Table Of ContentThe Photosynthetic Membrane
Rupan_ffirs.indd i 8/29/2012 5:31:53 PM
The Photosynthetic
Membrane
Molecular Mechanisms and Biophysics
of Light Harvesting
ALEXANDER RUBAN
School of Biological and Chemical Sciences,
Queen Mary, University of London, UK
Rupan_ffirs.indd iii 8/29/2012 5:31:53 PM
This edition first published 2013
© 2013 John Wiley & Sons, Ltd.
Registered Office
John Wiley & Sons, Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, United Kingdom
For details of our global editorial offices, for customer services and for information about how to apply for
permission to reuse the copyright material in this book please see our website at
www.wiley.com .
The right of the author to be identified as the author of this work has been asserted in accordance with the
Copyright, Designs and Patents Act 1988.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in
any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by
the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher.
Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be
available in electronic books.
Designations used by companies to distinguish their products are often claimed as trademarks. All brand names
and product names used in this book are trade names, service marks, trademarks or registered trademarks of their
respective owners. The publisher is not associated with any product or vendor mentioned in this book. This
publication is designed to provide accurate and authoritative information in regard to the subject matter covered.
It is sold on the understanding that the publisher is not engaged in rendering professional services. If professional
advice or other expert assistance is required, the services of a competent professional should be sought.
The publisher and the author make no representations or warranties with respect to the accuracy or completeness
of the contents of this work and specifically disclaim all warranties, including without limitation any implied
warranties of fitness for a particular purpose. This work is sold with the understanding that the publisher is not
engaged in rendering professional services. The advice and strategies contained herein may not be suitable for
every situation. In view of ongoing research, equipment modifications, changes in governmental regulations, and
the constant flow of information relating to the use of experimental reagents, equipment, and devices, the reader
is urged to review and evaluate the information provided in the package insert or instructions for each chemical,
piece of equipment, reagent, or device for, among other things, any changes in the instructions or indication of
usage and for added warnings and precautions. The fact that an organization or Website is referred to in this work
as a citation and/or a potential source of further information does not mean that the author or the publisher
endorses the information the organization or Website may provide or recommendations it may make. Further,
readers should be aware that Internet Websites listed in this work may have changed or disappeared between
when this work was written and when it is read. No warranty may be created or extended by any promotional
statements for this work. Neither the publisher nor the author shall be liable for any damages arising herefrom.
Library of Congress Cataloguing-in-Publication Data
Ruban, Alexander (Alexander V.)
The photosynthetic membrane : molecular mechanisms and biophysics of light harvesting / Alexander Ruban.
p. cm.
Includes index.
ISBN 978-1-119-96054-6 (cloth) – ISBN 978-1-119-96053-9 (pbk.)
1. Photosynthesis. 2. Photosynthetic pigments. 3. Light absorption. I. Title.
QK882.R83 2013
572′.46–dc23
2012025765
A catalogue record for this book is available from the British Library.
Set in 10/12pt Times by SPi Publisher Services, Pondicherry, India
1 2013
Rupan_ffirs.indd iv 8/29/2012 5:31:53 PM
Dedicated to my family
Rupan_ffirs.indd v 8/29/2012 5:31:53 PM
Contents
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
Rupan_ftoc.indd vii 8/29/2012 5:26:44 PM
viii Contents
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
Rupan_ftoc.indd viii 8/29/2012 5:26:45 PM
Contents ix
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
Rupan_ftoc.indd ix 8/29/2012 5:26:46 PM
x Contents
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
Rupan_ftoc.indd x 8/29/2012 5:26:47 PM
Preface
The science of biophysics of light harvesting has accumulated vast amount of knowledge
in the last 20 years about the workings of the photosynthetic membrane of higher plants.
The subject is a manifestation of a grand molecular design of the complex photosynthetic
machinery performing a sequence of primary energy transformation events. Hence, it
represents an excellent example for learning the principles of structure and mechanisms of
functioning of membrane proteins, their interactions with each other and their cofactors,
dynamics in the membrane and in the isolated state and various mechanisms of adaptation
to the environment. The author’s own 30 years’ experience in the field of biophysics of
photosynthesis and work done by his numerous colleagues has been presented in the
context of gradual explanation of complexity, historical development and multidisciplinary
character of the subject, T he Photosynthetic Membrane . The need for such a text is long
overdue, since it does not cover the whole photosynthesis but focuses on its light phase
processes, concentrating on the light harvesting: a well-structured and regulated process
that ensures phenomenal flexibility of adaptations of plants to light that are essential for
their survival. The book starts from a general introduction to the essential features of life;
one of the most important is the energy requirement that is fulfilled almost solely by sunlight.
Further, the advantages and peculiar physicochemical features of the nanoscale level of the
photosynthetic membrane organization are described and the general makeup is presented
setting the scene and preparing the reader for the detailed up-to-date description of numer-
ous methods of investigation of the photosynthetic membrane structure and functions,
light harvesting principles, atomic structure of light harvesting antenna complexes, the
macrostructural organization and integration of antennae within photosystem complexes,
dynamic nature of light harvesting proteins studied by various spectroscopies and adaptations
of the light harvesting machinery in the intact membrane to light. This book also contains
a chapter considering the potential of the educational and practical applications of the
knowledge obtained in studies of the photosynthetic membrane organization and light
harvesting p rocesses. The author contemplates the role of the fundamental knowledge in
general and explains possible ways it can be used in crop science, solar energy utilization
by mankind and in solving the problems associated with the global climate change.
The author addresses this book, first of all, to the final year undergraduate students of
various biology specializations. Therefore, he makes all effort to adapt it to different levels
of training in chemistry and physics. The level of complexity gradually increases towards
the end of the book making it relevant to postgraduate students and for a broader audience
of those involved in photosynthesis research as well as bioenergetic membranes in general.
With this book, the author hopes to awake an interest of a broad audience of students,
scientists and those who are attracted to the phenomenon of energy transformation
processes in living nature and welcomes any feedback.
Rupan_fpref.indd xi 8/29/2012 5:27:34 PM
Welch Schauspiel! Aber ach! Ein Schauspiel nur!
Wo fass ich dich, unendliche Natur?
Euch Brüste, wo? Ihr Quellen alles Lebens ,
An denen Himmel und Erde hängt ,
Dahin die welke Brust sich drängt -
Ihr quellt, ihr tränkt, und schmacht ich so vergebens?
(Ah! what a view! Alas and but a view!
Where shall I, endless Nature, seize on you?
Ye breasts, and where? Ye sources of all life
On which the heaven, the earth depends ,
Towards which the withered bosom tends —
Ye nourish, flow; yet vain my thirsty strife?)
Faust: Der Tragödie erster Teil
by
Johann Wolfgang von Goethe
For undergraduate and postgraduate students and also those with an interest in the
molecular engines of life.
Rupan_fpref.indd xii 8/29/2012 5:27:34 PM
