Biochemistry and Molecular Biology Education 29 (2001) 33}38

Book reviews

Protein structure prediction: Methods and protocols Advances in the "eld of structure prediction are as-
D.M. Webster (Ed.); Vol. 143, Methods in Molecular sessed by an ongoing biannual competition of &blind'
Biology J.M. Walker, Series Editor); Humana Press, prediction, the Critical Assessment of techniques for pro-
Totowa, NJ, 2000, ISBN 0-089603-637-5 tein Structure Prediction (CASP; http://predictioncen-
ter.llnl.gov/). Researchers from around the world can
Experimental techniques for the determination of access a list of sequences whose structures are soon to be
three-dimensional (3D) macromolecular structures can determined; then predicted structures are compared with
often involve months or even years of e!ort. As a result, the experimental results by a panel of experts. The online
the number of 3D structures available in the central results from CASP provide the most up-to-date assess-
repository for this information: the Protein Data Bank ment of the state of the art with regard to prediction
(http://www.rcsb.org/pdb/), is a tiny fraction of the num- techniques.
ber of sequences known. With the huge amount of se- Two main aspects detract from the overall quality of
quence data that constantly #ows out of various genomic the book. The "rst is that the inevitable delay in bringing
sequencing projects, this gap will continue to widen. such a book to publication means that many of the
The ultimate goal of structure prediction is to be able authors refer to CASP2 (from 1996), whereas CASP4
to feed a sequence into a computer and immediately took place in December 2000, also a number of URLs
generate a 3D structure, however, understanding the way cited are no longer accessible. The former point is less
that proteins fold remains one of the major challenges in serious since much of the progress made in the interven-
biology. Attacking the structure prediction problem from ing time is mainly due to improvements in the underlying
a number of angles simultaneously is leading to many computation, whereas the software interface to a novel
advances, and this book provides a timely review of the user may remain largely unchanged. The other irritation
current methodologies. The book is a collection of 18 relates to the editing. There are a number of small typo-
review articles, many written by distinguished experts in graphical errors, for example in URLs, and transposed
their "eld, providing an overview of the major aspects of labels of graphs and tables. Despite these, it is certainly
protein structure prediction. a useful reference to address for anyone thinking of
About half of the articles deal with speci"c software dipping their toes into this exciting "eld.
packages, many of which are free to academic users, Kurt Giles
where the author of the article is often the author of the Department of Experimental Psychology,
software discussed. This has the disadvantage of lacking a Oxford University,
critical comparison of techniques, but is more than made Oxford OX13UD, UK
up by the many useful hints and tips authors give on how
PII: S 1 4 7 0 - 8 1 7 5 ( 0 0 ) 0 0 0 6 3 - 1
to use their software. These comments add to the more
informal nature of the articles compared with standard
review papers, making them accessible to the novice. Fundamentals of enzymology (Third Edition)
Currently one of the most useful techniques in struc- Nicolas C. Price, Lewis Stevens; Oxford University Press,
ture prediction, is when the sequence of unknown struc- Oxford, 1999
ture is similar to one with a known structure. This is not
as unlikely as may be expected, since the number of The book Fundamentals of Enzymology, true to its
possible ways that proteins fold appears to be relatively title, is an overview of enzymology that can be used in
small (probably less than 2000). Unfortunately, detecting a survey course on the subject. The paperback book is
such similarities is a major obstacle. Predicting a struc- 449 pages in length, and the book includes in addition
ture in this way involves sequence and structure analysis, a 19-page appendix listing the common and Enzyme
as well as the practicalities of modelling a sequence onto Commission names and numbers of the enzymes men-
a structural template. All of these are covered in detail by tioned in the text, as well as an 8-page index. The book is
the book. However, it does not limit itself to these, but organized into a brief introductory chapter followed by
also covers less well-established topics as diverse as mod- chapters on puri"cation of enzymes, structure of en-
elling transmembrane helices, ab initio techniques, and zymes, introduction to enzyme kinetics, mechanism of
protein docking. enzyme action, control of enzyme activity, enzymes in
34 Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 33}38

organized systems, enzymes in the cell, enzyme turnover, Chapter 5 on mechanism of enzyme action is the lar-
clinical aspects of enzymology, and enzyme technology. gest subject in the book and has been skillfully "tted into
Because of the enormous scope of the book and its intent a limited space, thanks to the extensive structural cover-
as an introduction, the chapters are written as overviews age in Chapter 3. Theory is presented early, followed by
of principle topics in enzymology, rather than as in-depth a sampling of the more general methods that have been
perspectives. applied to studies of reaction mechanisms. This chapter
The introduction includes brief expositions of the sig- includes a few color graphics in representing overall
ni"cance of enzymes in terms of their biological func- enzyme structures. The authors have chosen, wisely, to
tions, speci"cities stereospeci"cities, and regulation. exemplify mechanistic analysis through an exposition of
Nomenclature and the functional basis for the formal examples of the elucidation of the mechanisms of action
classi"cation of enzymes are presented in outline. In this of speci"c enzymes. These include chymotrypsin, triose
connection, a few enzymes that will be used as speci"c phosphate isomerase, dehydroquinase, lactate dehydro-
examples later in the book are introduced by name. The genase, and DNA methyltransferase.
signi"cance of divalent metal ions and a few coenzymes The control of enzyme activity is discussed in consider-
that are central to the functions of enzymes that will be able detail in Chapter 6. Regulation by covalent modi"-
discussed in later chapters are mentioned brie#y. In keep- cation, as in phosphorylation}dephosphorylation, is
ing with the limitations of the coverage, "ve of the 20}30 presented "rst. The principal theories of allosteric regula-
known organic coenzymes are mentioned. Organometal- tion are presented in detail, including the concerted
lic coenzymes and cofactors are not included. transition and the ligand-induced conformational
The chapter on puri"cation is thorough and up-to- transition models. Treatment of data and graphical rep-
date. The role of enzyme assays in assessing puri"cation resentation of results allow the two main models to be
results is introduced early within the section on objec- exempli"ed and distinguished. A major part of the chap-
tives without special emphasis. A section could have been ter is devoted to case studies of the control of metabolic
devoted to this subject. The chapter includes sections on pathways, with glycolysis and glycogen synthesis serving
the extraction of enzymes from cells, separation methods, as concrete examples. Principles such as ampli"cation of
and the assessment of homogeneity by physical tech- signals are emphasized.
niques. Modern separation methods such as covalent Chapter 7 introduces organized enzyme systems as
chromatography and His-tag chromatography are in- multienzyme complexes. Speci"c examples are selected
cluded, as well as modern methods of analysis for homo- for detailed description. These include some familiar
geneity such as mass spectrometry. A very welcome cases such as the pyruvate dehydrogenase complexes,
feature is the inclusion of several speci"c examples of and interesting but less familiar cases such as the glycine
enzyme puri"cation in su$cient detail to convey the decarboxylase complex, The description of the structure
#avor of the puri"cation process. and tunnel function of tryptophan synthase is very wel-
The chapter on structure includes methods for deter- come. The book went to press before the tunneling func-
mining molecular weight, and amino acid composition is tion of carbamoyl phosphate (CAP) synthetase complex
treated in signi"cant detail. Primary, secondary, tertiary was known, so this aspect of the subject is treated as an
and quaternary structures are de"ned and methods of example of substrate channeling without mechanistic ex-
determination are discussed. Structures of amino acids position. However, the complex of the CAP synthetase
and the peptide bond are presented in detail. Three- and dihydroorotase is presented as a functional unit in
dimensional structure determinations by X-ray cry- pyrimidine biosynthesis. Other welcome examples pre-
stallography are discussed in signi"cant detail. The sented in signi"cant detail are the fatty acid synthase
structures of a number of enzymes are presented in vari- complex and the multidomain, multienzyme proteins in
ous ways, including chain folds, active site structures, the biosynthesis of aromatic amino acids. This is a rap-
space-"lled models, multisubunit models, domain struc- idly expanding "eld that includes new examples that
tures and so forth. An extensive section on chain folding could not be included in the chapter, but many of the
includes a delineation of the various forces that deter- principles of multienzyme systems are presented here.
mine three-dimensional structures. This chapter is by far Chapter 8 on enzymes in the cell explains how enzymes
the most complete and longest chapter in the book. within cells are generally localized in subcellular or-
Chapter 4 introduces enzyme kinetics with a primer on ganelles, membranes, or the cytosol. Intracellular com-
measuring rates and the systematic analysis of steady- partmentation of enzymes and of metabolic pathways as
state kinetic data. Conventional sections on Michaelis} well as the organization of membrane-bound enzymes
Menten kinetics, inhibition kinetics, analysis of pH ef- forms the subject matter for this chapter. This is a wel-
fects, and impact of temperature follow. Two-substrate come exposition of the actual state and function of
enzyme kinetics is given fairly thorough coverage, and enzymes in cells, especially eukaryotic cells. Chapter 9 on
three- and four-substrate kinetics are mentioned without enzyme turnover extends Chapter 8 to explain how en-
details. The subject of presteady-state kinetics is introduced. zymes produced in cells are degraded to regulate their
 Book reviews / Biochemistry and Molecular Biology Education 29 (2001) 33}38 35

activities and functions. Degradation mechanisms in- or RNA, a brief chapter on DNA cloning, a chapter on
cluding proteasome function and ubiquitin signaling are DNA sequencing, and a chapter on PCR. The writing is
delineated. clear and the protocols are easy to follow throughout.
The book is rounded out with very brief chapters on The indexing is good and all the chapters are richly
clinical enzymology and enzyme technology. A few of the referenced. The presentation of visual information is good
most common clinical assays for heart and liver diseases with one exception: all the photographs of electrophoresis
are described in Chapter 10, together with detection of gels are upside-down (with the origins unmarked); this is
de"ciencies of enzyme activities. Enzyme therapy is intro- going to confuse a lot of novices! I found no glaring
duced. In Chapter 11, enzyme technology is introduced. technical errors and only a few typographical errors.
Two main subjects are emphasized; the use of microor- I am impressed with Surzycki's attempts to alert stu-
ganisms in industrial processes and the use of immobi- dents to potential pitfalls throughout the manual. For
lized enzymes in industry. example, I appreciate (and so will students!) his dis-
The book is very well written and full of information. It cussion on handling very small nucleic acid pellets. Pro-
can serve as a useful text for a survey course in enzymol- fessor Surscyki reviews a variety of commercially
ogy. Students can acquire the well-known concepts for available techniques for the puri"cation of DNA and
most aspects of enzymology. Less attention is paid in this RNA, and includes some protocols that supplement
book to forward aspects of enzymology. This may be vendor's instructions. The chapters on DNA and RNA
well, for enzymology is a "eld that has resisted projection transfer to immobile membranes are excellent * all the
into the future. The book should work best for students key pitfalls are addressed. However, there are a couple of
in allied "elds who wish to be educated in the essential important technical omissions. In the discussion of plas-
aspects of enzymology. mid DNA isolation, Surzycki does not warn the reader to
Perry A. Frey be sure to remove ALL of the supernatant after centrifu-
University of Wisconsin, gation of bacteria out of the culture medium (this is
especially important with Terri"c Broth). Failure to do
Madison, WI, 53706 USA
this accounts for more problems with restriction diges-
PII: S 1 4 7 0 - 8 1 7 5 ( 0 0 ) 0 0 0 5 3 - 9 tion than any other step, save the careful removal of the
supernatant away from cold, high-salt/SDS precipitate.
Also the reader is not warned adequately to carefully mix
Basic techniques in molecular biology the NaOH solution or the neutral high-salt solution to
Stefan Surzycki; Springer, Berlin, 2000, 434 pages with avoid shearing genomic DNA (a signi"cant problem with
59 "gures, list price $79.95, ISBN 3-540-66678-8 large-scale plasmid isolations). An additional help to
novices here would be to suggest that the supernatant of
First things "rst, this is an excellent technical manual the high-salt/SDS precipitate be "ltered to avoid carrying
but rather limited in scope. Surzycki manages to mix along any #oating or dislodged precipitates. In the dis-
a nice blend of theory, detailed methods, and trouble- cussion of colony and plaque hybridization, Surzycki
shooting into a single 434 page, spiral-bound volume. avoids the use of India ink to mark plates and "lters. This
Advanced undergraduate students and their instructors is "ne for veterans but fraught with peril for novices.
are his target audience, and he does well reaching both. The potential buyer should also be warned that
Basic Techniques in Molecular Biology is not a collection the DNA cloning chapter is limited in scope. The chapter
of `experiments;a instead, it is a technical manual for is an excellent resource for DNA subcloning but the
novices and instructors covering the isolation and analy- nuances of cloning genomic DNA are ignored. On the
sis of nucleic acids, DNA cloning, DNA sequencing and other hand, the discussion of the stoichiometry of liga-
PCR. The "rst chapter, may be the best, gives a broad tion is the best that I have read in a long time. Unfortu-
introduction to the isolation and puri"cation of nucleic nately, complementary DNA cloning of reverse-
acids with a focus on DNA. This is a comprehensive transcribed RNA and PCR cloning are also ignored.
chapter in which Surzycki takes the reader through the Given that this is supposed to be an introductory text,
rationale for using a variety of reagents to break open I suppose this omission is acceptable.
cells, remove RNA, and achieve maximal deproteiniz- To my mind and bias, the weakest chapter is the PCR
ation of the lysate. He also gives a thorough discussion of chapter. The general guidelines for PCR are discussed
the concentration, storage, and assessment of DNA pu- well; however, the chapter would bene"t greatly with
rity. Even experienced researchers will "nd new know- a more thorough discussion of methods to enhance PCR
ledge here. The next three chapters focus on the recovery speci"city and yield. Surzycki is quick to reference com-
of genomic DNA from animal cells, plant cells, and mercial proprietary products in earlier chapters but not
bacteria. The "fth chapter covers the isolation of plasmid here (e.g., `hot starta products). In addition, heated-lid
DNA. There follows two chapters on RNA isolation, four thermal cyclers are ignored as an excellent device to get
chapters on "lter hybridization for the analysis of DNA high reproducibility at a reasonable price. I know of very