Crystallography Reviews

ISSN: 0889-311X (Print) 1476-3508 (Online) Journal homepage: https://www.tandfonline.com/loi/gcry20

Textbook of structural biology – Second edition

Xiao-Dong Su

To cite this article: Xiao-Dong Su (2018) Textbook of structural biology – Second edition,
Crystallography Reviews, 24:3, 209-211, DOI: 10.1080/0889311X.2018.1430142

To link to this article: https://doi.org/10.1080/0889311X.2018.1430142

Published online: 05 Feb 2018.

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 CRYSTALLOGRAPHY REVIEWS 209

materials. Thus, the book ends on a slightly speculative note: how far is the current state of the
art in crystal engineering from being able to design – and produce – the structure of the most
thermodynamically stable aggregate of a molecule or solvate crystal?
The book is well written and sensitively edited; despite the large number of authors involved,
the text flows and one can read consecutive chapters without particularly noticing the change in
authorship. The number of illustrations is reasonable, and they are clear and informative. Topi-
cal, and up to date, it includes chapters on relatively new techniques and those recently applied
to solid-state interactions (molecular beam spectroscopy, SSNMR, charge density methods), as
well as on relatively recently recognized and often underreported interactions such as hydro-
gen–hydrogen bonding and beryllium bonding. Keeping the focus firmly on the interactions
that occur in crystalline systems, the editor has ensured that crystal engineering remains the
clear goal to work in this area. As he states in the preface, ‘Improving our control of the outcome
of crystallization will only be possible after improving our control of the mechanism by which
intermolecular interactions compete’. While no one book can provide a complete overview of
a field as broad as intermolecular interactions, this text is an essential addition to any library in
the field. It works equally well as a book to be read in sequence or as a text to dip into and will
augment any collection on supramolecular or crystal chemistry.

Susan A. Bourne
Centre for Supramolecular Chemistry Research, Department of Chemistry, University of Cape
Town, Cape Town, South Africa
susan.bourne@uct.ac.za
© 2018 Susan A. Bourne
https://doi.org/10.1080/0889311X.2017.1420649

Textbook of structural biology – Second edition, by Anders Liljas, Lars Liljas,

Miriam-Rose Ash, Göran Lindblom, Poul Nissen and Morten Kjeldgaar, Singapore,
World Scientific, 2017, 572 pp., US$178(hardcover), ISBN 978-981-277-207-7,
US$95(paperback), http://www.worldscientific.com/worldscibooks/10.1142/10102

An excellent and extensive review for the first edition of the same book of ‘Textbook of struc-
tural biology’ appeared in this journal in 2009, see [1]. I well agree with the comments therein
and will start this review of the second edition by commenting on the major changes made. The
changes made are extensive and necessary, indeed making the second edition be a new book.
Except for Chap. 1, ‘Introduction’, most of the chapters of ‘Textbook of structural biology’
have undergone major rewriting and/or reshuffling to make relevant parts more logic and con-
sistent. Protein structure basics are now divided into two chapters: Chap. 2 ‘Basics of protein
structures’ and Chap. 3 ‘The folding, folds and functions of proteins’. These include most of the
contents of Appendix A from the first edition about chemical bonds and energetics relevant to
protein and nucleic acid structures, as well as the protein fold types. In Chap. 5 ‘Basics of nucleic
acid structure’ the authors have kept the main good style, but nucleosome and other genomics
parts were moved to the corresponding places of Chap. 9 ‘Genome structures, DNA replication
and recombination’. The two membrane biology related chapters, Chap. 4 ‘Basics of membrane
proteins’, and Chap. 6 ‘Basics lipids and membrane structures’, have been much expanded now
to reflect the rapid progress of membrane biology, and membrane protein structural and func-
tional research. Chap. 7 ‘Basics of carbohydrates’ is a completely new addition, which although
still quite short, makes this edition of the textbook of macromolecular structures more com-
plete. Chap. 8 ‘Enzymes’ has not changed dramatically, but in my opinion, this chapter would
210 BOOK REVIEWS

be better to become something like ‘Basics of Catalysis’ to make the basics of structural biology
complete. This far, almost half of the book has been dedicated to very detailed basic chemical
and physical properties and knowledge about structural biology related to all four major types
of biological macromolecules (proteins, nucleic acids, lipids and carbohydrates). This part is
really the highlight of this textbook, no other textbooks available so far cover such a broad
spectrum yet in-depth knowledge of structural biology. It is the most extensive and detailed
structural biology textbook I have ever seen, yet quite easy to read and to understand.
It is a well-known fact that for biological systems, no matter how diversified and complex as
they appear, their underlying mechanisms can only be understood at the atomic structure levels.
They all use the same sets of atoms that follow the same chemical and physical principles to
build various biological systems (organisms). This ‘atomicity’ puts an absolute scale for biology
and makes ‘structural biology’ a fundamental MUST for all biology disciplines, pretty much in
the same way that every field of modern biology requires biochemistry and molecular biology
knowledge.
The following four chapters, namely, Chap. 9 ‘Genome structures, DNA replication and
recombination’; Chap. 10 ‘Transcription’; Chap. 11 ‘Protein synthesis – translation’ and Chap.
12 ‘Protein folding and degradation’, can be collectively themed as the structural mechanisms
of the ‘central dogma’. The ‘central dogma’ is the greatest achievements of molecular biology
after the discovery of DNA double helix since 1953. This dogma governs all cellular life forms
found on earth, although not all details of the ‘central dogma’ are understood so far. The major
processes and participating molecules have been discovered. Many of these form large nucleic
acid–protein complexes such as replisomes, nucleosomes, ribosomes, spliceosomes, various
mediators, polymerase and helicase complexes, recombinases and telomerase complexes, DNA
repair complexes, transcription initiation complexes, etc. Most of them have representative 3D
structure models available, thanks to the rapid development of cryo-EM techniques and which
have been awarded Nobel prize in Chemistry in 2017. Indeed, the textbook has incorporated
very recent progress in these fields.
The rest of the book chapters, Chap. 13 ‘Transmembrane transport’; Chap. 14 ‘Signal
transduction’; Chap. 15 ‘Cell motility and transport’; Chap. 16 ‘Structural aspects of cell–cell
interaction’; Chap. 17 ‘The immune system’ and Chap. 18 ‘Virus structure and function’, have
addressed and summarized structural aspects on various branches of biology with varied
details. Membrane biology and signal transduction are no doubt among the fastest developing
fields in the recent years. They have been quite adequately covered in this textbook, however, the
rest of the chapters seem to need more pages particularly for the structural biology of immune
systems. Nevertheless, these later chapters have all been elegantly written and revised in this
second edition of the textbook.
Structural biology is narrowly defined as the ‘atomic structures of living things’. Any tech-
nique can become a structural biology ‘sharp weapon’ only when it can routinely reach a
resolution to observe and to be able to build atomic structure models. This has been shown
very clearly in the recent development of Cryo-EM, which is the latest ‘sharp weapon’, partic-
ularly for big molecular complexes. Another ‘sharp weapon’ can be computational structural
biology, including bioinformatics tools, which have been included in the last chapter, Chap. 19
‘Bioinformatics tools in structural biology’, not as Appendices as in the last edition. There could
also be included molecular dynamics simulation studies, which have not been mentioned much
in this textbook.
Overall, there are many, much improved/enhanced features in this second edition textbook.
I appreciate in particular the re-arranged, and many times re-drawn figures throughout the new
edition of the textbook. These new figures are lovely with much better contrast and colouration,
with particular consideration for colour-blindness.
 CRYSTALLOGRAPHY REVIEWS 211

Since 2009, the ‘Textbook of structural biology’ has been translated into several major lan-
guages including Chinese, Japanese and Russian. In China alone, more than 1000 copies have
been sold each year for the last 5–6 years. I believe that the second edition textbook will reach
the same or even more sales.

Reference
[1] Helliwell JR. Book review of the first edition of ‘Textbook of structural biology, by Anders Liljas, Lars Liljas,
Jure Piskur, Göran Lindblom, Poul Nissen and Morten Kjeldgaard’. Crystallogr Rev 2009; 15(4):295–297.

Xiao-Dong Su
State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging
Center (BIOPIC), School of Life Sciences, Peking University, Beijing, People’s Republic of China
xdsu@pku.edu.cn
© 2018 Xiao-Dong Su
https://doi.org/10.1080/0889311X.2018.1430142

Nucleic acid crystallography: methods and protocols, edited by Eric Ennifar,

Methods in molecular biology, New York, Springer Science + Business Media, 2016,
Volume 1320, 351 pp., e167,61 (hardback)/e128,16 (paperback)/e103,52 (ebook),
ISBN: 978-1-4939-2763-0

In contrast to proteins, the anionic surface area and the nature of base pairing in nucleic acids
create predictable secondary structure, although they can adopt intricate three-dimensional
architectures. As for their protein counterparts, X-ray crystallography has proved an ideal tool
for probing nucleic acid structure and in the last 20 years or so, advances in DNA and RNA sam-
ple preparation, crystallization techniques and increased access to synchrotron radiation have
boosted nucleic acid crystallography. However, nucleic acid crystallography presents technical
and practical challenges that often need to be addressed differently from protein crystallog-
raphy. Nucleic Acid Crystallography: Methods and Protocols represents an indispensable guide
for nucleic acid, and particularly for RNA, crystallography, introducing cutting-edge methods
while, at the same time, providing step-by-step protocols to achieve reproducible results.
Following an excellent Introduction by Eric Westhoff which highlights the perspectives
and pitfalls in nucleic acid crystallography with a particular emphasis to the importance of
implementing validation criteria before the deposition of structural models meant to be used
by worldwide researchers, the book is organized into three major parts, each addressing the
main challenges in nucleic acid crystallography: preparation of high-quality RNA samples at
large-scale and well-diffracting crystals (Part II); efficient data collection and structure deter-
mination (Part III) and biological relevance of the structure models (Part IV). Each individual
chapter comprises an introduction to contextualize the potential applications, a comprehensive
description of the protocols or methods and notes and advice from the authors. There is very
little redundancy between chapters and the accompanying illustrations and flowcharts are very
insightful for less experienced readers.
Part II of the book contains eight chapters dedicated to the production and crystallisation of
nucleic acids, both major bottlenecks in the structural biology of nucleic acids. Chapter 2 writ-
ten by Nikita Vasilyev and Alexandre Serganov focuses on the preparation of short RNAs with
different numbers of phosphates on the 5 terminus and elaborates strategies to reduce aberrant