cyclic Electron Transport in Eukaryotic Algae
5.1. Pyrrophyta, Dinophyta (Dinoflagellata)
5.1.1. Symbiodinium sp., the coral endosymbiont algae
5.2. Haptophyta
5.2.1. Prymnesiophyceae
5.3. Ochrophyta
5.3.1. Bacillariophyceae
5.3.2. Eustigmatophyceae
5.3.3. Phaeophyceae
5.4. Rhodophyta
5.4.1. Bangiophyceae
5.4.2. Floridiophyceae
6. The Role of CEF in Eukaryotic Algae in a Range of Habitats
6.1. Desiccation
6.2. Variations in salinity
6.3. Low temperature
6.4. High temperature
6.5. High light
6.6. Nitrogen deficiency
6.7. Iron deficiency
6.8. Summary and Conclusions
Acknowledgements
References
Index

Photosynthesis and Bioenergetics
This book is a tribute to three outstanding scientists, Professors Jan Anderson FRS, Leslie Dutton FRS and John Walker FRS, Nobel Laureate. Covering some of the most recent advances in the fields of Bioenergetics and Photosynthesis, this book is a compilation of contributions from leading scientists actively involved in understanding the natural biological processes associated with the flow of energy in biological cells. The lectures found in this significant volume were presented at a meeting in March 2016 in Singapore to commemorate the outstanding research in this area.The contents begin with the ideas, specially the contribution from Nobel Laureate Rudolph Marcus, who is well-known for creating the theory of electron transport reactions. This is followed by contributions of many others on various aspects of respiratory and photosynthetic transport chains as well as the dynamic regulation of light harvesting and electron transport events in oxygenic photosynthesis. The book is highly recommended to postgraduate students and researchers who are interested in various aspects of bioenergetic cycles.