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 xiii1 Life, Energy and Light 11.1 The Definition of Life 11.2 The Energy of Matter 21.2.1 The Source of Life’s Energy 31.3 Energy for the Future 31.4 Photosynthesis by Life 41.4.1 Photon Energy Transformations 5Reference 6Bibliography 62 The Space of the Cell 72.1 The Cell Concept: Fundamental Nature of Life 72.2 Compartmentalization: The Cult of the Membrane 92.3 Membrane Components: Fundamentals of Proteins 122.4 Functional Classification of Membrane Proteins 15Reference 16Bibliography 163 The Photosynthetic Membrane: Outlook 173.1 Knowledge of the Pre-Atomic Structure Era: Organization of the Photosynthetic Membrane System 173.2 Composition of the Photosynthetic Membrane 213.2.1 Lipids 213.2.2 Lipid-Related Compounds of the Photosynthetic Membrane 223.2.3 Proteins and Protein Complexes 253.3 Oligomerization, Interactions and Mobility of the Photosynthetic Proteins: Enabling Functions and Adaptations 283.3.1 Oligomerization and Clustering of Photosynthetic Membrane Proteins 283.3.2 Protein Mobility 30Reference 32Bibliography 324 Popular Methods and Approaches to Study Composition, Structure and Functions of the Photosynthetic Membrane 334.1 Biochemistry and Molecular Biology Approaches 334.1.1 Isolation of Chloroplasts and Subchloroplast Particles 334.1.2 Isolation of Membrane Protein Complexes 354.1.3 Analysis of Lipids and Pigments 374.1.4 Protein Expression and Reconstitution In Vitro 384.1.5 Reconstitution of Membrane Proteins in Liposomes 394.1.6 Mutagenesis and Transgenic Manipulations 404.2 Visualization Techniques 414.2.1 Optical Microscopy 414.2.2 Electron Microscopy (EM) 424.2.3 Atomic Force Microscopy (AFM) 454.2.4 Crystallography Methods 454.3 Function Probing Methods 484.3.1 Absorption-Based Approaches 494.3.2 Raman Spectroscopy 544.3.3 Fluorescence-Based Approaches 55References 65Bibliography 655 Primary Processes of the Light Phase of Photosynthesis: Principles of Light Harvesting in Antennae 675.1 The Nature of Light 675.2 Absorption of Light by Molecules 715.3 Fate of Absorbed Light Energy 735.4 The Need for the Photosynthetic Antenna and the Fifth Fate of Excitation Energy 755.5 Photosynthetic Antenna Pigments 815.5.1 Chlorophylls 825.5.2 Xanthophylls 875.6 Variety and Classification of Photosynthetic Antennae 915.7 Principles of Light Harvesting: Summary 935.8 Connecting Light Harvesting Antenna to the Photosystems: Red Energy Traps 96References 99Bibliography 996 Towards the Atomic Resolution Structure of Light Harvesting Antennae: On the Path of Discoveries 1016.1 Discovery and Primary Characterization of the Higher Plant Antenna Complex 1026.2 Development of Isolation Methods: Intactness, Purity and Quantity 1046.3 LHCII Crystallography: The Beginnings 1076.4 Revealing the Atomic Resolution Structure of LHCII Antenna Complexes 1116.4.1 Key Biochemical and Spectroscopic Advances that Aided the Emergence of the Current Atomic LHCIIb Structure 1116.4.2 The New Structure of LHCIIb 1156.5 Structure of a Minor LHCII Complex CP29 1266.6 Comparison of LHCII Structure with the Structure of a Simpler Light Harvesting Complex from Purple Bacteria, LH2 129References 133Bibliography 1347 Structural Integration of Antennae within Photosystems 1357.1 Light Harvesting Complexes Gene Family 1367.2 Toward the Structure of a Complete Photosystem II Unit: Supercomplexes 1377.3 Supramolecular Structure of Photosystem I: LHCI 1457.4 Photosynthetic Membrane Protein Landscapes 1477.5 Robustness of the Light Harvesting Antenna Design: Resurrecting the Structure to Preserve the Function 150References 156Bibliography 1578 Dynamics of Light Harvesting Antenna: Spectroscopic Insights 1598.1 Steady-State Optical Spectroscopy of LHCII: Composition and Order 1608.2 Time-Resolved Spectroscopy of LHCII: Energy Migration 1658.2.1 Time-Resolved Fluorescence Spectroscopy 1658.2.2 Time-Resolved Absorption Spectroscopy 1678.3 Spectral and Structural Identity of LHCII Xanthophylls 1708.4 Plasticity of Light Harvesting Antenna Design: Tailoring the Structure to Optimize the Function 1768.5 LHCII Oligomerization: Dynamics of the ‘Programmed Solvent’ 1798.5.1 Alterations in the Spectral Properties of LHCII 1798.5.2 Structural Changes within LHCII 1838.6 Kinetics of the Collective LHCII Transition into the Dissipative State: Exploring ‘The Switch’ Control 189References 194Bibliography 1959 Adaptations of the Photosynthetic Membrane to Light 1979.1 The Need for Light Adaptations and their Various Strategies 1989.2 Long-Term Regulation of the Photosystem Ratio and their Antenna Size: Acclimation 2019.3 Short-Term Adaptations to Light Quality: State Transitions 2029.3.1 The Phenomenology of State Transitions 2029.3.2 The Molecular Mechanism of State Transitions 2059.3.3 Chromatic Adaptations in Plants Lacking the Polypeptides of the Major LHC II Complex 2099.3.4 Future of State Transitions Research 2129.4 Short-Term Adaptations to Light Quantity 2149.4.1 Control of Excess Light Energy in Photosystem II – The Phenomenon of Nonphotochemical Chlorophyll Fluorescence Quenching (NPQ) 2149.4.2 The Molecular Components and Processes Involved in NPQ 2179.4.3 Future of qE Research 238References 238Bibliography 23910 What is in it for Plant, Biosphere and Mankind? 24110.1 Science and Society 24110.2 Energy Balance of Photosynthesis: A Wasteful Process? 24210.3 Crops and Light Harvesting 24710.4 Light Harvesting Principles for Future Applications: Liberation from Saturation Constraints 24910.5 Effects of Changing Climate – The Onset of Disorder 253Bibliography 25411 Conclusions 257Index 261

“I strongly recommend ‘‘The Photosynthetic Membrane’’, by Alexander Ruban, to all the advanced undergraduate and graduate students and even researchers of Plant Biology, Plant Sciences, Biochemistry, Biophysics, Molecular Biology, Biotechnology and Bioengineering.  Further, all libraries around the World must acquire a copy of this book for their students and teaching faculty. It is indeed a beautiful and refreshing book at a time when we are just too busy with only technical aspects of a problem.”  (Photosynth Res, 27 May 2014)“The Photosynthetic Membrane: Molecular Mechanisms of Light Harvesting will appeal to a wide audience of undergraduate and postgraduate students as well as researchers working in the fields of biochemistry, molecular biology, biophysics, plant science and bioengineering.”  (Biotechnology, Agronomy, Society, Environment, 1 December 2012)