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Photochemical & Photobiological Sciences
Comprehensive Series in Photochemical & Photobiological Sciences
Series Editors: Donat-Peter Häder, Friedrich-Alexander Universitat,
Erlangen, G
ermany
Giulio Jori, University of Padova, Italy
Initiated by the European Society for Photobiology, this series
provides comprehensive overviews on specific areas of photoscience.
It gives in-depth coverage of the very different fields related to light
effects and embraces both well-established and emerging areas.
www.rsc.org/photo
Primary Processes of Photosynthesis - Part 2
Principles and Apparatus
Renger
The primary processes of photosynthesis lead to transformation
of solar radiation into electrochemical Gibbs energy - the driving
force for life on Earth.
These intricate and fascinating processes have been researched
and analysed for generations and in this two part set the Editor
has brought together contributions from numerous leading
scientific experts providing a compendium of information offering
the most up-to-date understanding of the primary processes of
photosynthesis.
Part 2 of this set covers the following topics:
VI. S
tructure and Function of Reaction Centers and
Photosystems
VII.
Electron Transport Chains and Phosphorylation
VIII. Evolution
This outstanding work represents the activity of researchers across
the globe and will be of utmost interest to all those working in
the fields of Photochemistry, Bio-organic Chemistry, Bio-inorganic
Chemistry, Crystallography, Biological Sciences, Biochemistry and
related disciplines.
9 780854 042364
ISBN 978-0-85404-236-4
Comprehensive Series in Photochemical & Photobiological Sciences
Edited by Gernot Renger
Primary Processes of
Photosynthesis - Part 2
Principles and Apparatus

COMPREHENSIVE SERIES IN PHOTOCHEMISTRY AND PHOTOBIOLOGY
Series Editors
Donat P. Ha¨der
Professor of Botany
and
Giulio Jori
Professor of Chemistry
European Society for Photobiology

COMPREHENSIVE SERIES IN PHOTOCHEMISTRY AND PHOTOBIOLOGY
Series Editors: Donat P. Ha¨der and Giulio Jori
Titles in this Series:
Volume 1 UV Eﬀects in Aquatic Organisms and Ecosystems
Edited by E.W. Helbling and H. Zagarese
Volume 2 Photodynamic Therapy
Edited by T. Patrice
Volume 3 Photoreceptors and Light Signalling
Edited by A. Batschauer
Volume 4 Lasers and Current Optical Techniques in Biology
Edited by G. Palumbo and R. Pratesi
Volume 5 From DNA Photolesions to Mutations, Skin Cancer and Cell
Death
Edited by E´. Sage, R. Drouin and M. Rouabhia
Volume 6 Flavins: Photochemistry and Photobiology
Edited by E. Silva and A.M. Edwards
Volume 7 Photodynamic Therapy with ALA: A Clinical Handbook
Edited by R. Pottier, B. Krammer, R. Baumgartner, H. Stepp
Volume 8 Primary Processes of Photosynthesis, Part 1: Principles and
Apparatus
Edited by G. Renger
Volume 9 Primary Processes of Photosynthesis, Part 2: Principles and
Apparatus
Edited by G. Renger
Visit our website at http://www.rsc.org/Publishing/Books/PPS

COMPREHENSIVE SERIES IN PHOTOCHEMISTRY AND
PHOTOBIOLOGY–VOLUME 9
Primary Processes of
Photosynthesis, Part 2
Principles and Apparatus
Editor
Gernot Renger
Technische Universita¨t Berlin
Max-Volmer-Laboratorium fu¨r Biophysikalische Chemie
Sekr. PC 14
Strasse des 17. Juni 135
D–10623 Berlin, Germany

ISBN: 978-0-85404-236-4
ISBN of set: 978-0-85404-364-4
A catalogue record for this book is available from the British Library
rEuropean Society of Photobiology 2008
All rights reserved
Apart from fair dealing for the purposes of research for non-commercial purposes or for
private study, criticism or review, as permitted under the Copyright, Designs and Patents
Act 1988 and the Copyright and Related Rights Regulations 2003, this publication may not
be reproduced, stored or transmitted, in any form or by any means, without the prior
permission in writing of The Royal Society of Chemistry, or in the case of reproduction in
accordance with the terms of licences issued by the Copyright Licensing Agency in the UK,
or in accordance with the terms of the licences issued by the appropriate Reproduction
Rights Organization outside the UK. Enquiries concerning reproduction outside the terms
stated here should be sent to The Royal Society of Chemistry at the address printed on this
page.
Published by The Royal Society of Chemistry,
Thomas Graham House, Science Park, Milton Road,
Cambridge CB4 0WF, UK
Registered Charity Number 207890
For further information see our web site at www.rsc.org

Preface for the ESP Series in
Photochemical and Photobiological Sciences
‘‘Its not the substance, it’s the dose which makes something poisonous!’’ When
Paracelsius, a German physician of the 14th century made this statement he
probably did not think about light as one of the most obvious environmental
factors. But his statement applies as well to light. While we need light, for
example for vitamin D production, too much light might cause skin cancer. The
dose makes the diﬀerence. These diverse ﬁndings of light eﬀects have attracted
the attention of scientists for centuries. The photosciences represent a dynamic
multidisciplinary ﬁeld that includes such diverse subjects as behavioral re-
sponses of single cells, cures for certain types of cancer and the protective
potential of tanning lotions. It also includes photobiology and photochemistry,
photomedicine as well as the technology for light production, ﬁltering and
measurement. Light is a common theme in all these areas. In recent decades a
more molecular centered approach has changed both the depth and the quality
of the theoretical as well as the experimental foundation of photosciences.
An example of the relationship between global environment and the bio-
sphere is the recent discovery of ozone depletion and the resulting increase in
high-energy ultraviolet radiation. The hazardous eﬀects of high-energy ultra-
violet radiation on all living systems is now well established. This discovery of
the result of ozone depletion put photosciences at the center of public interest
with the result that, in an unparalleled eﬀort, scientists and politicians worked
closely together to come to international agreements to stop the pollution of the
atmosphere.
The changed recreational behavior and the correlation with several diseases
in which sunlight or artiﬁcial light sources play a major role in the causation of
clinical conditions (e.g., porphyrias, polymorphic photodermatoses,Xeroderma
pigmentosumand skin cancers) have been well documented. As a result, in some
countries (e.g., Australia) public services inform people about the potential risk
of extended periods of sun exposure every day. The problems are often
aggravated by the phototoxic or photoallergic reactions produced by various
environmental pollutants, food additives or therapeutic and cosmetic drugs.
However, if properly used, light-stimulated processes can induce important
beneﬁcial eﬀects in biological systems, such as the elucidation of several aspects
of cell structure and function. Novel developments are centered around
v

photodiagnostic and phototherapeutic modalities for the treatment of cancer,
arthrosclerosis, several autoimmune diseases, neonatal jaundice and others. In
addition, classic research areas such as vision and photosynthesis are still very
active. Some of these developments are unique to photobiology, since the
peculiar physicochemical properties of electronically excited biomolecules often
lead to the promotion of reactions that are characterized by high levels of
selectivity in space and time. Besides the biologically centered areas, technical
developments have paved the way for the harnessing of solar energy to produce
warm water and electricity or the development of environmentally friendly
techniques for addressing problems of large social impact (e.g., the deconta-
mination of polluted waters). While also in use in Western countries, these
techniques are of great interest for developing countries.
The European Society for Photobiology (ESP) is an organization that aims
to develop and coordinate the very diﬀerent ﬁelds of photosciences in terms of
public knowledge and scientiﬁc interests. Owing to the ever increasing demand
for a comprehensive overview of the photosciences the ESP decided to initiate
an encyclopedic series, the ‘‘Comprehensive Series in Photochemical and
Photobiological Sciences’’. This series is intended to give an in-depth coverage
over all the very diﬀerent ﬁelds related to light eﬀects. It will allow investiga-
tors, physicians, students, industry and laypersons to obtain an updated record
of the state-of-the-art in speciﬁc ﬁelds, including ready access to the recent
literature. Most importantly, such reviews give a critical evaluation of the
directions that the ﬁeld is taking, outline hotly debated or innovative topics and
even suggest a redirection if appropriate. It is our intention to produce the
monographs at a suﬃciently high rate to generate a timely coverage of both
well established and emerging topics. As a rule, the individual volumes are
commissioned; however, comments, suggestions or proposals for new subjects
are welcome.
Donat-P. Ha¨der and Giulio Jori
Spring 2002
vi PREFACE

Volume Preface
The interaction of living matter with electromagnetic radiation in the near-
ultraviolet (NUV), visible (Vis) and near-infrared (NIR) regions is a most
important topic in life sciences. The radiation from a huge extraterrestrial
fusion reactor, the sun, not only provides the unique Gibbs energy for the
development and sustenance of almost all forms of life on our planet but also
plays a key role in several regulatory functions such as synchronizing biological
clocks and information transfer processes (e.g., vision, photomorphogenesis,
phototaxis, communication via bioluminescence signals).
It is, therefore, not surprising that the sun played a central role in mankind’s
cultural development and religious admiration throughout the world, ranging
from the great Aton hymn of the old Egyptians, to the worshippers of the sun in
India and to the highly advanced ancient Indian societies (Mayas and Incas) in
the Western hemisphere.
Among the diﬀerent light-induced processes, photosynthesis is fundamental
and unique because it enables the biological transformation of solar radiation
into (electro)chemical Gibbs energy. Furthermore, it is the most abundant
chemical reaction on the earth’s surface (land and oceans), with an estimated
turnover of 300–500 billion tons of CO
2per year, converted into carbohydrates
and subsequent products. The crucial role of photosynthesis can be best
summarized in only four words: ‘‘Life is bottled sunshine’’ [Wynword Read,
Martyrdom of Man, 1924].
Studies on photosynthesis date back to the early days of the development of
natural sciences. The fundamental principles of energy transformation in
general and photosynthesis in particular, described by the ﬁrst and second
law of thermodynamics, were outlined in the nineteenth century by R. J. Mayer
and L. Boltzmann, respectively (Chapter 1). Nowadays, the unraveling of the
underlying structural and functional organization of photosynthesis focuses on
intensive research activities. The high scientiﬁc relevance of topics related to the
subject is best illustrated by the impressive list of about 20 Nobel laureates that
were awarded the Prize for their work performed in this ﬁeld, starting with
Richard Willsta¨tter in 1915 and Hans Fischer in 1930 and their pioneering
studies on the chemistry of chlorophylls as the key pigments of the photo-
synthetic apparatus [for an excursion into the history of photosynthesis
vii

research, I recommend the excellent bookDiscoveries in Photosynthesis
(Govindjee, J. T. Beatty, H. Gest, J. F. Allen, eds.), Springer, 2005].
The overall process of photosynthesis consists of several reactions, which
take place in quite diﬀerent time domains, covering a range from femtoseconds
(light absorption) up to hours (long-term acclimation) and even days or months
(plant growth). Within this wide time region the light-driven reactions leading
to the primary metabolites (‘‘energy rich’’ bound hydrogen and ATP) are the
fastest reactions, which are accomplished within milliseconds and referred to as
‘‘Primary Processes of Photosynthesis’’. Research on this topic is not only a
fascinating part of pure science but it can also oﬀer nature’s masterpiece for
solar energy exploitation as a blueprint for the technical development of devices
aiming at contributing to solutions of mankind’s Gibbs energy demands.
This edition of two volumes is restricted to topics on the ‘‘Primary Processes
of Photosynthesis’’. As several books in this ﬁeld already exist (see, for example,
Advances in Photosynthesis and Respiration, Series editor Govindjee, Springer),
one might ask: Why publish another two? The major reason for doing so is the
enormous progress achieved in molecular biology and X-ray diﬀraction crystal-
lography of membrane proteins during the last two decades, which has enabled,
in combination with developments of sophisticated spectroscopic methods of
very high time resolution, much deeper insight into the mechanisms and
structure of the apparatus down to the level of atomic dimensions. Furthermore,
signiﬁcant advances in the methodology of theory (quantum chemistry, mole-
cular mechanics) oﬀer a new basis for a better understanding of structure–
function relationships, including the role of dynamic processes.
This publication is an ambitious attempt to provide a synoptic state-of-the-
art picture of the primary processes of photosynthesis by casting together the
mosaics of detailed knowledge described by leading experts in the ﬁeld. Twenty
two chapters have been written by 42 authors from Europe, USA, Japan and
Australia. The wealth of information appears to be best presented in two
diﬀerent volumes (Parts 1 and 2). Part 1 describes the photophysical principles,
photosynthetic pigments and light harvesting/adaptation/stress. It is divided
into ﬁve sections: Section I is an introduction to the ﬁeld, giving an overview
on the primary processes of photosynthesis in a single chapter presented by
G. Renger. Section II also contains a single chapter, by T. Renger, which
provides the basic theoretical background of the underlying photophysical
principles (excitation energy and electron transfer) for light harvesting and the
electron transport chain. Section III describes the properties of the main
pigments in two chapters, i.e. the chlorophylls in Chapter 3 by H. Scheer and
the carotenoids in Chapter 4 by Koyama et al. In Section IV, ﬁve chapters deal
with light harvesting, regulatory control of excitation energy ﬂuxes and
Chapter 5, presented by Law and Cogdell, provides an insight into the structure
and function of the antenna system of anoxygenic photosynthetic bacteria, and
in Chapter 6, presented by Mimuro et al., the properties of the antenna system
of oxygenic cyanobacteria are Morosinotto and Bassi, in Chapter 7, and van
Amerongen and Croce, in Chapter 8, summarize our knowledge on the antenna
systems of Photosystem I and Photosystem II, respectively, of higher plants.
viii VOLUME PREFACE

Chapter 9, by Gilmore and Li, presents information on the regulatory control
of the antenna function in plants. Section V describes, in a single Chapter 10 by
Vass and Aro, the eﬀects induced by light stress.
Part 2 is divided into three sections: Section VI (the numbering is continued
from Part 1) is devoted to the structure and function of reaction centers in
anoxygenic photosynthetic bacteria and the two photosystems of oxygen
evolving organisms. Lancaster in Chapter 11 and Parson in the complementary
Chapter 12 summarize the current state of knowledge on the structure and the
functional pattern, respectively, of reaction centers in anoxygenic bacteria.
Analogously, structure and functional pattern of Photosystem I (PS I) and
Photosystem II (PS II) in oxygen-evolving organisms are described in the foll-
owing ﬁve chapters presented by Fromme et al. (Chapter 13: structure of PS I),
Setif and Leibl (Chapter 14: functional pattern of PSI), Zouni (Chapter 15:
structure of PS II), G. Renger (Chapter 16: functional pattern of PS II) and
J. Messinger and G. Renger (Chapter 17: oxygen evolution). Section VII on
electron transport chains and photophosphorylation contains four chapters:
anoxygenic bacteria are described by Verme´glio (Chapter 18), oxygen-evolving
cyanobacteria by Peschek (Chapter 19), the cytochrome b
6f complex by Cramer
et al. (Chapter 20), and in Chapter 21 Junge summarizes our knowledge on
photophosphorylation. In Section VIII, Larkum describes, in Chapter 22, the
evolution of photosynthetic organisms.
All the chapters in these two parts provide a modern and updated view of the
corresponding topics. Accordingly, this edition is not only a most valuable text
for graduate students but it is also addressed to all scientists who are interested
in the ﬁeld of the primary processes of photosynthesis. It is my sincere hope that
these two books will entice young people into this exciting research area with
the aim of addressing successfully the challenging problems of high relevance
that are still awaiting a satisfactory answer.
I have many people to thank. First of all, the authors for their eﬀorts to oﬀer
the reader excellent chapters and for their positive responses to my suggestions.
Without their invaluable cooperation there would be no books. My thanks also
go to Susanne Renger and Solweig Nothing for their continuous help in the
preparation of electronic versions of ﬁgures and typing of manuscripts,
respectively.
I am most grateful to my wife Eva for all her enthusiasm in supporting this
work and her invaluable help during periods of frustration and disappointment
by sharing her optimism in ﬁnally reaching the desired goal.
I wish all readers a pleasant and stimulating journey through the fascinating
‘‘world’’ of the primary processes of photosynthesis.
Gernot Renger
ixVOLUME PREFACE

Contents
Part 1: Photophysical Principles, Pigments and Light Harvesting/Adaptation/
Stress
I. Introduction
Chapter 1 Overview of Primary Processes of Photosynthesis 5
Gernot Renger
II. Basic Photophysical Principles
Chapter 2 Absorption of Light, Excitation Energy Transfer and
Electron Transfer Reactions 39
Thomas Renger
III. Pigments
Chapter 3 Chlorophylls 101
Hugo Scheer
Chapter 4 Photophysical Properties and Light-Harvesting and
Photoprotective Functions of Carotenoids in Bacterial
Photosynthesis: Structural Selections 151
Yasushi Koyama, Yoshinori Kakitani and
Yasutaka Watanabe
IV. Structure and Function of Antenna Systems
Chapter 5 The Light-Harvesting System of Purple Anoxygenic
Photosynthetic Bacteria 205
Christopher J. Law and Richard J. Cogdell
Chapter 6 Oxygen-Evolving Cyanobacteria 261
Mamoru Mimuro, Masami Kobayashi, Akio Murakami,
Tohru Tsuchiya and Hideaki Miyashita
xi

Chapter 7 Antenna System of Higher Plants’ Photosystem I and Its
Interaction with the Core Complex 301
Tomas Morosinotto and Roberto Bassi
Chapter 8 Structure and Function of Photosystem II
Light-Harvesting Proteins (Lhcb) of Higher Plants 329
Herbert van Amerongen and Roberta Croce
Chapter 9 Regulatory Control of Antenna Function in Plants 369
Adam M. Gilmore and Xiao-Ping Li
V. Light Stress
Chapter 10 Photoinhibition of Photosynthetic Electron Transport 393
Imre Vass and Eva-Mari Aro
Subject Index 427
Part 2: Reaction Centers/Photosystems, Electron Transport Chains,
Photophosphorylation and Evolution
VI. Structure and Function of Reaction Centers and Photosystems
Chapter 11 Structures of Reaction Centers in Anoxygenic Bacteria 5
C. Roy D. Lancaster
Chapter 12 Functional Pattern of Reaction Centers in Anoxygenic
Photosynthetic Bacteria 57
William W. Parson
Chapter 13 Structure and Function of Photosystem I 111
Raimund Fromme, Ingo Grotjohann and Petra Fromme
Chapter 14 Functional Pattern of Photosystem I in Oxygen Evolving
Organisms 147
Pierre Se´tif and Winfried Leibl
Chapter 15 From Cell Growth to the 3.0 A
˚
Resolution Crystal
Structure of Cyanobacterial Photosystem II 193
Athina Zouni
Chapter 16 Functional Pattern of Photosystem II 237
Gernot Renger
xii CONTENTS

Chapter 17 Photosynthetic Water Splitting 291
Johannes Messinger and Gernot Renger
VII. Electron Transport Chains and Phosphorylation
Chapter 18 Anoxygenic Bacteria 351
Andre´Verme´glio
Chapter 19 Electron Transport Chains in Oxygenic Cyanobacteria 383
Gu¨nter A. Peschek
Chapter 20 Structure–Function of the Cytochromeb
6fComplex: A
Design that has Worked for Three Billion Years 417
William A. Cramer, Huamin Zhang, Jivsheny Yan,
Genji Kurisu, Eiki Yamashita, Naranbaatar Dashdorj,
Hanyovp Kim and Sergei Savikhin
Chapter 21 Photophosphorylation 447
Wolfgang Junge
VIII. Evolution
Chapter 22 The Evolution of Photosynthesis 489
Anthony W.D. Larkum
Subject Index 523
xiiiCONTENTS

Contributors
Eva-Mari Aro,Department of Biology, University of Turku, Turku, Finland
Roberto Bassi,Dipartimento Scientiﬁco e Tecnologico, Universita`di Verona.
Strada Le Grazie, 15-37134 Verona, Italy
Richard J. Cogdell,Microbial Photosynthesis Laboratory, Division of
Biochemistry & Molecular Biology, Institute of Biomedical and Life Sciences,
University of Glasgow, Glasgow G12 8QQ, UK
W. A. Cramer,Department of Biological Sciences, Purdue University, West
Lafayette, IN 47907, USA
Roberta Croce,Institute of Biophysics CNR, C/o ITC. 38100 Povo, Trento, Italy
Present address: Biophysical Chemistry, University of Groningen, Nijenborg 4,
9747 AG Groningen, The Netherlands
N. Dashdorj,Department of Physics, Purdue University, West Lafayette,
IN 47907, USA
Petra Fromme,Department of Chemistry and Biochemistry, Arizona State
University, Box 871604, 85287-1607 Tempe, Arizona, USA
Raimund Fromme,Department of Chemistry and Biochemistry, Arizona State
University, Box 871604, 85287-1607 Tempe, Arizona, USA
Adam M. Gilmore,Fluorescence Division, Horiba Jobin Yvon Inc., 3880 Park
Avenue, Edison, NJ 08820, USA
Ingo Grotjohann,Department of Chemistry and Biochemistry, Arizona State
University, Box 871604, 85287-1607 Tempe, Arizona, USA
Wolfgang Junge,Department of Biophysics, University of Osnabru¨ck, 49069
Osnabru¨ck, Germany
Yoshinori Kakitani,Faculty of Science and Technology, Kwansei Gakuin Uni-
versity, 2-1 Gakuen, Sanda 669-1137, Japan
H. Kim,Department of Physics, Purdue University, West Lafayette,
IN 47907, USA
Masami Kobayashi,Institute of Materials Science, University of Tsukuba,
Tsukuba, Ibaraki 305–8573, Japan
Yasushi Koyama,Faculty of Science and Technology, Kwansei Gakuin
University, 2-1 Gakuen, Sanda 669-1337, Japan
G. Kurisu, Department of Biological Sciences, Purdue University, West
Lafayette, IN 47907, USA
xv

Present address: Department of Life Sciences, Graduate School of Arts and
Sciences, University of Tokyo, Komaba 3–8-1, Meguro-ku, Tokyo 153–8902,
Japan
C. Roy D. Lancaster,Max Planck Institute of Biophysics, Department of
Molecular Membrane Biology, P.O. Box 55 03 53, D-60402, Frankfurt am
Main, Germany
Anthony W.D. Larkum,School of Biological Sciences, University of Sydney and
Sydney University Biological Information and Technology Centre (SUBIT),
Medical Foundation Building, University of Sydney, NSW 2006, Australia
Christopher J. Law,Microbial Photosynthesis Laboratory, Division of
Biochemistry & Molecular Biology, Institute of Biomedical and Life Sciences,
University of Glasgow, Glasgow G12 8QQ, UK
Winfried Leibl,Service de Bioe´nerge´tique and URA CNRS 2096, De´partement
de Biologie Joliot-Curie, CEA Saclay, 91191 Gif sur Yvette, France
Xiao-Ping Li,Biotechnology Center for Agriculture and the Environment, Foran
Hall, Cook Campus, Rutgers, The State University of New Jersey, 59 Dudley
Road, New Brunswick, NJ 08901–8520, USA
Johannes Messinger,Max-Planck-Institut fu¨r Bioanorganische Chemie, Stift-
strasse 34–36, D-45470 Mu¨lheim an der Ruhr, Germany
Mamoru Mimuro,Department of Technology and Ecology, Hall of Global
Environmental Research, and Graduate School of Human and Environmental
Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606–8501,
Japan
Hideaki Miyashita,Department of Technology and Ecology, Hall of Global
Environmental Research, and Graduate School of Human and Environmental
Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606–8501,
Japan
Tomas Morosinotto,Dipartimento Scientiﬁco e Tecnologico, Universita`di
Verona. Strada Le Grazie, 15-37134 Verona, Italy
Present address: Dipartmento of Biologia, Universita`di Padova, Via Ugo
Bassi 58 B, 35131 Padova, Italy
Akio Murakami,Kobe University Research Center for Inland Seas, Iwaya,
Awaji, Hyogo 656–2401, Japan
William W. Parson,Department of Biochemistry, Box 35–7350, University of
Washington, Seattle, WA 98195–7350, USA
Gu¨nter A. Peschek,Molecular Bioenergetics Group, Institute of Physical Chemi-
stry, University of Vienna, Althanstrasse 14, A-1090 Wien, Austria
Gernot Renger,Technische Universita¨t Berlin, Institut fu¨r Chemie,
Max-Volmer-Laboratorium fu¨r Biophysikalische Chemie, Straße des 17. Juni
135, D-10623 Berlin, Germany
Thomas Renger,Institut fu¨r Chemie (Kristallographie), Freie Universita¨t Berlin,
Takustrasse 6, D-14195 Berlin, Germany
S. Savikhin,Department of Physics, Purdue University, West Lafayette, IN
47907, USA
H. Scheer,Dept. Biologie I-Bereich Botanik, Universita¨tMu¨nchen, Menzinger Str.
67, D-80638 Mu¨nchen, Germany
xvi CONTRIBUTORS

Pierre Se´tif,Service de Bioe´nerge´tique and URA CNRS 2096, De´partement de
Biologie Joliot-Curie, CEA Saclay, 91191 Gif sur Yvette, France
Tohru Tsuchiya,Department of Technology and Ecology, Hall of Global
Environmental Research, and Graduate School of Human and Environmental
Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606–8501,
Japan
Herbert van Amerongen,Laboratory of Biophysics, Wageningen University, P.O.
Box 8128, 6700 ET Wageningen, The Netherlands
Imre Vass,Institute of Plant Biology, Biological Research Center, Hungarian
Academy of Sciences, 6726 Szeged, Temesva´ri krt. 62, Hungary
Andre´Verme´glio,Laboratoire de Bioe´nerge´tique Cellulaire, UMR 6191 CNRS-
CEA-Aix-Marseille II DEVM CEA, Cadarache 13108, Saint Paul lez Dur-
ance, France
Yasutaka Watanabe,Faculty of Science and Technology, Kwansei Gakuin
University, 2-1 Gakuen, Sanda 669–1137, Japan
E. Yamashita,Department of Biological Sciences, Purdue University, West
Lafayette, IN 47907, USA
J. Yan,Department of Biological Sciences, Purdue University, West Lafayette,
IN 47907, USA
Present address: Department of Pharmacology, University of California-
Davis, Davis, CA 95616, USA
H. Zhang,Department of Biological Sciences, Purdue University, West Lafay-
ette, IN 47907, USA
Athina Zouni,Institute for Chemistry/Max Volmer Laboratory for Biophysical
Chemistry, Technical University Berlin, Strasse des 17. Juni 135, D-10623
Berlin, Germany
xviiCONTRIBUTORS

Abbreviations and Symbols
AorA
0, special chlorophyllamolecules acting as electron acceptors in type I
RCs
A, antheraxanthin
A
1, special phylloquinone molecule(s) acting as electron acceptor in PS I (see
also PhQ
Aand PhQB)
aa or AA, amino acid
Acc, electron acceptor
ALA, 5-aminolevulinic acid
APC, allophycocyanin
ATP, adenosine triphosphate
B
A,BB, ‘‘accessory’’ BChls in proteobacterial RCs
BC, before Christ
(B)Chl, (bacterio)chlorophyll
(B)Pheo or (B)Phe, (bacterio)pheophytin
BIC, butyl isocyanide
B
X,By, higher energy optical absorption bands (Soret bands) of (bacterio)
chlorins and porphyrins
CAB, chlorophylla/bbinding protein
CAC, chlorophylla/cbinding protein
CAM crassulacean acid metabolism
Car, carotenoid
CcO, cytochromecoxidase
CD, circular dichroism
CM, cytoplasmic or plasma membrane(s)
CPX, chlorophyll binding protein of molecular massX
cyt, cytochrome
d.w., dry weight
D1, D2, central polypeptides of PS II RCs
DBMIB, 2,5-dibromo-3-methyl-6- isopropyl-p-benzoquinone
DCCD, dicyclohexylcarbodiimide
DCMU, 3-(3,4-dichlorophenyl)-1,1-dimethylurea
DGDG, digalactosyldiacylglycerol
DOPC, dioleoyl-phosphatidylcholine
EET, excited state energy transfer (excitation energy transfer)
xix

ELIP, early light induced protein
EM, electron microscopy
E
m, midpoint oxidation–reduction potential
ENDOR, electron nuclear double resonance
EPR, electron paramagnetic resonance
ER, endoplasmatic reticulum
ESEEM, electron spin echo envelope modulation
ESR, electron spin resonance
ET, electron transfer
ETC, Electron transport chain
ETP, electron transport phosphorylation
EXAFS, extended X-ray absorption ﬁne structure
F
A,F
B,F
x, Iron-sulfur centers in PS I and chlorobial RCs
F
ABprotein, subunit PsaC of photosystem I which binds the two iron-sulfur
clusters F
Aand FB
FCWD, Franck–Condon weighted density of states
Fd or fd, ferredoxin
FDP, ﬂavo-diiron proteins
FIOP, ﬂash-induced oxygen evolution pattern
Fld, ﬂavodoxin
FNR, ferredoxin-NADP
1
-oxidoreductase
FTIR, Fourier-transform infrared
FWHM, full-width at half-maximum
Ga, giga years ago
GAP, glyceraldehyde 3-phosphate
GAP-DH, glyceraldehyde 3-phosphate dehydrogenase
H
A,HB, bacteriopheophytins in proteobacterial RCs
HiPIP, high-potential iron-sulfur protein
HLIP, high light-induced protein
IC, internal conversion
ICM, intracytoplasmic membrane
IChM, inner chloroplast membrane
IEF, isoelectric focusing
IEP, (pH of) isoelectric point
IR, infrared
ISC, intersystem crossing
isiA, iron stress-induced protein A
ISP, iron-sulfur protein
ISP-s, 139 residuep-side soluble domain of the ISP
K
z, equilibrium binding (association) constant between Z (or A) and one PS II
unit;
L, lutein
L, M, H, subunits of proteobacterial RCs
LD, linear dichroism
LH, light harvesting
xx ABBREVIATIONS AND SYMBOLS

LHC I, II (or Lhc I, II), light-harvesting chlorophyll complexes of Photosystem
I, II
LH(C)P, light harvesting (chlorophyll) protein
MDGD, monogalactosyldiacylglycerol
MgDVP, Mg-2, 4-divinyl phaeoporphyrin methyl ester
MIMS, membrane inlet mass spectrometry
MK, MKH
2, menaquinone, menaquinol
MSH, membrane spanning helix (see also TMH)
N, neoxanthin
NAD
+
, NADH, nicotinamide adenine dinucleotide (oxidized and reduced,
respectively)
NHFe, nonheme iron
NIR, near-infrared spectral range (700–1200 nm)
NMR, nuclear magnetic resonance
NPQ, nonphotochemical quenching (of PS II chlorophyll ﬂuorescence)
NQNO, 2-n-nonyl-4-hydroxyquinoline N-oxide
OChM, outer chloroplast membrane
OEC oxygen evolving complex
p- andn-, electrochemically positive and negative sides of the membrane
P, special pair, photochemically active pigment of bacterial RCs
P870, special pair in proteobacterial RCs
p.m.f., proton motive force
P680 (or P
680), photochemically active pigment of PS II
P700, photochemically active pigment (or electron donor) in PS I
P798, photochemically active pigment in heliobacterial RCs
P840, photochemically active pigment in chlorobial RCs
PAR, photosynthetically active radiation
PBRC (or PbRC), purple bacteria reaction center
PC, phycocyanin
PC, also used as abbreviation for plastocyanin
pcb, prochlorophyte chlorophyll binding protein
PCET, proton coupled electron transfer
PE, phycoerythrin
PEC, phycoerythrocyanin
PET, photosynthetic electron transport
PG, Phosphatidylglycerol
PhQ
Aand PhQ
B, the two phylloquinones A- of PS I associated to the A- and
B-branches of electron transfer
PQ, plastoquinone
(P)Chlide, (Proto)Chlorophyllide
Proto, protoporphyrin IX
PS I (or PS1), Photosystem I (1)
PS II (or PS2), Photosystem II (2)
PS II CC, PS II core complex
PsaA, PsaB, subunits of PS I RCs
PsbS (also called CP22), 22 kDa PS II protein
xxiABBREVIATIONS AND SYMBOLS

PscA, PscB, polypeptides of chlorobial RCs
Q
A, primary quinone electron acceptor of type II RCs
Q
B, secondary plastoquinone acceptor of type II RCs
Q
x,Q
y, low energy optical absorption bands of (bacterio)chlorins and
porphyrins
RC, reaction centre
RET, respiratory electron transport
RIXS, resonant inelastic x-ray scattering
ROS reactive oxygen species
rRNA ribosomal ribose nucleic acid
S (or S
i) states, formal oxidation states of the water-oxidizing complex
SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis
SQDG, sulfoquinovosyldiacylglycerol
TA, transient absorption
TDS, tridecyl-stigmatellin
TMH, trans-membrane helix (see also MSH)
TRO, terminal respiratory oxidase
T-S, triplet minus singlet
UQ, ubiquinone (coenzyme Q)
UV, ultraviolet spectral range (200–400 nm)
V, violaxanthin
VDE, violaxanthin de-epoxidase
Vis, Visible spectral range (400–700 nm)
W
f,Ws,, fast and slowly exchanging substrate (water) molecules bound to the
WOC
WOC, water-oxidizing complex (¼OEC, oxygen-evolving complex)
WT, wild type
XANES, X-ray absorption near edge structure
Xanth, xanthophyll
XRD(C), X-ray diﬀraction (crystallography)
Y
Z,YD, redox active tyrosine of polypeptides D1 and D2, respectively, in PS II
Z, zeaxanthin
DpH, trans-membrane diﬀerence of pH
D~m
H
1, trans-membrane proton electrochemical potential diﬀerence
e, molar extinction coeﬃcient (
M
ﬀ1
cm
ﬀ1
)
l, wavelength (nm)
mE, micro Einstein (Einstein is the unit for one mole photons)
xxii ABBREVIATIONS AND SYMBOLS

Part 2: Reaction Centers/Photosystems,
Electron Transport Chains,
Photophosphorylation and Evolution

VI. Structure and Function of Reaction
Centers and Photosystems

Chapter 11
Structures of Reaction Centers in
Anoxygenic Bacteria
C. Roy D. Lancaster
Table of Contents
11.1 Introduction........................................ 7
11.2 Structural Overview.................................. 9
11.2.1 Subunit Composition and Molecular Characterization . . . . 9
11.2.2 Crystallization................................. 12
11.2.3 X-Ray Crystal Structures of the RCs from Anoxygenic
Purple Bacteria................................. 13
11.3 Arrangement of the Cofactors . . ......................... 18
11.4 Structure of the Protein Subunits......................... 18
11.4.1 L Subunit..................................... 18
11.4.2 M Subunit.................................... 20
11.4.3 H Subunit.................................... 21
11.4.4 C Subunit.................................... 21
11.5 Cofactor Conformation and Protein–Cofactor Interactions...... 21
11.5.1 Primary Electron Donor . ......................... 21
11.5.2 Accessory Bacteriochlorophylls..................... 25
11.5.3 Bacteriopheophytins............................. 25
11.5.4 The Primary Electron Acceptor Q
Aand the Non-Heme
Iron......................................... 25
11.5.5 Heme-Iron Site Geometries........................ 28
11.6 Substrate Binding Sites................................ 29
11.6.1 The Electron-Acceptor Substrate Q
Band the Binding of
Inhibitors ..................................... 29
11.6.2 The Electron-Donor Substrate, Cytochrome c
2or HiPiP . . . 32
11.7 Aspects of Membrane Protein Structure.................... 34
11.7.1 Side-Chain Distributions . ......................... 34
11.7.2 Bound Water.................................. 36
11.7.3 Phospholipid Binding............................ 37
5

11.8 Structures of Modiﬁed Reaction Centers................... 39
11.8.1 Variant Reaction Centers ......................... 39
11.8.2 Dark-Adapted Versus Light-Adapted Reaction Centers . . . 43
11.9 Comparison with Photosystem II......................... 44
11.10 Conclusions and Future Perspectives...................... 45
References.............................................. 45
6 C. ROY D. LANCASTER

Abstract
Photosynthetic reaction centers from anoxygenic bacteria are the best-characterized
membrane protein complexes. This chapter compares over 50 X-ray crystal structures
of reaction centers fromRhodopseudomonas(Blastochloris)viridis,Rhodobacter
sphaeroides, and Thermochromatium tepidumon the basis of data quality and quan-
tity, maximum resolution limits, and structural features. Not only the overall architec-
ture of the reaction centers and the relevant positions and orientations of the
prosthetic groups, but also speciﬁc structural features are conserved. Small structural
diﬀerences might provide a basis for the explanation of the observed spectral and
functional discrepancies between the three species. Particular points of focus in this
chapter are, ﬁrst, the site of binding of the secondary quinone (Q
B) where electron
transfer is coupled to the uptake of protons from the cytoplasm; second, the respec-
tive binding sites of the electron donor proteins; third the increasing number of struc-
tures of variant reaction centers; and, fourth, the binding of phospholipids to these
membrane protein complexes. Finally, recent progress in the structure determination
of Photosystem II allows a comparison of the structures of bacterial RCs to that of
Photosystem II.
11.1 Introduction
A large proportion of photosynthetically active organisms consists of anoxy-
genic photosynthetic bacteria. Purple bacteria ﬁnd their ecological niche in
deeper layers of stagnant bodies of water. In all purple bacteria, the photosyn-
thetic pigments and the photosynthetic apparatus are located within a more or
less extended system of invaginated intracytoplasmic membranes. Located
within these photosynthetic membranes, reaction centers (RCs) [1–8] are deﬁned
as the minimal functional units that can catalyze light-induced electron transfer
reactions, thus stabilizing the separation of charged species across the mem-
brane. In contrast to the higher plants, algae, and cyanobacteria of oxygenic
photosynthesis, which contain the two membrane-bound Photosystems I and II,
each of the anoxygenic photosynthetic bacteria has only one type of reaction
center. While the iron-sulfur type RCs of heliobacteria and anaerobic green
sulfur bacteria resemble that of Photosystem I, the pheophytin-quinone type
RCs of purple bacteria are more similar to the RC of Photosystem II. The RC
essentially functions as a [reduced soluble electron carrier protein]:quinone
photo-oxidoreductase (Figure 1).
The absorption of two photons of light leads to two one-electron oxidations of
a soluble electron carrier protein in the periplasm and to the two-electron
reduction of a quinone, which is coupled to the uptake of two protons from the
cytoplasm. The resulting quinol then leaves its binding site, diﬀuses in the
photosynthetic membrane and is reoxidized by a second membrane protein
complex, the cytochromebc
1complex, which results in proton release to the
periplasm. The electrons are transferred to re-reduce the soluble electron carrier
protein in the periplasm. This net proton transport produces a transmembrane
7STRUCTURES OF REACTION CENTERS

electrochemical proton potential that can drive ATP synthesis [9] through a third
membrane-spanning complex, the ATP synthase (see Chapter 21 for details).
Unlike Photosystem II, however, the purple bacterial RC is incapable of
extracting electrons from water. Instead it must oxidize inorganic or organic
molecules available in the environment. According to their electron donor
requirements, sulfur and non-sulfur purple bacteria have traditionally been
8 C. ROY D. LANCASTER

distinguished. In contrast to sulfur purple bacteria (Chromatiaceae, Ectothio-
rhodospira), non-sulfur purple bacteria (Rhodospirillaceae) do not require
inorganic sulfur compounds, such as hydrogen sulﬁde, but instead use organic
electron donors such as malate or succinate as electron donors. Most of what is
known today about purple bacterial RCs results from studies on RCs from
non-sulfur purple bacteria. These are currently the best characterized mem-
brane protein complexes [1–8].
11.2 Structural Overview
11.2.1 Subunit Composition and Molecular Characterization
Most bacterial reaction centers contain four protein subunits (Figure 2),
referred to as H, M, L, and C (a tetraheme cytochromec). Some, however,
such as the RCs ofRhodobacter(Rb.)sphaeroides,Rb.capsulatus, and Rhodo-
spirillum(Rs.)rubrum, contain only the H, M, and L subunits. The related RC
of the green aerobic thermophilic bacteriumChloroﬂexus(Cf.)aurantiacus
lacks the H subunit. References to representative amino acid sequence infor-
mation of RC subunits have been compiled [7]. The gene for the H subunit lies
on a diﬀerent operon than those for the other subunits and has been examined
less frequently.
Generally, RCs from purple bacteria have been isolated and characterized
fromRhodopseudomonas(Rp.)viridis[10], more recently referred to asBlast-
ochloris(Bl.) [11]viridis,Rb. sphaeroides[12],Thermochromatium(Tc.)tepidum
[13],Rb. capsulatusand several other purple bacteria [12,14]. Variant RCs have
been isolated and characterized fromRb. capsulatus[15–17],Rb. sphaeroides
[18,19], andBl. viridismutants [20–23]. The methods for isolation (and
Figure 1.Structure and function of the photosynthetic RC. (a) Light-induced cyclic
electron ﬂow and the generation and utilization of a transmembrane electrochemical
potential in the purple bacteriumBl. viridis.The structure of theBl. viridisRC is
represented schematically, showing the heterotetramer of C, L, M, and H subunits as Ca
traces in green, brown, blue, and purple, respectively, plus the 14 cofactors, which have
been projected on to the molecule for better visibility. Also for the sake of clarity, the
quinone tails are truncated after the ﬁrst isoprenoid unit and the phytyl side-chains of
the bacteriochlorophyll and bacteriopheophytin molecules have been omitted, as have
those atoms of the carotenoid molecule not observed in the electron density and assigned
zero occupancy in the PDB entry 2PRC (see Table 2 for reference). Carbon, nitrogen,
and oxygen atoms are drawn in yellow, blue, and red, respectively. Prepared with
programs MolScript [168] and Raster3D [169]. [Adapted from [170]]. (b) Equilibrium
oxidation–reduction potentials of theBl. viridisRC cofactors as reported in [22,117,171–
174] as a function of inter-cofactor distance. The soluble electron donor protein
cytochromec
2has been included as suggested by [175] and [176]. The photochemical
excitation is indicated by a dashed arrow and unphysiological charge recombination
reactions are shown as dotted arrows. [Adapted from [7]]. (c) Quinone reduction cycle.
Reduced quinones are in bold. Steps 2, 4, 5, and 6 are reversible. See text for details.
9STRUCTURES OF REACTION CENTERS

Figure 2.Subunit and cofactor arrangement in the photosynthetic RC fromBl. viridis:
Schematic representation of the structure of theBl. viridisRC, showing the hetero-
tetramer of C, L, M, and H subunits as Catraces in green, brown, blue, and purple,
respectively, plus the 14 cofactors. For the sake of clarity, the quinone tails are truncated
after the ﬁrst isoprenoid unit and the phytyl side-chains of the bacteriochlorophyll and
bacteriopheophytin molecules have been omitted, as have those atoms of the carotenoid
molecule not observed in the electron density and assigned zero occupancy. PDB
entry 2PRC.
10 C. ROY D. LANCASTER

crystallization) of the RCs fromRb. sphaeroidesandBl. viridishave been
reviewed [7,24]. The puriﬁcation procedures consist of disrupting the bacteria
by ultrasonication, isopycnic centrifugation of the chromatophores in a sucrose
gradient, and solubilization of the RCs with the detergentN,N-dime-
thyldodecylamineN-oxide (LDAO) at concentrations of 6% (Bl. viridis)and
of 0.5% (Rb. sphaeroides), respectively. The RCs are further puriﬁed by a
combination of column chromatography steps. In the case ofBl. viridisRCs,
molecular sieve chromatography is used exclusively [25]. For the RCs ofRb.
sphaeroides, various modiﬁcations of a combination of anion exchange chro-
matography and molecular sieve chromatography [26] have been employed. A
procedure for the rapid isolation using Ni
21
-nitrilotriacetic acid (NTA) aﬃnity
chromatography ofRb. sphaeroidesRCs with an engineered poly-histidine tag
fused to the C terminus of the M subunit has been published [27], and successful
crystallization of the isolated material has been reported [28]. A procedure with
an engineered His
6-tag fused to the C-terminus of the C subunit of recombinant
Bl. viridisRC has yielded material that could be crystallized [23].
The L, M, and H subunits of theBl. viridisRC contain 273, 323, and 258
amino acid residues (M
r¼30.5, 35.9, 28.3 kDa), respectively [29,30]. The C
subunit ofBl. viridis(336 residues,M
r¼40.5 kDa) [31] is a lipoprotein and is
anchored in the membrane by a diacylglycerol moiety, which is covalently
bound to the N-terminal Cys side-chain via a thioether bond [32]. A recognition
site for the covalent attachment of a diglyceride and removal of the signal
peptide by signal peptidase II is present inBl. viridisandRv. gelatinosusbut not
inCf. aurantiacus.
RC preparations have a non-heme iron and four magnesium-containing
bacteriochlorophyll cofactors per RC [12], as measured by atomic absorption
spectroscopy [33]. InRb. sphaeroidesandBl. viridis, these are bacteriochlorophyll
aand bacteriochlorophyllb, respectively (Figure 3). Those preparations with a
tightly bound C subunit have four iron-containing heme groups that are
covalently bound to the protein. Apart from these fourc-type heme groups, all
other cofactors are non-covalently bound by the L and M subunits. In addition to
the metal-containing cofactors, these comprise two bacteriopheophytin groups, a
carotenoid, and two quinones. InRb. sphaeroides, these are bacteriopheophytina,
spheroidene, and ubiquinone-10, respectively, whereasBl. viridiscontains ba-
cteriopheophytinb, 1,2-dihydroneurosporene, menaquinone-9 and ubiquinone-9.
Similar to theRb. sphaeroidesRC, theTc. tepidumRC contains four bacterio-
chlorophyllaand two bacteriopheophytinagroups. Similar to theBl. viridisRC,
theTc. tepidumRC contains fourc-type heme groups, menaquinone-8 and
ubiquinone-8. The carotenoid in theTc. tepidumRC is spirilloxanthin.
Apart from the availability of high resolution crystal structures discussed
below, one major reason why, despite its complexity, the purple bacterial RC
has become the ‘‘hydrogen atom of protein electron transfer’’ ([34], see also
[35,36]) is the richness of its characterization by optical absorption, electron
paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR),
Fourier-transform infrared (FTIR), resonance Raman (RR), ﬂuorescence, Stark
eﬀect, and other types of spectroscopy; comprehensively reviewed in [1–8].
11STRUCTURES OF REACTION CENTERS

11.2.2 Crystallization
Crystals of theBl. viridisRC were ﬁrst grown by vapor diﬀusion from a protein
droplet containing 1.5
M(NH4)2SO4, 0.1%N,N-dimethyldodecylamineN-oxide
(lauryl-N,N-dimethylN-oxide, LDAO) and 3% heptane-1,2,3-triol against a
Figure 3.Chemical structures of RC cofactors (a–c) and inhibitors at the QBsite (d, e).
(a) Bacteriochlorophyllb, as bound in theBl. viridisRC. The bacteriochlorophylla
bound in theRb. sphaeroidesRC diﬀers by the presence of a C8 ethyl group instead of
the C8 ethylidene group indicated in red. Bacteriopheophytins (aorb) are the metal-free
variants of the bacteriochlorophylls (aorb) with two protons bonded to the nitrogens of
the unsaturated pyrrole rings A and C. (b) Menaquinone-n . The native Q
Ain the
Bl. viridisRC is menaquinone-9. In theTc. tepidumRC, Q
Ais menaquinone-8. (c)
Ubiquinone-n . The native Q
Bin theBl. viridisRC is ubiquinone-9. In theTc. tepidum
RC, Q
Bis ubiquinone-8. In theRb. sphaeroidesRC, both Q Aand QBare ubiquinone-10.
(d) Atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine). (e) Stigmatellin A.
12 C. ROY D. LANCASTER

reservoir containing 2–3M(NH4)2SO4[25]. They are tetragonal, space group
P4
3212witha¼b¼223.5 A˚,c¼113.6 A˚[37], and one molecule per asymmetric
unit (crystal form ‘‘A’’ in Table 1). Using these crystals, the structure of theBl.
viridisRC was solved by multiple isomorphous replacement [37,38] and reﬁned to
a crystallographicR-factor of 19.3% up to a resolution of 2.3 A˚[39,40]. More
recentcrystalsdiﬀracttoatleast1.8A
˚
resolution (CRD Lancaster, unpublished
observations), and the structure has been reﬁned with complete data to 2.0 A
˚
resolution (see Table 2 below) [41].
Three kinds of well-diﬀracting crystals have been obtained of theRb. sphaero-
idesRC (as reviewed by Fritzsch [24]). They are orthorhombic, [42–45]
trigonal [46] and tetragonal [47] (crystal forms ‘‘B’’, ‘‘C’’, and ‘‘D’’, respectively,
in Table 1). Orthorhombic crystals are grown in the presence of 10–12%
poly(ethylene glycol) 4000 (PEG4000), 0.06% LDAO and 3.5–3.9% heptane-
1,2,3-triol or 0.8%n-octyl-ß-
D-glucopyranoside against a reservoir buﬀer con-
taining 18–25% PEG4000. The space group is P2
12121. The best resolution is 2.8
A˚in the direction of the long axis, but worse in the other directions. Using a
partially reﬁned coordinate set of theBl. viridisRC for molecular replacement,
three diﬀerent groups used these orthorhombic crystal forms with slightly
diﬀerent cell dimensions to determine the structure of theRb. sphaeroidesRC.
As discussed earlier [48], for all RC structures based on these orthorhombic
crystals, the number of observed unique reﬂections,n
obs, is less than the number
of parameters,n
par, required to deﬁne the model (cf. Tables 2 and 3 below).
Trigonal crystals can be obtained in the presence of 0.5–1.0
Mpotassium
phosphate, pH 6.5–7.5, 0.06–0.15% LDAO and 1.8–3.0% heptane-1,2,3-triol
against a reservoir buﬀer containing 1.4–1.7
Mpotassium phosphate. The space
group is P3
121. The best crystals diﬀract to 1.8 A˚[49]. To date, this is the crystal
form of theRb. sphaeroidesRC, which has yielded by far the largest number of
well-deﬁned structures (cf. Tables 2 and 3 below).
Tetragonal crystals are grown in the presence of 6% PEG4000, 0.85%
n-octyl-b-
D-glucopyranoside, 2.5% heptane-1,2,3-triol and 0.4% benzamidine
hydrochloride against a reservoir solution containing 32% PEG4000 [47].
Crystals belong to the space group P4
3212 with two RCs per asymmetric unit.
Data from these crystals have been collected to 2.2 A
˚
resolution [50].
More recently, crystals of theRb. sphaeroidesRC have been obtained using
the cubic lipid phase technique [51] of membrane protein crystallization (crystal
form ‘‘E’’ in Table 1). Data from these crystals have been collected to 2.35 A˚
resolution [52].
For theTc. tepidumRC, orthorhombic crystals have been obtained in the
presence of 47% (w/v) PEG4000 as a precipitant in a 15 m
Mphosphate buﬀer,
pH 7.0, together with 0.36
MNaCl, 0.1% (w/v) NaN3, and 0.1 mMEDTA
(crystal form ‘‘H’’ in Table 1) [53]. Data from these crystals have been collected
to 2.2 A
˚
resolution [54].
11.2.3 X-Ray Crystal Structures of the RCs from Anoxygenic Purple Bacteria
Tables 2 and 3 list the coordinate sets of those RC structures deposited in the
PDB as of 1 August, 2005. Table 3 (below) contains all coordinate sets of variant
13STRUCTURES OF REACTION CENTERS

Table 1.Crystal forms of bacterial reaction centers
Crystal
form Sample
Space
groupa(A
˚
)b(A
˚
)c(A
˚
)a(1)b(1)c(1)
No. of PDB
depositions References
a
ABlastochloris viridisRCP4
3
2
1
2 223.5 223.5 113.6 90 90 90 10[25]
BRhodobacter sphaeroidesRCP2
1
2
1
2
1
143.7 139.8 78.7 90 90 90 5[42–45]
CRhodobacter sphaeroidesRCP3
1
21 141.3 141.3 187.2 90 90 120 26[46]
DRhodobacter sphaeroidesRCP4
3
2
1
2 140.1 140.1 271.6 90 90 90 7[47]
ERhodobacter sphaeroidesRCin cubo P4
2
2
1
2 100.0 100.0 237.2 90 90 90 3[52]
FRhodobacter sphaeroidesvariant RC
with PSII-like Mn
21
-binding site
P4
2
22 203.8 203.8 119.9 90 90 90 1[152]
GRhodobacter sphaeroidesvariant RC
with PSII-like Mn
21
-binding site
P4
2
22 207.8 207.8 107.5 90 90 90 1[152]
HThermochromatium tepidumRCP2
1
2
1
2
1
133.3 196.6 84.2 90 90 90 1[53]
XRhodobacter sphaeroidesRC-cytc
2
complex
P2
1
78.2 115.7 79.7 90 110.3 90 1[153]
YRhodobacter sphaeroidesRC-cytc
2
complex
P2
1
77.9 80.3 246.6 90 92.4 90 1[153]
ZRhodopseudomonas palustrisRC-LH1
core complex
P1 76.0 119.0 130.4 69.3 72.7 66.5 1[154]
a
In general, only the ﬁrst publication is cited, although the precise crystallization conditions and unit cell dimensions may vary in subsequent publications.
14 C. ROY D. LANCASTER

Table 2.Reaction center structures (excluding Rb. sphaeroidesRC variants)
a
PDB
ID Remarks (if any) Crystal form
b
High-resolution
limit (A
˚
)R
cryst
c
(%)R
f
ree
d
(%)n
obs
/n
par
e
Reference
Blastochloris viridis
1DXR His L168-Phe variant; terbutryn complex A 2.00 19.4 21.8 4.44 [41]
1VRN A 2.20 19.1 21.2 2.78 [135]
2JBL Stigmatellin complex (replaces 4PRC) A 2.40 19.0 20.6 2.46 [155]
6PRC Triazine DG-420314 complex A 2.30 18.4 22.5 2.43 [58]
1PRC A 2.30 19.3 n/a 2.38 [40]
5PRC Atrazine complex A 2.35 19.0 23.6 2.20 [58]
3PRC Q
B
-depletedA2.4017.8 21.5 2.07 [66]
2PRC Ubiquinone-2 complexA2.4518.2 22.9 1.89 [66]
4PRC Stigmatellin complexA2.4019.1 24.1 1.82 [66]
7PRC Triazine DG-420315 complexA2.6518.4 23.1 1.73 [58]
1R2CA2.8620.2 22.8 1.58 [156]
Rhodobacter sphaeroides
1RG5 Carotenoidless RCC2.5015.5 18.2 2.51 [157]
1M3XC2.5518.5 20.9 2.34 [158]
1AIJ Ground stateD2.2021.6 27.0 1.95 [50]
1PCRC2.6518.6 n/a1.91 [55]
1RQK Carotenoidless RC reconstituted with 3,
4-dihydrospheroidene
C2.7016.4 19.4 1.82 [157]
1OGV Lipid cubic phase crystalE2.3521.4 24.4 1.74 [52]
1DV6 Zn 21
-complex; ground stateD2.5023.8 26.5 1.65 [92]
1DV3 Cd
21
-complex; charge-separated state D2.5022.6 25.2 1.61 [92]
1DS8 Cd
21
-complex; ground stateD2.5022.7 25.6 1.61 [92]
1L9B Cytochromec
2
-RC complexX2.4022.0 26.4 1.55 [153]
1RGN Carotenoidless RC reconstituted with
spheroidene
C2.8019.1 23.2 1.48 [157]
2BNS Lipid cubic phase crystal; charge-separated
state
E2.5021.1 24.7 1.41 [136]
15STRUCTURES OF REACTION CENTERS

Table 2
(continued)
PDB
ID Remarks (if any) Crystal form
b
High-resolution
limit (A
˚
)R
cryst
c
(%)R
f
ree
d
(%)n
obs
/n
par
e
Reference
1AIG Charge-separated stateD2.6021.5 29.9 1.26 [50]
2BNP Lipid cubic phase crystal; ground state E2.7021.2 24.9 1.16 [136]
1K6LC3.1019.3 19.4 1.08 [28]
4RCRB2.8022.7 n/a0.81 [159,160,161]
1PSSB3.0022.3 n/a0.79 [109]
1L9J Cytochromec
2
-RC complexY3.2524.8 28.7 0.77 [153]
1YSTB3.0023.4 n/a0.69 [162]
2RCRB3.1022.0 n/a0.64 [163]
1Z9KG4.6033.0 33.0 0.57 [152]
Thermochromatium tepidum
1EYSH2.2023.1 28.7 2.37 [54]
Rhodopseudomonas palustris
1PYH RC-LH1 core complexZ4.8046.9 49.1 n/a[154]
a
Continuously updated versions of Tables 1–3 will be provided online at http://www.mpibp-frankfurt.mpg.de/lancaster/rc/
b
As deﬁned in Table 1.
c
R
cryst
¼S
(hkl)
||F
o
|–|F
c
||/S
(hkl)
|F
o
|. Statistics are quoted as supplied with the PDB entries and are not necessarily consistent with the respective publications.
d
R
free
¼S
(hkl)AT
||F
o
|–|F
c
||/S
(hkl)AT
|F
o
|, where T is the test set [164].
e
n
obs
¼number of observed unique reﬂections used in the working set; n
par
¼number of parameters necessary to deﬁne the model; this includes three to four
parameters (x,y,zcoordinates, plus an isotropic atomic Bfactor, where applicable) per atom.
16 C. ROY D. LANCASTER

Table 3.Rb. sphaeroidesRC variant structures; see Table 2 footnotes for details
PDB
ID Remarks
Crystal
form
High resolution
limit (A
˚
)R
cryst
(%)R
free
(%)n
obs
/n
par
Reference
1RZH Asp L213-Asn/Arg M233-Cys variantC1.8022.1 23.3 6.21 [49]
1QOV Ala M260-Trp variantC2.1016.9 18.6 4.27 [114,165]
1RY5 Asp L213-Asn variantC2.1021.1 22.6 3.96 [49]
1E6D Trp M115-Phe/Phe M197-Arg variantC2.3017.4 20.0 3.10 [166]
1YF6 Quintuple variant (Phe L181-Tyr/Gly M203-Asp/
Tyr M210-Phe/Leu M214-His/Ala M260-Trp)
C2.2519.7 21.6 2.82 [115]
2BOZ Gly M203-Leu variantC2.4017.5 19.8 2.55 [102]
1FNQ Pro L209-Glu variantC2.6021.7 24.7 2.16 [119]
1FNP Pro L209-Phe variantC2.6021.6 24.8 2.14 [119]
1KBY His M202-Leu variantC2.5019.5 22.4 2.00 [106]
1MPS Tyr M177-Phe /Phe M197-Arg variantC2.5519.4 21.7 1.92 [110]
1E14 Phe M197-Arg/Gly M203-Asp variantC2.7022.6 26.8 1.85 [167]
1RVJ Asp L213-Asn/Arg H177-His variantC2.7521.8 23.7 1.84 [49]
1JGW Thr M21-Leu variantC2.8021.1 23.7 1.81 [126]
1RZZ Asp L213-Asn/Arg M233-Cys variant; Ground
state
D2.4021.6 23.8 1.81 [49]
1UMX Arg M267-Leu variantC2.8022.5 24.9 1.79 [125]
1F6N Pro L209-Tyr variantC2.8022.1 25.0 1.75 [119]
1JGZ Tyr M76-Lys variantC2.7021.5 24.9 1.56 [126]
1JGX Thr M21-Asp variantC3.0121.1 24.9 1.44 [126]
1S00 Asp L213-Asn/Arg M233-Cys variant; charge-
separated state
D2.6022.6 26.8 1.38 [49]
1JGY Tyr M76-Phe variantC2.7021.8 25.7 1.32 [126]
1K6N Glu L212-Ala/Asp L213-Ala variantC3.1020.3 20.7 1.02 [28]
1JH0 Glu L205-LeuC3.5022.5 26.9 0.99 [126]
1PST His M202-Leu variantB3.0021.8 n/a 0.82 [109]
1Z9J Multiple variant (Leu L131-His/Leu M160-His/Arg
M164-Tyr/Met M168-Glu/Phe M197-His/Gly
M288-Asp) with PSII-like Mn
21
-binding site
F4.5029.9 33.8 0.59 [152]
17STRUCTURES OF REACTION CENTERS

Rb. sphaeroidesRC structures, while Table 2 list all other coordinate sets.
Coordinate sets are ordered by their ratio of the number of observed unique
reﬂections,n
obs, to the number of parameters required to deﬁne the respective
atomic model,n
par. The structures based on the trigonal crystal form satisfy
these criteria best, so we shall primarily refer to these when comparing the RC
structure from this species to that ofBl. viridis.The structure of the four-subunit
Bl. viridisRC is shown schematically in Figures 1 and 2. The RC from
Rb. sphaeroideswould appear almost identical except for the cytochrome
subunit at the top, which would be missing. TheRb. sphaeroidesandBl. viridis
RC structures have been compared in detail previously [55,56].
TheBl. viridisRC has an overall length of 130 A
˚
in the direction perpen-
dicular to the membrane. Parallel to the membrane, the maximum width is
about 70 A
˚
. The central core of the RC is formed by the L subunit and the M
subunit, which possess ﬁve membrane-spanning segments each. Both subunits
are closely associated and non-covalently bind ten cofactors as detailed above
and shown in Figures 1 and 2. Large parts of the L and M subunits and their
associated cofactors are related by a two-fold axis of symmetry perpendicular
to the plane of the membrane. The H subunit is anchored to the membrane by a
single membrane-spanning helix and is attached to the LM core on the
cytoplasmic side. On the periplasmic side, the C subunit with its four covalently
bound heme groups is attached. The N-terminal diacylglycerol moiety is not
visible in the electron density map.
11.3 Arrangement of the Cofactors
The pigments form two symmetry-related branches, also shown in Figure 2,
each consisting of two bacteriochlorophylls, one bacteriopheophytin and one
quinone, which both cross the membrane starting from the ‘‘special pair’’ P of
two closely associated bacteriochlorophylls near the periplasmic side, followed
by the ‘‘accessory’’ bacteriochlorophyll, B, one bacteriopheophytin, H, and a
quinone, Q. As indicated in Figure 1, only the branch more closely associated
with L subunit is used in the light-driven electron transfer. It is called the
A-branch, the inactive one the B-branch. The active branch ends with the
primary quinone Q
A, the inactive one with the secondary quinone Q
B. Halfway
between both quinones, a non-heme iron is located. The carotenoid, which has a
cis double bond at the 15–15
0
position in its RC-bound state [57,58], is in van der
Waals contact with B
Band disrupts the two-fold symmetry. In both species the
crystallographic temperature factors, which are a measure for the rigidity of the
structure, are considerably higher along the B-branch than along the A-branch.
11.4 Structure of the Protein Subunits
11.4.1 L Subunit
Figure 4(a) shows the Catrace of the L subunit of theBl. viridisRC. The
dominant features are the ﬁve long membrane-spanning helices (A–E). They
18 C. ROY D. LANCASTER

are 21 (helix A), 24 (helices C and E), or 28 (helices B and D) residues long [39].
On the periplasmic side, the connection of transmembrane helices C and D
contains a helix (‘‘cd’’) of eleven residues and the connection between trans-
membrane helix E and the C-terminus a helix (‘‘ect’’) of nine residues. On the
cytoplasmic side, the connection of transmembrane helices D and E contains a
helix (‘‘de’’) of twelve residues. This region of the structure forms the binding
site of the secondary electron acceptor Q
B, which is also included in Figure 4(a).
In projection, viewed from the top of the membrane, the transmembrane helices
form a semicircular arrangement in the order A, B, C, E, and D [39]. Trans-
membrane helices A, B, and D are straight, helix E is smoothly curved, and
helix C possesses a kink of more than 301. When the L subunits fromBl. viridis,
Tc. tepidum, and Rb. sphaeroidesare compared (Figure 4b), an additional eight
amino acid residues are found at the C-terminus in theRb. sphaeroidesRC [56].
Figure 4.Stereo views: The Catrace of the L subunit of theBl. viridisRC (a) and its
comparison with those of theTc. tepidumandRb. sphaeroidesRCs (b). The letters ‘‘A’’
to ‘‘E’’ designate the ﬁve transmembrane helices. The additional helices ‘‘cd’’, ‘‘de’’, and
‘‘ect’’ are detailed in the text (PDB entries used: 2PRC, 1EYS, 1PCR).
19STRUCTURES OF REACTION CENTERS

11.4.2 M Subunit
The M subunit of theBl. viridisRC is displayed in Figure 5(a). As indicated
already by the sequence identity of around 30% between the L and M subunits,
the overall protein fold is very similar. The ﬁve transmembrane helices of the M
subunit are 24 (C), 25 (A,E), 26 (D) or 27 (B) residues long. The connecting
helices ‘‘cd’’ (twelve residues) and ‘‘ect’’ (seven residues) on the periplasmic side
as well as ‘‘de’’ (14 residues) on the cytoplasmic side, forming part of the Q
A
site, are also present. Accompanied by an insertion of seven amino acids
(compared with the L subunit), short additional helices are found in the
Figure 5.Stereo views: Catrace of the M subunit of theBl. viridisRC (a) and its
comparison with those of theTc. tepidumandRb. sphaeroidesRCs (b). ‘‘A’’–‘‘E’’
designate the ﬁve transmembrane helices. The additional helices ‘‘ab’’, ‘‘cd’’, ‘‘dde’’,
‘‘de’’, and ‘‘ect’’ are detailed in the text (PDB entries 2PRC, 1EYS, 1PCR).
20 C. ROY D. LANCASTER

connections of transmembrane helices A and B (helix ‘‘ab’’, seven residues) on
the periplasmic side, and between transmembrane helix D and the connecting
helix ‘‘de’’ on the cytoplasmic side (helix ‘‘dde’’, six residues).
On the cytoplasmic side, the L and M subunits are tightly interwoven. When
the L and M subunits are compared, the M subunits are 26 (Bl. viridis)or25
(Rb. sphaeroides, Figure 5b) residues longer at the N-termini than the L
subunits. At the C terminus, the M subunit fromRb. sphaeroidesis nine amino
acids shorter than the L subunit. The M subunit fromBl. viridispossesses an
additional 18 amino acids at the C-terminus, which interact with the C subunit
(see also Figures 1 and 2).
11.4.3 H Subunit
The N-terminus of the H subunit (Figure 6) is located on the periplasmic side of
the membrane. Residues H12 to H35 form a membrane-spanning helix (Figure
6a), which is ana-helix at its beginning but ap-helix at its very end. The next 70
residues are preferentially in contact with the LM complex. A globular region
follows that has been referred to as the ‘‘PRC barrel’’ [59] and contains an
extended system of antiparallel and parallelb-sheets. Close to the C-terminus,
ana-helix is found.
11.4.4 C Subunit
The structure of the tetraheme cytochrome or C subunit (Figure 7) has been
described in detail [40]. It is not related to other known tetraheme protein
structures and consists of ﬁve segments, an N-terminal segment (C1–C66), the
ﬁrst heme-binding segment (C67–C142), a connecting segment (C143–C225), a
second heme-binding segment (C226–C315), and the C-terminal seg-
ment(C316–C336). Apart from ana-helix (C25–C34) in the N-terminal seg-
ment, the three non-heme-binding segments contain little regular secondary
structure. The four hemes and the two heme-binding segments make up the
core of the cytochrome subunit. The ﬁrst heme-binding segment contains the
binding sites for heme-1 (c
554) and heme-2 (c
556), the second those for heme-3
(c
559) and heme-4 (c
552). Each heme-binding site consists of ana-helix that runs
parallel to the heme plane, a loop, and the heme attachment site with the
sequence Cys-X-Y-Cys-His.
11.5 Cofactor Conformation and Protein–Cofactor Interactions
11.5.1 Primary Electron Donor
The primary electron donor (‘‘special pair’’) is located at the interface of the L
and M subunits near the periplasmic side (Figures 1, 2, and 8). It interacts with
residues of the transmembrane helices C, D, E and the connections of helices C
21STRUCTURES OF REACTION CENTERS

and D. The special pair bacteriochlorophylls are held in their position by speciﬁc
interactions with the protein matrix (Figure 8). The ﬁrst four ligands to the ﬁve-
coordinated bacteriochlorophyll magnesium are provided by the bacteriochlorin
ring nitrogen atoms, and the ﬁfth ligand is provided by the Neatom of a His
side-chain (Figure 8). For the ‘‘special pair’’ bacteriochlorophylls, these His
residues (L173 and M200) are close to the N-terminal ends of the L and M
subunit transmembrane helices D, respectively. Apart from binding the Mg
21
ion, the protein displays several hydrogen bonding interactions with the bacte-
riochlorophyll molecules, as deduced from the structures [55,60] (Figure 8).
The ring I acetyl group (Figure 3a) of P
Lis hydrogen bonded to a His residue
Figure 6.Stereo views: Catrace of the H subunit of theBl. viridisRC (a) and its
comparison with those of theTc. tepidumandRb. sphaeroidesRCs (b). Residues H47 to
H53 (on the right) are not observed in the electron density. This region is included as a
very thin line to facilitate chain tracing (PDB entries 2PRC, 1EYS, 1PCR).
22 C. ROY D. LANCASTER

(His L168 in both theBl. viridisandRb. sphaeroidesRC, His L176 in the
Tc. tepidumRC) in all three RCs. The symmetry-related amino-acid residue near
P
Mis Phe M197 inRb. sphaeroides.Thus, no hydrogen bond can be formed. In
Bl. viridisandTc. tepidum, the respective residues are Tyr M195 and Tyr M196,
which donate hydrogen bonds to the acetyl carbonyl oxygen of ring I.
Thr L248 donates a hydrogen bond to the ring V keto carbonyl (Figure 3a) of
P
LinBl. viridis, which, in combination with the presence of the bulky Met L127
Figure 7.Stereo views: Catrace of the C subunit of theBl. viridisRC (a) and its
comparison with those of theTc. tepidumRC (b). The N-terminal segment drawn in
blue, the ﬁrst heme-binding segment in green, the connecting segment in yellow, the
second heme-binding segment in red, and the C-terminal segment in purple. The
cofactor heme groups and the side-chains of their ligands are displayed as atomic
models (PDB entries 1PRC, 1EYS).
23STRUCTURES OF REACTION CENTERS

Figure 8.Stereo pairs of the regions of the special pair and the accessory bacterio-
chlorophyll molecules of theBl. viridisRC (a),Tc. tepidumRC (b), andRb. sphaeroides
RC (c). Hydrogen bonds and ligand binding Mg-His are indicated as purple lines. (PDB
entries 2PRC, 1EYS, 1PCR.)
24 C. ROY D. LANCASTER

on the opposite side of the ring, results in ring V being bent towards Thr L248
(Figure 8a). This ring is oriented in the opposite direction inTc. tepidumandRb.
sphaeroides, where Ala residues are found at the position of theBl. viridisMet
L127, and theBl. viridisresidues Gly L247 and Thr L248 correspond to Cys L247
and Met L248 inRb. sphaeroides, and to Cys L255 and Ile L256 inTc. tepidum.
11.5.2 Accessory Bacteriochlorophylls
The accessory bacteriochlorophylls B
Aand BBare located between P and the
respective bacteriopheophytins H
Aand HBand are in van der Waals contact
with both respective neighboring cofactors. The His ligands for the accessory
bacteriochlorophylls, L153 (L161 inTc. tepidum) and M180 (M181 inTc.
tepidumand M182 inRb. sphaeroides), are situated close to the N-terminal end
of the L and M subunit periplasmic helices ‘‘cd’’, respectively. The average His
Ne–Mg distance is 2.1 A
˚
, as is the average distance between the bacteriochlorin
N atoms and the respective Mg
21
. Signiﬁcant conformational diﬀerences
between the reaction centers are found only at the ethyl groups – caused by
the structural diﬀerence between the ethyl group of bacteriochlorophyllaand
the ethylidene group of bacteriochlorophyllb(Figure 3a). In all three RCs, the
ring V carbonyl oxygen atoms are hydrogen-bonded via a water molecule
(‘‘water A’’) to His M200 (M201 inTc. tepidum,M202inRb. sphaeroides) and
(via ‘‘water B’’) to His L173, respectively (Figure 8).
11.5.3 Bacteriopheophytins
Figure 9 shows the location of the bacteriopheophytin H
Abetween BAand QA
for all three reaction centers. At the top, Tyr M208 (M209, M210) appears to be
of importance since it is in van der Waals contact with P
M,P
L,andB
A.The
symmetry-related residue in the L subunit is Phe L181 (L189, L181). The pattern
of hydrogen bonding formed by H
Aand HBwith the protein matrix is identical
in both species. Trp L100 (L108, L100) and Trp M127 (M128, M129), respec-
tively, donate a hydrogen bond to the ester carbonyls of ring V of H
Aand HB.
The carboxyl group of Glu L104 (L112, L104) is calculated [63,77,78] to be
protonated and donates a hydrogen bond to the H
Aring V keto group (Figure 9)
[60]. This is responsible for the 10 nm redshift of the H
AQxband compared with
the H
BQ
xband [61], but is not a dominant contributor to the directionality of
electron transfer in RCs. The bacteriopheophytin H
Ais surrounded by a
signiﬁcant number of Phe residues (Figure 9). Around H
B, these bulky residues
are replaced to a large extent by smaller amino acid residues. As seen in Figures 9
and 10, Trp M250 (M251, M252), with its large aromatic side-chain, bridges the
gap between H
Aand QAin all three reaction centers.
11.5.4 The Primary Electron Acceptor Q
Aand the Non-Heme Iron
Figure 10 shows the binding site of the primary electron acceptor quinone Q
A
for all three reaction centers. Q
Ais located on the A side where the L subunit
25STRUCTURES OF REACTION CENTERS

Figure 9.Stereo pairs of the regions of the bacteriopheophytin molecules H
Aof theBl.
viridisRC (a),Tc. tepidumRC (b), andRb. sphaeroidesRC (c). (PDB entries 1DXR,
1EYS, 1PCR.)
26 C. ROY D. LANCASTER

Figure 10.Stereo pairs of the regions of the Q Amolecules and the non-heme iron
atoms of the RCs ofBl. viridis(a),Tc. tepidum(b), andRb. sphaeroides(c). (PDB entries
1DXR, 1EYS, 1PCR.)
27STRUCTURES OF REACTION CENTERS

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determining medical practice by laws, and presuming every one
to know it
Government by fixed laws is better than lawless government by
unscientific men, but worse than lawless government by
scientific men. It is a second-best
ib.
Comparison of unscientific governments. The one despot is the
worse. Democracy is the least bad, because it is least of a
government
270
The true governor distinguished from the General, the Rhetor,
&c. They are all properly his subordinates and auxiliaries
271
What the scientific Governor will do. He will aim at the
formation of virtuous citizens. He will weave together the
energetic virtues with the gentle virtues. Natural dissidence
between them
272
If a man sins by excess of the energetic element, he is to be
killed or banished: if of the gentle, he is to be made a slave.
The Governor must keep up in the minds of the citizens an
unanimous standard of ethical orthodoxy
272
Remarks — Sokratic Ideal — Title to govern mankind derived
exclusively from scientific superiority in an individual person
273
Different ways in which this ideal is worked out by Plato and
Xenophon. The man of speculation and the man of action
ib.
The theory in the Politikus is the contradiction to that theory
which is assigned to Protagoras in the Protagoras
274
Points of the Protagorean theory — rests upon common
sentiment
275
Counter-Theory in the Politikus. The exigencies of the Eleate in
the Politikus go much farther than those of Protagoras
276

The Eleate complains that under the Protagorean theory no
adverse criticism is allowed. The dissenter is either condemned
to silence or punished
ib.
Intolerance at Athens, not so great as elsewhere. Plato
complains of the assumption of infallibility in existing societies,
but exacts it severely in that which he himself constructs
277
Theory of the Politikus — distinguished three gradations of
polity. Gigantic individual force the worst
278
Comparison of the Politikus with the Republic. Points of analogy
and difference
279
Comparison of the Politikus with the Kratylus. Dictatorial,
constructive, science or art, common to both: applied in the
former to social administration — in the latter to the formation
and modification of names
281
Courage and Temperance are assumed in the Politikus. No
notice taken of the doubts and difficulties raised in Lachês and
Charmidês
282
Purpose of the difficulties in Plato’s Dialogues of Search — To
stimulate the intellect of the hearer. His exposition does not
give solutions
284

CHAPTER XXXI.
KRATYLUS.
Persons and subjects of the dialogue Kratylus — Sokrates has
no formed opinion, but is only a Searcher with the others
285

Argument of Sokrates against Hermogenes — all proceedings of
nature are conducted according to fixed laws — speaking and
naming among the rest
286
The name is a didactic instrument; fabricated by the law-giver
upon the type of the Name-Form, and employed as well as
appreciated, by the philosopher
287
Names have an intrinsic aptitude for signifying one thing and
not another
289
Forms of Names, as well as Forms of things nameable —
essence of the Nomen, to signify the Essence of its Nominatum
ib.
Exclusive competence of a privileged lawgiver, to discern these
essences, and to apportion names rightly
290
Counter-Theory, which Sokrates here sets forth and impugns —
the Protagorean doctrine — Homo Mensura
291
Objection by Sokrates — That Protagoras puts all men on a
level as to wisdom and folly, knowledge and ignorance
292
Objection unfounded — What the Protagorean theory really
affirms — Belief always relative to the believer’s mind
ib.
Each man believes others to be wiser on various points than
himself — Belief on authority — not inconsistent with the
affirmation of Protagoras
293
Analogy of physical processes (cutting and burning) appealed to
by Sokrates — does not sustain his inference against Protagoras
294
Reply of Protagoras to the Platonic objections 295
Sentiments of Belief and Disbelief, common to all men —
Grounds of belief and disbelief, different with different men and
different ages
295
Protagoras did not affirm, that Belief depended upon the will or
inclination of each individual but that it was relative to the
297

circumstances of each individual mind
Facts of sense — some are the same to all sentient subjects,
others are different to different subjects. Grounds of unanimity
298
Sokrates exemplifies his theory of the Absolute Name or the
Name-Form. He attempts to show the inherent rectitude of
many existing names. His etymological transitions
299
These transitions appear violent to a modern reader. They did
not appear so to readers of Plato until this century. Modern
discovery, that they are intended as caricatures to deride the
Sophists
302
Dissent from this theory — No proof that the Sophists ever
proposed etymologies
304
Plato did not intend to propose mock-etymologies, or to deride
any one. Protagoras could not be ridiculed here. Neither
Hermogenes nor Kratylus understand the etymologies as
caricature
306
Plato intended his theory as serious, but his exemplifications as
admissible guesses. He does not cite particular cases as proofs
of a theory, but only as illustrating what he means
308
Sokrates announces himself as Searcher. Other etymologists of
ancient times admitted etymologies as rash as those of Plato
310
Continuance of the dialogue — Sokrates endeavours to explain
how it is that the Names originally right have become so
disguised and spoiled
312
Letters, as well as things, must be distinguished with their
essential properties, each must be adapted to each
313
Essential significant aptitude consists in resemblance ib.
Sokrates assumes that the Name-giving Lawgiver was a believer
in the Herakleitean theory
314

But the Name-Giver may be mistaken or incompetent — the
rectitude of the name depends upon his knowledge
315
Changes and transpositions introduced in the name — hard to
follow
315
Sokrates qualifies and attenuates his original thesis 316
Conversation of Sokrates with Kratylus; who upholds that
original thesis without any qualification
ib.
Sokrates goes still farther towards retracting it 317
There are names better and worse — more like, or less like to
the things named: Natural Names are the best, but they cannot
always be had. Names may be significant by habit, though in an
inferior way
318
All names are not consistent with the theory of Herakleitus:
some are opposed to it
319
It is not true to say, That Things can only be known through
their names
320
Unchangeable Platonic Forms — opposed to the Herakleitean
flux, which is true only respecting sensible particulars
ib.
Herakleitean theory must not be assumed as certain. We must
not put implicit faith in names
321
Remarks upon the dialogue. Dissent from the opinion of
Stallbaum and others, that it is intended to deride Protagoras
and other Sophists
ib.
Theory laid down by Sokrates à priori, in the first part — Great
difficulty, and ingenuity necessary, to bring it into harmony with
facts
322
Opposite tendencies of Sokrates in the last half of the dialogue
— he disconnects his theory of Naming from the Herakleitean
doctrine
324

Ideal of the best system of naming — the Name-Giver ought to
be familiar with the Platonic Ideas or Essences, and apportion
his names according to resemblances among them
325
Comparison of Plato’s views about naming with those upon
social institutions. Artistic, systematic construction — contrasted
with unpremeditated unsystematic growth
327
Politikus compared with Kratylus 328
Ideal of Plato — Postulate of the One Wise Man — Badness of
all reality
329
Comparison of Kratylus, Theætêtus, and Sophistês, in treatment
of the question respecting Non-Ens, and the possibility of false
propositions
331
Discrepancies and inconsistencies of Plato, in his manner of
handling the same subject
332
No common didactic purpose pervading the Dialogues — each is
a distinct composition, working out its own peculiar argument
ib.

CHAPTER XXXII.
PHILEBUS.
Character, Personages, and Subject of the Philêbus 334
Protest against the Sokratic Elenchus, and the purely negative
procedure
335
Enquiry — What mental condition will ensure to all men a
happy life? Good and Happiness — correlative and co-extensive.
ib.

Philêbus declares for Pleasure, Sokrates for Intelligence
Good — object of universal choice and attachment by men,
animals, and plants — all-sufficient — satisfies all desires
ib.
Pleasures are unlike to each other, and even opposite cognitions
are so likewise
336
Whether Pleasure, or Wisdom, corresponds to this description?
Appeal to individual choice
337
First Question submitted to Protarchus — Intense Pleasure,
without any intelligence — He declines to accept it
338
Second Question — Whether he will accept a life of Intelligence
purely without any pleasure or pain? Answer — No
ib.
It is agreed on both sides, That the Good must be a Tertium
Quid. But Sokrates undertakes to show, That Intelligence is
more cognate with it than Pleasure
339
Difficulties about Unum et Multa. How can the One be Many?
How can the Many be One? The difficulties are greatest about
Generic Unity — how it is distributed among species and
individuals
ib.
Active disputes upon this question at the time 340
Order of Nature — Coalescence of the Finite with the Infinite.
The One — The Finite Many — The Infinite Many
ib.
Mistake commonly made — To look only for the One, and the
Infinite Many, without looking for the intermediate subdivisions
341
Illustration from Speech and Music 342
Plato’s explanation does not touch the difficulties which he had
himself recognised as existing
343
It is nevertheless instructive, in regard to logical division and
classification
344

At that time little thought had been bestowed upon
classification as a logical process
ib.
Classification — unconscious and conscious 345
Plato’s doctrine about classification is not necessarily connected
with his Theory of Ideas
ib.
Quadruple distribution of Existences. 1. The Infinite. 2. The
Finient 3. Product of the two former. 4. Combining Cause or
Agency
346
Pleasure and Pain belong to the first of these four Classes —
Cognition or Intelligence belongs to the fourth
347
In the combination, essential to Good, of Intelligence with
Pleasure, Intelligence is the more important of the two
constituents
ib.
Intelligence is the regulating principle — Pleasure is the
Indeterminate, requiring to be regulated
348
Pleasure and Pain must be explained together — Pain arises
from the disturbance of the fundamental harmony of the
system — Pleasure from the restoration of it
ib.
Pleasure presupposes Pain 349
Derivative pleasures of memory and expectation belonging to
mind alone. Here you may find pleasure without pain
ib.
A life of Intelligence alone, without pain and without pleasure,
is conceivable. Some may prefer it: at any rate it is second-best
ib.
Desire belongs to the mind, presupposes both a bodily want,
and the memory of satisfaction previously had for it. The mind
and body are here opposed. No true or pure pleasure therein
350
Can pleasures be true or false? Sokrates maintains that they are
so
351

Reasons given by Sokrates. Pleasures attached to true opinions,
are true pleasures. The just man is favoured by the Gods, and
will have true visions sent to him
ib.
Protarchus disputes this — He thinks that there are some
pleasures bad, but none false — Sokrates does not admit this,
but reserves the question
352
No means of truly estimating pleasures and pains — False
estimate habitual — These are the false pleasures
ib.
Much of what is called pleasure is false. Gentle and gradual
changes do not force themselves upon our notice either as
pleasure or pain. Absence of pain not the same as pleasure
353
Opinion of the pleasure-hating philosophers — That pleasure is
no reality, but a mere juggle. There is no reality except pain,
and the relief from pain
354
Sokrates agrees with them in part, but not wholly ib.
Theory of the pleasure-haters — We must learn what pleasure
is by looking at the intense pleasures — These are connected
with distempered body and mind
355
The intense pleasures belong to a state of sickness; but there is
more pleasure, on the whole, enjoyed in a state of health
356
Sokrates acknowledges some pleasures to be true. Pleasures of
beautiful colours, odours, sounds, smells, &c. Pleasures of
acquiring knowledge
ib.
Pure and moderate pleasures admit of measure and proportion357
Pleasure is generation, not substance or essence: it cannot
therefore be an End, because all generation is only a means
towards substance — Pleasure therefore cannot be the Good
ib.
Other reasons why pleasure is not the Good 358

Distinction and classification of the varieties of Knowledge or
Intelligence. Some are more true and exact than others,
according as they admit more or less of measuring and
computation
ib.
Arithmetic and Geometry are twofold: As studied by the
philosopher and teacher: As applied by the artisan
359
Dialectic is the truest and purest of all Cognitions. Analogy
between Cognition and Pleasure: in each, there are gradations
of truth and purity
360
Difference with Gorgias, who claims superiority for Rhetoric.
Sokrates admits that Rhetoric is superior in usefulness and
celebrity: but he claims superiority for Dialectic, as satisfying
the lover of truth
ib.
Most men look to opinions only, or study the phenomenal
manifestations of the Kosmos. They neglect the unchangeable
essences, respecting which alone pure truth can be obtained
361
Application. Neither Intelligence nor Pleasure separately, is the
Good, but a mixture of the two — Intelligence being the most
important. How are they to be mixed?
ib.
We must include all Cognitions — not merely the truest, but the
others also. Life cannot be carried on without both
362
But we must include no pleasures except the true, pure, and
necessary. The others are not compatible with Cognition or
Intelligence — especially the intense sexual pleasures
ib.
What causes the excellence of this mixture? It is Measure,
Proportion, Symmetry. To these Reason is more akin than
Pleasure
363
Quintuple gradation in the Constituents of the Good. 1.
Measure. 2. Symmetry. 3. Intelligence. 4. Practical Arts and
364

Right Opinions. 5. True and Pure Pleasures
Remarks. Sokrates does not claim for Good the unity of an
Idea, but a quasi-unity of analogy
365
Discussions of the time about Bonum. Extreme absolute view,
maintained by Eukleides: extreme relative by the Xenophontic
Sokrates. Plato here blends the two in part; an Eclectic doctrine
ib.
Inconvenience of his method, blending Ontology with Ethics366
Comparison of Man to the Kosmos (which has reason, but no
emotion) is unnecessary and confusing
367
Plato borrows from the Pythagoreans, but enlarges their
doctrine. Importance of his views in dwelling upon systematic
classification
368
Classification broadly enunciated, and strongly recommended —
yet feebly applied — in this dialogue
369
What is the Good? Discussed both in Philêbus and in Republic.
Comparison
370
Mistake of talking about Bonum confidently, as if it were known,
while it is subject of constant dispute. Plato himself wavers
about it; gives different explanations, and sometimes professes
ignorance, sometimes talks about it confidently
ib.
Plato lays down tests by which Bonum may be determined: but
the answer in the Philêbus does not satisfy those tests
371
Inconsistency of Plato in his way of putting the question — The
alternative which he tenders has no fair application
372
Intelligence and Pleasure cannot be fairly compared — Pleasure
is an End, Intelligence a Means. Nothing can be compared with
Pleasure, except some other End
373
The Hedonists, while they laid down attainment of pleasure and
diminution of pain, postulated Intelligence as the governing
374

agency
Pleasures of Intelligence may be compared, and are compared
by Plato, with other pleasures, and declared to be of more
value. This is arguing upon the Hedonistic basis
375
Marked antithesis in the Philêbus between pleasure and
avoidance of pain
377
The Hedonists did not recognise this distinction — They
included both in their acknowledged End
ib.
Arguments of Plato against the intense pleasures — The
Hedonists enforced the same reasonable view
378
Different points of view worked out by Plato in different
dialogues — Gorgias, Protagoras, Philêbus — True and False
Pleasures
379
Opposition between the Gorgias and Philêbus, about Gorgias
and Rhetoric
380
Peculiarity of the Philêbus — Plato applies the same principle of
classification — true and false — to Cognitions and Pleasures
382
Distinction of true and false — not applicable to pleasures ib.
Plato acknowledges no truth and reality except in the Absolute
— Pleasures which he admits to be true — and why
385
Plato could not have defended this small list of Pleasures, upon
his own admission, against his opponents — the Pleasure-
haters, who disallowed pleasures altogether
387
Sokrates in this dialogue differs little from these Pleasure-haters389
Forced conjunction of Kosmology and Ethics — defect of the
Philêbus
391
Directive sovereignty of Measure — how explained and applied
in the Protagoras
ib.

How explained in Philêbus — no statement to what items it is
applied
393
Classification of true and false — how Plato applies it to
Cognitions
394
Valuable principles of this classification — difference with other
dialogues
395
Close of the Philêbus — Graduated elements of Good 397
Contrast between the Philêbus and the Phædrus, and
Symposion, in respect to Pulchrum, and intense Emotions
generally
398

CHAPTER XXXIII.
MENEXENUS.
Persons and situation of the dialogue 401
Funeral harangue at Athens — Choice of a public orator —
Sokrates declares the task of the public orator to be easy —
Comic exaggeration of the effects of the harangue
401
Sokrates professes to have learnt a funeral harangue from
Aspasia, and to be competent to recite it himself. Menexenus
entreats him to do so
402
Harangue recited by Sokrates 403
Compliments of Menexenus after Sokrates has finished, both to
the harangue itself and to Aspasia
ib.
Supposed period — shortly after the peace of Antalkidasib.

Custom of Athens about funeral harangues. Many such
harangues existed at Athens, composed by distinguished
orators or logographers — Established type of the harangue
404
Plato in this harangue conforms to the established type —
Topics on which he insists
405
Consolation and exhortation to surviving relatives 407
Admiration felt for this harangue, both at the time and
afterwards
407
Probable motives of Plato in composing it, shortly after he
established himself at Athens as a teacher — His competition
with Lysias — Desire for celebrity both as rhetor and as
dialectician
ib.
Menexenus compared with the view of rhetoric presented in the
Gorgias — Necessity for an orator to conform to established
sentiments
409
Colloquial portion of the Menexenus is probably intended as
ridicule and sneer at Rhetoric — The harangue itself is serious,
and intended as an evidence of Plato’s ability
410
Anachronism of the Menexenus — Plato careless on this point411

CHAPTER XXXIV.
KLEITOPHON.
Persons and circumstances of Kleitophon 413

Conversation of Sokrates with Kleitophon alone: he alludes to
observations of an unfavourable character recently made by
Kleitophon, who asks permission to explain
ib.
Explanation given. Kleitophon expresses gratitude and
admiration for the benefit which he has derived from long
companionship with Sokrates
414
The observations made by Sokrates have been most salutary
and stimulating in awakening ardour for virtue. Arguments and
analogies commonly used by Sokrates
ib.
But Sokrates does not explain what virtue is, nor how it is to be
attained. Kleitophon has had enough of stimulus, and now
wants information how he is to act
415
Questions addressed by Kleitophon with this view, both to the
companions of Sokrates and to Sokrates himself
416
Replies made by the friends of Sokrates unsatisfactory ib.
None of them could explain what the special work of justice or
virtue was
417
Kleitophon at length asked the question from Sokrates himself.
But Sokrates did not answer clearly. Kleitophon believes that
Sokrates knows, but will not tell
417
Kleitophon is on the point of leaving Sokrates and going to
Thrasymachus. But before leaving he addresses one last
entreaty, that Sokrates will speak out clearly and explicitly
418
Remarks on the Kleitophon. Why Thrasyllus placed it in the
eighth Tetralogy immediately before the Republic, and along
with Kritias, the other fragment
419
Kleitophon is genuine, and perfectly in harmony with a just
theory of Plato
420
It could not have been published until after Plato’s death ib.

Reasons why the Kleitophon was never finished. It points out
the defects of Sokrates, just as he himself confesses them in
the Apology
421
The same defects also confessed in many of the Platonic and
Xenophontic dialogues
422
Forcible, yet respectful, manner in which these defects are set
forth in the Kleitophon. Impossible to answer them in such a
way as to hold out against the negative Elenchus of a Sokratic
pupil
423
The Kleitophon represents a point of view which many objectors
must have insisted on against Sokrates and Plato
424
The Kleitophon was originally intended as a first book of the
Republic, but was found too hard to answer. Reasons why the
existing first book was substituted
ib.

CHAPTER XXVI.

These two are the two
erotic dialogues of Plato.
Phædrus is the originator
of both.
Eros as conceived by Plato.
Different sentiment
prevalent in Hellenic
antiquity and in modern
times. Position of women in
Greece.
PHÆDRUS — SYMPOSION.
I put together these two dialogues,
as distinguished by a marked
peculiarity. They are the two erotic
dialogues of Plato. They have one
great and interesting subject common
to both: though in the Phædrus, this subject is blended with, and
made contributory to, another. They agree also in the circumstance,
that Phædrus is, in both, the person who originates the
conversation. But they differ materially in the manner of handling, in
the comparisons and illustrations, and in the apparent purpose.
The subject common to both is, Love
or Eros in its largest sense, and with its
manifold varieties. Under the totally
different vein of sentiment which
prevails in modern times, and which
recognises passionate love as
prevailing only between persons of
different sex — it is difficult for us to enter into Plato’s eloquent
exposition of the feeling as he conceives it. In the Hellenic point of
view,1 upon which Plato builds, the attachment of man to woman
was regarded as a natural impulse, and as a domestic, social,
sentiment; yet as belonging to a common-place rather than to an
exalted mind, and seldom or never rising to that pitch of enthusiasm
which overpowers all other emotions, absorbs the whole man, and
aims either at the joint performance of great exploits or the joint

prosecution of intellectual improvement by continued colloquy. We
must remember that the wives and daughters of citizens were
seldom seen abroad: that the wife was married very young: that she
had learnt nothing except spinning and weaving: that the fact of her
having seen as little and heard as little as possible, was considered
as rendering her more acceptable to her husband:2 that her sphere
of duty and exertion was confined to the interior of the family. The
beauty of women yielded satisfaction to the senses, but little
beyond. It was the masculine beauty of youth that fired the Hellenic
imagination with glowing and impassioned sentiment. The finest
youths, and those too of the best families and education, were seen
habitually uncovered in the Palæstra and at the public festival-
matches; engaged in active contention and graceful exercise, under
the direction of professional trainers. The sight of the living form, in
such perfection, movement, and variety, awakened a powerful
emotional sympathy, blended with aesthetic sentiment, which in the
more susceptible natures was exalted into intense and passionate
devotion. The terms in which this feeling is described, both by Plato
and Xenophon, are among the strongest which the language affords
— and are predicated even of Sokrates himself. Far from being
ashamed of the feeling, they consider it admirable and beneficial;
though very liable to abuse, which they emphatically denounce and
forbid.3 In their view, it was an idealising passion, which tended to
raise a man above the vulgar and selfish pursuits of life, and even
above the fear of death. The devoted attachments which it inspired
were dreaded by the despots, who forbade the assemblage of
youths for exercise in the palæstra.4
1 Schleiermacher (Einleit. zum Symp. p. 367) describes this view of
Eros as Hellenic, and as “gerade den anti-modernen and anti-
christlichen Pol der Platonischen Denkungsart”. Aristotle composed

Θέσεις Ἐρωτικαὶ or Ἐρωτικάς, Diogenes Laert. v. 22-24. See Bernays,
Die Dialoge des Aristoteles, p. 133, Berlin, 1863.
Compare the dialogue called Ἐρωτικός, among the works of
Plutarch, p. 750 seq., where some of the speakers, especially
Protogenes, illustrate and enlarge upon this Platonic construction of
Eros — ἀληθινοῦ δὲ Ἔρωτος οὐδ’ ὁτιοῦν τῇ γυναικωνίτιδι μέτεστιν,
&c. (750 C, 761 B, &c.)
In the Treatise De Educatione Puerorum (c. 15, p. 11 D-F)
Plutarch hesitates to give a decided opinion on the amount of
restriction proper to be imposed on youth: he is much impressed
with the authority of Sokrates, Plato, Xenophon, Æschines, Kebês,
καὶ τὸν πάντα χόρον ἐκείνων τῶν ἀνδρῶν, οἱ τοὺς ἄῤῥενας
ἐδοκίμασαν ἔρωτας, &c. See the anecdote about Episthenes, an
officer among the Ten Thousand Greeks under Xenophon, in
Xenophon, Anabasis, vii. 4, 7, and a remarkable passage about Zeno
the Stoic, Diog. Laert. vii. 13. Respecting the general subject of
παιδεραστία in Greece, there is a valuable Excursus in Bekker’s
Charikles, vol. i. pp. 347-377, Excurs. ii. I agree generally with his
belief about the practice in Greece, see Cicero, Tusc. Disp. iv. 33, 70.
Bekker quotes abundant authorities, which might be farther
multiplied if necessary. In appreciating the evidence upon this point,
we cannot be too careful to keep in mind what Sokrates says (in the
Xenophontic Symposion, viii. 34) when comparing the Thebans and
Eleians on one side with the Athenians and Spartans on the other —
Ἐκείνοις μὲν γὰρ ταῦτα νόμιμα, ἡμῖν δὲ ἐπονείδιστα. We must
interpret passages of the classical authors according to their fair and
real meanings, not according to the conclusions which we might
wish to find proved.

If we read the oration of Demosthenes against Neæra (which is
full of information about Athenian manners), we find the speaker
Apollodôrus distributing the relations of men with women in the
following manner (p. 1386) — τὸ γὰρ συνοικεῖν τοῦτ’ ἐστίν, ὃς ἂν
παιδοποιῆται καὶ εἰσάγῃ εἴς τε τοὺς δημότας καὶ τοὺς φράτορας τοὺς
υἱεῖς, καὶ τὰς θυγατέρας ἐκδιδῷ ὡς αὐτοῦ οὔσας τοῖς ἀνδράσι. Τὰς
μὲν γὰρ ἑταίρας, ἡδονῆς ἕνεκα ἔχομεν — τὰς δὲ παλλακάς, τῆς καθ’
ἡμέραν θεραπείας τοῦ σώματος — τὰς δὲ γυναῖκας, τοῦ
παιδοποιεῖσθαι γνησίως, καὶ τῶν ἕνδον φύλακα πίστην ἔχειν.
To the same purpose, the speaker in Lysias (Ὑπὲρ τοῦ
Ἐρατοσθένους φόνου — sect. 7), describing his wife, says — ἐν μὲν
οὖν τῷ πρώτῳ χρόνῳ πασῶν ἦν βελτίστη· καὶ γὰρ οἰκονόμος δεινὴ
καὶ φειδωλὸς ἀγαθὴ καὶ ἀκριβῶς πάντα διοικοῦσα.
Neither of these three relations lent itself readily to the Platonic
vein of sentiment and ideality: neither of them led to any grand
results either in war — or political ambition — or philosophical
speculation; the three great roads, in one or other of which the
Grecian ideality travelled. We know from the Republic that Plato did
not appreciate the value of the family life, or the purposes for which
men marry, according to the above passage cited from
Demosthenes. In this point, Plato differs from Xenophon, who, in his
Œconomicus, enlarges much (in the discourse of Ischomachus) upon
the value of the conjugal union, with a view to prudential results and
good management of the household; while he illustrates the
sentimental and affectionate side of it, in the story of Pantheia and
Abradates (Cyropædia).
2 See the Œconomicus of Xenophon, cap. iii. 12, vii. 5.

3 The beginning of the Platonic Charmidês illustrates what is here
said, pp. 154-155; also that of the Protagoras and Lysis, pp. 205-
206.
Xenophon, Sympos. i. 8-11; iv. 11, 15. Memorab. i. 3, 8-14 (what
Sokrates observes to Xenophon about Kritobulus). Dikæarchus
(companion of Aristotle) disapproved the important influence which
Plato assigned to Eros (Cicero, Tusc. D. iv. 34-71).
If we pass to the second century after the Christian Era, we find
some speakers in Athenæus blaming severely the amorous
sentiments of Sokrates and the narrative of Alkibiades, as recited in
the Platonic Symposium (v. 180-187; xi. 506-508 C). Athenæus
remarks farther, that Plato, writing in this strain, had little right to
complain (as we read in the Republic) of the licentious compositions
of Homer and other poets, and to exclude them from his model city.
Maximus Tyrius, in one of his four discourses (23-5) on the ἐρωτικὴ
of Sokrates, makes the same remark as Athenæus about the
inconsistency of Plato in banishing Homer from the model city, and
composing what we read in the Symposion; he farther observes that
the erotic dispositions of Sokrates provoked no censure from his
numerous enemies at the time (though they assailed him upon so
many other points), but had incurred great censure from
contemporaries of Maximus himself, to whom he replies — τοὺς νυνὶ
κατηγόρους (23, 6-7). The comparisons which he institutes (23, 9)
between the sentiments and phrases of Sokrates, and those of
Sappho and Anakreon, are very curious.
Dionysius of Halikarnassus speaks of the ἐγκώμια on Eros in the
Symposion, as “unworthy of serious handling or of Sokrates”. (De
Admir. Vi Dic. Demosth. p. 1027.)

Eros, considered as the
great stimulus to improving
philosophical communion.
Personal Beauty, the great
point of approximation
between the world of sense
and the world of Ideas.
Gradual generalisation of
the sentiment.
But the most bitter among all the critics of Plato, is Herakleitus —
author of the Allegoriæ Homericæ. Herakleitus repels, as unjust and
calumnious, the sentence of banishment pronounced by Plato
against Homer, from whom all mental cultivation had been derived.
He affirms, and tries to show, that the poems of Homer — which he
admits to be full of immorality if literally understood — had an
allegorical meaning. He blames Plato for not having perceived this;
and denounces him still more severely for the character of his own
writings — ἐῤῥίφθω δὲ καὶ Πλάτων ὁ κόλαξ, Ὁμήρου συκοφάντης —
Τοὺς δὲ Πλάτωνος διαλόγους, ἄνω καὶ κάτω παιδικοὶ καθυβρίζουσιν
ἔρωτες, οὐδαμοῦ δε οὐχι τῆς ἀῤῥένος ἐπιθυμίας μεστός ἐστιν ὁ ἀνήρ
(Herakl. All. Hom., c. 4-74, ed. Mehler, Leiden, 1851).
4 Plato, Sympos. 182 C. The proceedings of Harmodius and
Aristogeiton, which illustrate this feeling, are recounted by
Thucydides, vi. 54-57. These two citizens were gratefully recollected
and extensively admired by the Athenian public.
Especially to Plato, who combined
erotic and poetical imagination with
Sokratic dialectics and generalising
theory — this passion presented itself
in the light of a stimulus introductory to
the work of philosophy — an impulse
at first impetuous and undistinguishing,
but afterwards regulated towards
improving communion and colloquy
with an improvable youth. Personal
beauty (this is5 the remarkable doctrine of Plato in the Phædrus) is
the main point of visible resemblance between the world of sense
and the world of Ideas: the Idea of Beauty has a brilliant

representative of itself among concrete objects — the Ideas of
Justice and Temperance have none. The contemplation of a beautiful
youth, and the vehement emotion accompanying it, was the only
way of reviving in the soul the Idea of Beauty which it had seen in
its antecedent stage of existence. This was the first stage through
which every philosopher must pass; but the emotion of love thus
raised, became gradually in the better minds both expanded and
purified. The lover did not merely admire the person, but also
contracted the strongest sympathy with the feelings and character,
of the beloved youth: delighting to recognise and promote in him all
manifestations of mental beauty which were in harmony with the
physical, so as to raise him to the greatest attainable perfection of
human nature. The original sentiment of admiration, having been
thus first transferred by association from beauty in the person to
beauty in the mind and character, became gradually still farther
generalised; so that beauty was perceived not as exclusively
specialised in any one individual, but as invested in all beautiful
objects, bodies as well as minds. The view would presently be
farther enlarged. The like sentiment would be inspired, so as to
worship beauty in public institutions, in administrative arrangements,
in arts and sciences. And the mind would at last be exalted to the
contemplation of that which pervades and gives common character
to all these particulars — Beauty in the abstract — or the Self-
Beautiful — the Idea or Form of the Beautiful. To reach this highest
summit, after mounting all the previous stages, and to live absorbed
in the contemplation of “the great ocean of the beautiful,” was the
most glorious privilege attainable by any human being. It was indeed
attainable only by a few highly gifted minds. But others might make
more or less approach to it: and the nearer any one approached, the

All men love Good, as the
means of Happiness, but
they pursue it by various
means. The name Eros is
confined to one special
case of this large variety.
greater measure would he ensure to himself of real good and
happiness.6
5 Plato, Phædrus, pp. 249 E, 250 B-E.
6 Plato, Sympos. pp. 210-211.
Respecting the Beautiful, I transcribe here a passage from Ficinus,
in his Argument prefixed to the Hippias Major, p. 757.
“Unumquodque è singulis pulchris, pulchrum hoc Plato vocat:
formam in omnibus, pulchritudinem; speciem et ideam supra omnia,
ipsum pulchrum. Primum sensus attingit opinioque. Secundum ratio
cogitat. Tertium mens intuetur.
“Quid ipsum Bonum? Ipsum rerum omnium principium, actus
purus, actus sequentia cuncta vivificans. Quid ipsum Pulchrum?
Vivificus actus e primo fonte bonorum effluens, Mentem primo
divinam idearum ordine infinité decorans, Numina deinde sequentia
mentesque rationum serie complens, Animas tertio numerosis
discursibus ornans, Naturas quarto seminibus, formis quinto
materiam.”
Such is Plato’s conception of Eros or
Love and its object. He represents it as
one special form or variety of the
universal law of gravitation pervading
all mankind. Every one loves, desires,
or aspires to happiness: this is the
fundamental or primordial law of
human nature, beyond which we cannot push enquiry. Good, or
good things, are nothing else but the means to happiness:7
accordingly, every man, loving happiness, loves good also, and
desires not only full acquisition, but perpetual possession of good. In

this wide sense, love belongs to all human beings: every man loves
good and happiness, with perpetual possession of them — and
nothing else.8 But different men have different ways of pursuing this
same object. One man aspires to good or happiness by way of
money-getting, another by way of ambition, a third by gymnastics —
or music — or philosophy. Still no one of these is said to love, or to
be under the influence of Eros. That name is reserved exclusively for
one special variety of it — the impulse towards copulation,
generation, and self-perpetuation, which agitates both bodies and
minds throughout animal nature. Desiring perpetual possession of
good, all men desire to perpetuate themselves, and to become
immortal. But an individual man or animal cannot be immortal: he
can only attain a quasi-immortality by generating a new individual to
replace himself.9 In fact even mortal life admits no continuity, but is
only a succession of distinct states or phenomena: one always
disappearing and another always appearing, each generated by its
antecedent and generating its consequent. Though a man from
infancy to old age is called the same, yet he never continues the
same for two moments together, either in body or mind. As his
blood, flesh, bones, &c., are in perpetual disappearance and
renovation, always coming and going — so likewise are his
sensations, thoughts, emotions, dispositions, cognitions, &c. Neither
mentally nor physically does he ever continue the same during
successive instants. The old man of this instant perishes and is
replaced by a new man during the next.10 As this is true of the
individual, so it is still more true of the species: continuance or
immortality is secured only by perpetual generation of new
individuals.
7 Plato, Sympos. pp. 204-205. Φέρε, ὁ ἐρῶν τῶν ἀγαθῶν, τί ἐρᾷ;
Γενέσθαι, ἦν δ’ ἐγώ, αὐτῷ. Καὶ τί ἔσται ἐκείνῳ ᾧ ἂν γένηται τἀγαθά;

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Primary Processes Of Photosynthesis Part 2 Principles And Apparatus G Renger

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