Photosynthesis: Molecular Approaches to Solar Energy Conversion

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