Photosynthesis: Molecular Approaches to Solar Energy Conversion

✍ Scribed by Jian-Ren Shen, Kimiyuki Satoh, Suleyman I. Allakhverdiev

• Publisher: Springer
• Year: 2021
• Tongue: English
• Leaves: 646
• Series: Advances in Photosynthesis and Respiration
• Edition: 1
• Category: Library

✦ Synopsis

In the modern world, to meet increasing energy demands we need to develop new technologies allowing us to use eco-friendly carbon-neutral energy sources. Solar energy as the most promising renewable source could be the way to solve that problem, but it is variable depending on day time and season. From this side, the understanding of photosynthesis process could be of significant help for us to develop effective strategies of solar energy capturing, conversion, and storage. Plants, algae, and cyanobacteria perform photosynthesis, annually producing around 100 billion tons of dry biomass. Presently, the detailed studies of photosynthetic system structure make functional investigations of the photosynthetic process available, allowing scientists to construct artificial systems for solar energy transduction. This book summarizes exciting achievements in understanding of photosynthetic structures and mechanisms of this process made by world leaders in photosynthesis field, and contains information about modern ideas in development of revolutionary new technologies of energy conversion. Organized according to the natural sequence of events occurring during photosynthesis, the book includes information of both photosynthetic structures and mechanisms and its applications in bioenergetics issues.

✦ Table of Contents

From the Series Editors
Advances in Photosynthesis and Respiration Including Bioenergy and Related Processes
Authors of Volume 47
Our Books
Future Advances in Photosynthesis and Respiration and Other Related Books
Series Editors
Foreword
References
Preface
A Tribute to Vyacheslav (Slava) Vasilyevich Klimov (1945–2017)
Reminiscences
References
Contents
Editors
Contributors
Part I: Natural and Artificial Water Oxidation
Chapter 1: Structure, Electron Transfer Chain of Photosystem II and the Mechanism of Water Splitting
Summary
I. Introduction
II. Structure of PS II
A. Structure of Cyanobacterial PS II
1. Organization and Structure of Protein Subunits
Trans-Membrane Subunits
Extrinsic Subunits
2. Arrangement of Pigments
3. Other Cofactors
B. Structure of Red Algal PS II
C. Structure of Diatom PS II
D. Structure of Green Algal PS II
E. Structure of Higher Plant PS II
III. Electron Transfer Chain of PS II
IV. Structure of the Mn4CaO5-Cluster and the Mechanism of Water Oxidation
A. Structure of the Mn4CaO5-Cluster
1. S1-State
Structure of the Mn4CaO5-Cluster in the S1-State
Oxidation States of the Mn Ions in the S1-State
Chloride Ions
Hydrogen-Bond Networks
2. S2-State
3. S3-State
B. Mechanism of Water Splitting
Concluding Remarks and Perspectives
Acknowledgements
References
Chapter 2: Mechanism of Water Oxidation in Photosynthesis Elucidated by Interplay Between Experiment and Theory
Summary
I. Introduction
II. Structure and Bonding of MnxOy Clusters
A. The Nature of High-Valent Mn=O Bonds
B. Lewis Acid Effects for Metal-Oxo Bonds
C. Exchange Coupling Between Local Spins
D. Spin Frustrations of Mn3O4 and Mn4O4
E. Jahn-Teller (JT) Effects by Mn(III) Ion
III. High-Resolution XRD Structure of PS II
A. XRD Geometry of the CaMn4O5 Cluster
B. Theoretical Study of the CaMn4O5 Cluster
C. Full Geometry Optimizations by HDFT
D. EPR Results for the S1 State of OEC
IV. Electronic and Spin Structures of the S2 State
A. Full Geometry Optimizations with HOS
B. Full Geometry Optimizations with LOS
V. System Structures of OEC of PS II
A. Proton Release and Water Inlet Pathways
B. H-Bond Networks for Tyr161 and Ca Ion
C. Water Inlet Pathway (WIP)
D. Proton Release Pathway (PRP)
E. QM/MM Calculations of Other Networks
VI. Possible Intermediates in the S3 State
A. Water Insertion in the S3 State
B. XFEL Results for the S3 State
C. EPR Results for the S3 State
VII. Possible Mechanisms for Water Oxidation
A. Reaction Sites Revealed by Frontier MO
B. Possible Mechanisms for Water Oxidation
C. Perspectives
VIII. Concluding Remarks
Acknowledgements
References
Chapter 3: On the Nature of the Functional S-States in the Oxygen Evolving Centre of Photosystem II—What Computational Chemistry Reveals About the Water Splitting Mechanism
Summary
I. Introduction
II. The Oxidation State Possibilities
III. X-Ray Structures, Extended X-Ray Absorption Fine Structure
IV. Substrate Exchange Kinetics
V. X-Ray Spectroscopy
VI. Low Paradigm Functional S-States
VII. Mechanism of Oxygen Evolution
VIII. Conclusions
Acknowledgements
References
Chapter 4: Toward Molecular Mechanisms of Solar Water Splitting in Semiconductor/Manganese Materials and Photosystem II
Summary
I. Introduction
II. Photosystem II Water Splitting Chemistry
III. Manganese-based Photosystem II Functional Models
A. Synthesis, Structure, and Electrochemistry of the Manganese-Oxo Dimer Complex
B. Water Oxidation Mechanism by the Manganese-Oxo Dimer Complex
C. Stability of the Manganese-Oxo Dimer Complex
IV. Semiconductor/Manganese Systems Mimicking Photosytem II
A. Design, Synthesis, and Structural Characterization of Manganese/Tungsten Oxide Nanostructures
B. Catalytic Activity of Manganese/Tungsten Oxide Nanostructures
C. Mechanism of the Manganese/Tungsten Oxide System
V. Concluding Remarks
Acknowledgements
References
Part II: Light-Harvesting Systems
Chapter 5: Chlorophyll Species and Their Functions in the Photosynthetic Energy Conversion
Summary
I. Introduction
II. The Diversity of Chlorophylls and Related Pigments
A. Chlorophyll a
B. Pheophytin a
C. Chlorophyll b
D. Divinyl Chlorophyll a and Divinyl Chlorophyll b
E. Chlorophyll c
III. Red-Shifted Chlorophylls
A. Chlorophyll d
1. Ecological Distribution and Biology
2. Chemical Properties
3. The Role of Chlorophyll d in Photosynthesis
a. PS I in A. marina
b. Energetics of PS I in A. marina
c. PS II in A. marina
d. Stoichiometry of Pigments in PS II Reaction Center
e. The Special Pair of PS II
f. Presence of Chl a and Its Function in PS II
g. Energetics of PS II in A. marina
B. Chlorophyll f
1. Ecological Distribution and Chemical Properties
2. Functions of Chlorophyll f
3. Structure of Chlorophyll f-containing PS I
Acknowledgments
References
Chapter 6: Structure, Organization and Function of Light-Harvesting Complexes Associated with Photosystem II
Summary
I. Introduction
II. Compositions and Functions of Various Types of Light-Harvesting Complexes II
A. Functions of Light-Harvesting Complex II
B. Protein Compositions and Their Sequence Comparisons
C. Chlorophylls
D. Carotenoids
E. Lipids, Water Molecules and Metal Ions
III. Structures of LHCII and FCPII
A. Structures of LHCII
1. Major Trimeric LHCII of Plants and Green Algae
2. Minor LHCII Antennae CP29, CP26 and CP24
B. Structures of FCPII of Diatoms
1. Major Dimeric and Tetrameric FCPIIs
2. Minor, Monomeric FCPIIs
IV. Organization of LHC Antennae in the PS II-LHCII Supercomplexes
V. Energy Transfer Pathways and Photoprotection
A. Energy Transfer Pathways
B. Energy Balance Between the Two Photosystems and Photoprotection
VI. Perspectives
Acknowledgements
References
Chapter 7: Structure, Function, and Evolution of Photosystem I-Light Harvesting Antenna I Complexes
Summary
I. Introduction
II. Structure of Cyanobacterial PS I and Evolution of the PS I Core Complex
III. Structure of the PS I Supercomplex of Higher Plants
A. Overall Structure of the PS I-LHCI Supercomplex
B. Structure and Function of Unique Core Subunits PsaH, PsaN, and PsaO
C. Structure of LHCI of Higher Plants
D. Possible Excitation Energy Transfer Pathways from LHCI to the PS I Core Complex
IV. Structure of the PS I-LHCR Supercomplex from Red Algae
A. Overall Structure of Red Algal PS I-LHCR
B. Arrangement of Chlorophylls and Carotenoids in LHCR
C. Possible Excitation Energy Transfer Pathways from LHCR to the PS I Core
V. Structure of the PS I-LHCI Supercomplex of Green Algae
A. Architecture of the PS I-LHCI Supercomplex from Green Algae
B. Identification and Arrangement of LHCI Antenna Proteins
C. Structural Features of the Green Algal LHCI Apoproteins
D. Arrangement of Chlorophylls and Carotenoids in Green Algal LHCI Subunits
VI. Chlorophyll Arrangement of PS I-LHCI and its Possible Effect on Excitation Energy Transfer Pathways
VII. Evolution of the PS I Complex
Acknowledgements
References
Chapter 8: Light Harvesting Modulation in Photosynthetic Organisms
Summary
I. Introduction
II. Light-Harvesting Protein Complexes
A. Phycobilin-Based Antenna
1. Hemidiscoidal Phycobilisomes
2. Atypical Phycobilisome Structures
B. Chlorophyll-Binding Three-Helix Light-Harvesting Protein Complexes
1. Light-Harvesting Complex I
2. Light-Harvesting Complex II
C. CP43-Like Six-Helix Chlorophyll-Binding Proteins
1. Iron-Stress-Induced Protein A
2. Prochlorophyte Chlorophyll a/b Protein
III. Light Acclimation and Adaptation
A. Phycobilisome-Based Chromatic Acclimation
B. Far-Red-Light-Induced Red-Shifted Phycobilisomes
1. Halomicronema Hongdechloris
2. Leptolyngbya sp. JSC-1
3. Synechococcus sp. PCC 7335
IV. Characteristics and Extended Functions of Light-Harvesting Protein Complex Superfamily Members
A. High-Light-Induced Proteins
B. One-Helix Proteins
C. Stress-Enhanced Proteins
D. Stress-Induced Early Light-Inducible Proteins
E. Four-Helix Light-Harvesting-Like Proteins
F. Evolutionary Relationships Among Chlorophyll-Binding Proteins
Acknowledgements
References
Chapter 9: Red-Shifted and Red Chlorophylls in Photosystems: Entropy as a Driving Force for Uphill Energy Transfer?
Summary
I. Introduction
II. “Uphill” Energy Transfer and Anti-Stokes Luminescence
III. “Red” vs. “Red-Shifted” Chlorophylls
A. “Red” Chlorophylls in Photosynthesis (Mainly LHCs, Photosystem I)
B. Far-Red Light Photoacclimation and Red-Shifted Chlorophylls
C. Red-Shifted Chlorophylls: Chlorophyll d from Acharyochloris Marina
D. Red-Shifted Chlorophylls: Chlorophyll f from Halomicronema hongdechloris
1. Fluorescence Emission and Excitation Spectra
2. Time-Resolved Fluorescence Spectra and Decay-Associated Spectra
3. Modeling of Energy Transfer Processes
4. Anti-Stokes Fluorescence Detection
IV. How Entropy Gain Supports “Uphill” Energy Transfer
V. Conclusions
Acknowledgements
References
Chapter 10: Modification of Energy Distribution Between Photosystems I and II by Spillover Revealed by Time-Resolved Fluorescence Spectroscopy
Summary
I. Introduction
II. Analysis of Energy Transfer
III. Energy Transfer Involving Antenna
IV. Evolution of Spillover Mechanisms
V. Benefits of the Direct-Type and Bridged-Type Spillovers
VI. Thylakoid Structure and Spillover
VII. Position of Quenching Site: Reaction Center or Peripheral Antenna
VIII. Concluding Remarks
Acknowledgements
References
Chapter 11: Perception of State Transition in Photosynthetic Organisms
Summary
I. Introduction
II. Photosystem Architecture
III. State Transitions
IV. Redox Poise of the Plastoquinone Pool
V. Role of Kinases and Phosphatases
VI. Phosphorylation of Thylakoid Membrane Proteins
VII. Thylakoid Membrane Dynamics in State Transitions
VIII. State Transitions and Cyclic Electron Flow
IX. Abiotic Stress and State Transition
X. Concluding Remarks
Acknowledgments
References
Part III: Photo-Induced Charge Separation and Primary Electron Transfer Processes
Chapter 12: Molecular Mechanism of Asymmetric Electron Transfer on the Electron Donor Side of Photosystem II
Summary
I. Introduction
II. Asymmetric Charge Distribution on the Radical Cation of the Chlorophyll Dimer P680
A. FTIR Detection of a Charge Distribution on P680+
B. Genetic Introduction of a Hydrogen Bond to the 131-keto C=O Group of PD1 and PD2
C. Identification of the Charge Localized Chlorophyll from the Assignments of the 131-keto C=O Bands of P680+
III. Asymmetric Photoreactions of Redox-Active Tyrosines, YZ and YD
A. Proton-Coupled Electron Transfer Reactions of YZ and YD
B. FTIR Detection of Proton Release from YD to the Bulk
IV. Mechanism of Asymmetric Electron Transfer from Tyrosines to P680+
V. Conclusions
Acknowledgements
References
Part IV: Membrane Dynamics and Regulation of Excitation Energy/Electron Transfer Processes
Chapter 13: Structure-Function Relationships in Chloroplasts: EPR Study of Temperature-Dependent Regulation of Photosynthesis, an Overview
Summary
I. Introduction
II. Electron and Proton Transport in Chloroplasts
A. Structural and Functional Organization of Photosynthetic Electron Transport Chain
1. Photosystem I
2. Photosystem II
3. Cytochrome b6f Complex
4. Lateral Heterogeneity of Thylakoids, Linear and Cyclic Electron Transport
B. Rate-Limiting Steps in the Chain of the Intersystem Electron Transport
C. Proton Pumping Across the Thylakoid Membrane and ATP Synthesis
III. Lipid-Soluble Nitroxide Radicals as Molecular Probes for Membrane Fluidity
IV. Temperature-Dependent Regulation of Electron and Proton Transport and ATP Synthesis in Chloroplasts
A. Regulation of Electron Transport
1. Photosystem II
2. The Intersystem Electron Transport
B. Proton Transport, ATP Synthesis, and Carbon Fixation
1. Trans-thylakoid Transfer of Protons
2. ATP Synthesis and ATP Hydrolysis
3. Chloroplasts In Situ: Electron Transport and Carbon Fixation
V. Discussion and Concluding Remarks
Acknowledgements
References
Chapter 14: Plasticity of Photosystem II. Fine-Tuning of the Structure and Function of Light-Harvesting Complex II and the Reaction Center
Summary
I. Introduction
II. Plasticity of Light-Harvesting Complex II
A. Light-Harvesting Complex II – The Peripheral Photosystem II Antenna
B. Functional Plasticity of Light-Harvesting Complex II; Non-photochemical Quenching
C. Structural Changes in Different Molecular Environments
D. Spectral Signatures in Reconstituted Light-Harvesting Complex II Membranes
E. Fluorescence Quenching and Excited-State Dynamics
III. Plasticity of Photosystem II
A. Two Different Physical Mechanisms Involved in Fv
B. Rate-Limiting Steps in Photosystem II
Acknowledgements
References
Chapter 15: Role of Lipids and Fatty Acids in the Maintenance of Photosynthesis and the Assembly of Photosynthetic Complexes During Photosystem II Turnover
Summary
I. Introduction
II. Biosynthesis of Glycerolipids and Fatty Acids Is a Genuine Plastid Process
III. Chloroplast Membrane Lipids Have Different Composition with Respect to the Rest of the Cell Membranes
IV. Thylakoid Lipids Are Enriched in Polyunsaturated Fatty Acids
V. Role of Lipids in the Maintenance of Photosynthetic Activity
A. MGDG
B. DGDG
C. SQDG
D. PG
E. PUFAs
VI. Role of Lipids and Fatty Acids in the Assembly and Turnover of Photosystem II
VII. Concluding Remarks
Acknowledgements
References
Chapter 16: Evolution and Function of the Extrinsic Subunits of Photosystem II
Summary
I. Introduction
II. Localization of Extrinsic Subunits in Photosystem II Structures
III. Functions of Each Extrinsic Subunit
A. PsbO
B. PsbV
C. PsbU
D. PsbP
E. PsbQ
F. Psb31
IV. Molecular Evolution of PsbP and PsbQ Family Proteins
V. Concluding Remarks
Acknowledgements
References
Chapter 17: Effect of Trehalose on the Functional Properties of Photosystem II
Summary
I. Introduction
II. Effects of Trehalose on the Oxygen-Evolving PS II Complexes
III. Effects of Trehalose on the Manganese-Depleted PS II Complexes
IV. Discussion
A. Trehalose Effects in Solution
B. Trehalose Effects in Dry Glassy Matrix
Acknowledgements
References
Chapter 18: Dynamic Models for the Electron Transfer Processes in Thylakoid Membranes
Summary
I. Introduction: Kinetic and Agent-Based Models
II. Modelling the Processes in Photosynthetic Membranes
A. Master Equations for the Description of the Processes in Multi-subunit Enzyme Complexes
B. Fluorescence Intensity Is Proportional to the Chlorophyll Concentration in the Excited State
C. Model of the Processes in PS II: Simulation of the Fluorescence Induction Curve
D. Electrical and Electrochemical Membrane Potentials
III. Modeling the Fluorescence Kinetics after Illumination by a Saturating Laser Pulse
IV. Detailed Kinetic Model of the Processes in Photosynthetic Membranes
V. Simplified Models
VI. Direct Multiparticle Models of Brownian Dynamics for the Description of Electron Transfer Involving Mobile Carriers
VII. Productive and Futile (Non-productive) Encounter Complexes
VIII. Probabilistic Models of Monte Carlo Type
IX. Models of Electron Fluxes Switching in Microalgae that Release Molecular Hydrogen
A. Organization of Photosynthetic Electron Flow in Hydrogen-Releasing Algae
B. Kinetic Models of Electron Flow Switching in PS II under Stress Conditions
C. Switching of Electron Fluxes at the Acceptor Side of PS I: Kinetic and Multiparticle Brownian Models
X. Concluding Remarks and Perspectives
Acknowledgements
References
Chapter 19: Photoacoustics Reveals Specific Thermodynamic Information in Photosynthesis
Summary
I. Introduction
A. Theory of Pulsed Photoacoustic Methodology
B. Thermodynamic Parameters of Photoreactions
II. Photoacoustic Measurements on PS I
A. Quinones in PS I
B. Physiological, Structural, and Kinetic Studies of the menA and menB Null Mutants
C. Thermodynamics of menA and menB Null Mutants
III. Thermodynamics of Charge Separation and S-State Cycle in PS II
A. Quantum Yield
B. Molecular Volume Changes
C. Enthalpy Changes In Vitro and In Vivo
D. Entropy Changes
E. Comparison of the Thermodynamics of Bacterial, Photosytem I, and PS II Reaction Centers
IV. Limitations and Potential Problems
V. Conclusions
Acknowledgements
References
Chapter 20: Plasticity of the Photosynthetic Energy Conversion and Accumulation of Metabolites in Plants in Response to Light Quality
Summary
I. Introduction
II. Spectral Effects on Photosynthesis
A. Photosynthetic Responses to Red Light
B. Photosynthetic Responses to Blue Light
C. Photosynthetic Responses to Green Light
D. Photoinhibition in Response to the Light Quality
E. Effects of Monochromatic Light Treatments on Photosynthetic Parameters
III. Accumulation of Photoprotective Compounds Under Different Light Spectra
A. Effects of Different Light Spectra on Carotenoid Content in Leaves
B. Effects on Anthocyanins by Different Light Spectra
IV. Concluding Remarks
Acknowledgements
References
Part V: Photosynthetic Hydrogen Production
Chapter 21: Feasibility of Sustainable Photosynthetic Hydrogen Production
Summary
I. Global Energy Economy – A Matter of Magnitude
II. Global Thermodynamics – only Solar Energy
III. Green Microalgae – A Complex Energy Managing Machine
A. Energy Currency – NADPH and ATP
B. Energy Harvest – Light Reactions
C. Energy Storage – CO2 Fixation and Storage
D. Energy Consumption – Mitochondrial Respiration and Fermentation
E. Energy Flux Management and Balance
IV. H2 Economy – The Way to Go
V. Microalgal H2 – Engineering a Photosynthetic Biorefinery
A. Dealing with the O2
1. Developed Methods
2. Efficiencies Vs Costs
B. Improving H2 Yield
C. Upscaling
1. Target Organism
2. Added Values
3. Bioreactor
VI. Conclusions
Acknowledgments
References
Chapter 22: Recent Advances in Microalgal Hydrogen Production
Summary
I. Introduction
II. Hydrogen Production by Microalgae
A. Light-Dependent Hydrogen Production
B. Dark Hydrogen Evolution
III. Hydrogenases
IV. Overcoming the Oxygen Toxicity for Hydrogen Production
A. Sulfur-Deprived Cultures
B. Phosphorous-Deprived Cultures
C. Nitrogen-Deprived Cultures
D. Carbon and Other Element Limitation/Deprivation
E. Application of Light Pulses
V. Genetic Approaches Improving Hydrogen Production
A. Directed Genetic Modulation of Photosystem II Activity
B. Decrease of Electron Distribution as an Alternative to Hydrogen Production Routes
C. Elimination of Electrons Dissipation to Cyclic Electron Flow
D. Influence of High Proton Gradient on Linear Electron Flow
VI. Conclusions
References
Author Index
Subject Index