The Photosynthetic Membrane

Professor Alexander V. Ruban, School of Biological and Chemical Sciences, Queen Mary University of London, UK. Professor Ruban is a Professor in Biophysics at Queen Mary University of London and holds a 'Professeur des Universites (Biochimie et biologie moleculaire)' title awarded by the French Ministry of Education. He obtained his PhD at the Institute of Plant Physiology at the Academy of Sciences of the Ukraine. His research has been instrumental in the discovery of the molecular basis of photoprotection in LHCII and the in vivo configuration and dynamics of higher plant xanthophylls in the thylakoid membrane. The Ruban Lab at Queen Mary is engaged in mechanistic photosynthesis research with a multidisciplinary approach applies molecular spectroscopy, biophysics and biochemistry to important problems in plant physiology, specifically, the role of the various components (proteins, lipids, pigments) and macrostructure in the functions and adaptive mechanisms of the photosynthetic membrane related to light harvesting and photoprotection in plants and algae. In addition, professor Ruban is interested in the universal properties of carotenoids in biological membranes, the molecular dynamics of these molecules in the modulation of membrane protein conformation and their functions.

Preface xi Acknowledgements xiii

1 Life, Energy and Light 1

1.1 The Definition of Life 1

1.2 The Energy of Matter 2

1.2.1 The Source of Life’s Energy 3

1.3 Energy for the Future 3

1.4 Photosynthesis by Life 4

1.4.1 Photon Energy Transformations 5

Reference 6

Bibliography 6

2 The Space of the Cell 7

2.1 The Cell Concept: Fundamental Nature of Life 7

2.2 Compartmentalization: The Cult of the Membrane 9

2.3 Membrane Components: Fundamentals of Proteins 12

2.4 Functional Classification of Membrane Proteins 15

Reference 16

Bibliography 16

3 The Photosynthetic Membrane: Outlook 17

3.1 Knowledge of the Pre-Atomic Structure Era: Organization of the Photosynthetic Membrane System 17

3.2 Composition of the Photosynthetic Membrane 21

3.2.1 Lipids 21

3.2.2 Lipid-Related Compounds of the Photosynthetic Membrane 22

3.2.3 Proteins and Protein Complexes 25

3.3 Oligomerization, Interactions and Mobility of the Photosynthetic Proteins: Enabling Functions and Adaptations 28

3.3.1 Oligomerization and Clustering of Photosynthetic Membrane Proteins 28

3.3.2 Protein Mobility 30

Reference 32

Bibliography 32

4 Popular Methods and Approaches to Study Composition, Structure and Functions of the Photosynthetic Membrane 33

4.1 Biochemistry and Molecular Biology Approaches 33

4.1.1 Isolation of Chloroplasts and Subchloroplast Particles 33

4.1.2 Isolation of Membrane Protein Complexes 35

4.1.3 Analysis of Lipids and Pigments 37

4.1.4 Protein Expression and Reconstitution In Vitro 38

4.1.5 Reconstitution of Membrane Proteins in Liposomes 39

4.1.6 Mutagenesis and Transgenic Manipulations 40

4.2 Visualization Techniques 41

4.2.1 Optical Microscopy 41

4.2.2 Electron Microscopy (EM) 42

4.2.3 Atomic Force Microscopy (AFM) 45

4.2.4 Crystallography Methods 45

4.3 Function Probing Methods 48

4.3.1 Absorption-Based Approaches 49

4.3.2 Raman Spectroscopy 54

4.3.3 Fluorescence-Based Approaches 55

References 65

Bibliography 65

5 Primary Processes of the Light Phase of Photosynthesis: Principles of Light Harvesting in Antennae 67

5.1 The Nature of Light 67

5.2 Absorption of Light by Molecules 71

5.3 Fate of Absorbed Light Energy 73

5.4 The Need for the Photosynthetic Antenna and the Fifth Fate of Excitation Energy 75

5.5 Photosynthetic Antenna Pigments 81

5.5.1 Chlorophylls 82

5.5.2 Xanthophylls 87

5.6 Variety and Classification of Photosynthetic Antennae 91

5.7 Principles of Light Harvesting: Summary 93

5.8 Connecting Light Harvesting Antenna to the Photosystems: Red Energy Traps 96

References 99

Bibliography 99

6 Towards the Atomic Resolution Structure of Light Harvesting Antennae: On the Path of Discoveries 101

6.1 Discovery and Primary Characterization of the Higher Plant Antenna Complex 102

6.2 Development of Isolation Methods: Intactness, Purity and Quantity 104

6.3 LHCII Crystallography: The Beginnings 107

6.4 Revealing the Atomic Resolution Structure of LHCII Antenna Complexes 111

6.4.1 Key Biochemical and Spectroscopic Advances that Aided the Emergence of the Current Atomic LHCIIb Structure 111

6.4.2 The New Structure of LHCIIb 115

6.5 Structure of a Minor LHCII Complex CP29 126

6.6 Comparison of LHCII Structure with the Structure of a Simpler Light Harvesting Complex from Purple Bacteria, LH2 129

References 133

Bibliography 134

7 Structural Integration of Antennae within Photosystems 135

7.1 Light Harvesting Complexes Gene Family 136

7.2 Toward the Structure of a Complete Photosystem II Unit: Supercomplexes 137

7.3 Supramolecular Structure of Photosystem I: LHCI 145

7.4 Photosynthetic Membrane Protein Landscapes 147

7.5 Robustness of the Light Harvesting Antenna Design: Resurrecting the Structure to Preserve the Function 150

References 156

Bibliography 157

8 Dynamics of Light Harvesting Antenna: Spectroscopic Insights 159

8.1 Steady-State Optical Spectroscopy of LHCII: Composition and Order 160

8.2 Time-Resolved Spectroscopy of LHCII: Energy Migration 165

8.2.1 Time-Resolved Fluorescence Spectroscopy 165

8.2.2 Time-Resolved Absorption Spectroscopy 167

8.3 Spectral and Structural Identity of LHCII Xanthophylls 170

8.4 Plasticity of Light Harvesting Antenna Design: Tailoring the Structure to Optimize the Function 176

8.5 LHCII Oligomerization: Dynamics of the ‘Programmed Solvent’ 179

8.5.1 Alterations in the Spectral Properties of LHCII 179

8.5.2 Structural Changes within LHCII 183

8.6 Kinetics of the Collective LHCII Transition into the Dissipative State: Exploring ‘The Switch’ Control 189

References 194

Bibliography 195

9 Adaptations of the Photosynthetic Membrane to Light 197

9.1 The Need for Light Adaptations and their Various Strategies 198

9.2 Long-Term Regulation of the Photosystem Ratio and their Antenna Size: Acclimation 201

9.3 Short-Term Adaptations to Light Quality: State Transitions 202

9.3.1 The Phenomenology of State Transitions 202

9.3.2 The Molecular Mechanism of State Transitions 205

9.3.3 Chromatic Adaptations in Plants Lacking the Polypeptides of the Major LHC II Complex 209

9.3.4 Future of State Transitions Research 212

9.4 Short-Term Adaptations to Light Quantity 214

9.4.1 Control of Excess Light Energy in Photosystem II – The Phenomenon of Nonphotochemical Chlorophyll Fluorescence Quenching (NPQ) 214

9.4.2 The Molecular Components and Processes Involved in NPQ 217

9.4.3 Future of qE Research 238

References 238

Bibliography 239

10 What is in it for Plant, Biosphere and Mankind? 241

10.1 Science and Society 241

10.2 Energy Balance of Photosynthesis: A Wasteful Process? 242

10.3 Crops and Light Harvesting 247

10.4 Light Harvesting Principles for Future Applications: Liberation from Saturation Constraints 249

10.5 Effects of Changing Climate – The Onset of Disorder 253

Bibliography 254

11 Conclusions 257

Index 261