DNA topology

104

Protein Biotechnology

DNA Topology

E d i t e d by F F r a n k s . p p 592. T h e H u m a n a Press, N J, U S A . 1993. $89.50 ISBN 0-89603-230-2

by A D B a t e s a n d A Maxwell. pp 114. I R L Press at O x f o r d U n i v e r s i t y Press, O x f o r d . 1993. £8.95 ISBN ()-19-963349-5 (pbk)

Proteins play central roles in all life processes. In recent years we have seen tremendous progress in understanding protein structure and function. This book provides a comprehensive introduction to protein isolation, characterization and stabilization. Although there is an ever growing literature available on proteins, this book emphasizes the distinction between physiological and technological function and performance and between results obtained from in vivo and in vitro analysis and characterization. This book is a compilation of fifteen chapters or better, sections, contributed by six authors (including editor who has contributed seven sections). These are entitled, Proteins: description and classification, In vitro characterization: economics and technology, Analytical chromatography of amino acids, peptides, and proteins, Internal structure and organization: relationship to function, Solution properties of proteins, Posttranslational processing of proteins, Protein fragmentation, Peptide sequence determination, Electrophoretic techniques of analysis and isolation, Production and application of polyclonal and monoclonal antibodies, Conformational stability of proteins, Protein hydration, Recombinant protein technology, Storage stabilization of proteins, and Process purification. The overall look of the book is impressive and a good continuity has been maintained from one section to another. There are a few errors/additions outlined below. Section 1, Table 2, in the list of metalloproteins, ones requiring nickel could be included. As of this writing, four nickel-containing enzymes have been detected and isolated (urease, hydrogenases, methyl coenzyme M reductase, CO dehydrogenase). Table 6, shows the mol wt of tryptophan synthetase (E coli) as 117 000. Tryptophan synthase (E coli) is an o~2132complex with tool wt 143 430 that can be dissociated reveribly into two monomeric ~ subunits, mol wt 28 727 (Nichols and Yanofsky, 1979, PNAS 76, 5244) and one dimeric [32 subunit, tool wt 85 976 (Crawford et al, 1980, JMB 12, 489). In section 4, terms like 'Torsional angle map' and "hard-sphere steric maps' have been used for a more popular "Ramachandran Plots'. In the same section, a small discussion finds a place on multienzyme complexes with only the example of yeast pyruvate dehydrogenase. More recently, the 3-D structure of the tryptophan synthase multienzyme complex from S typhimurium revealed a 25 A-long hydrophobic tunnel (Hyde et al, 1988, JBC 263, 785) where data support of substrate channelling seem unequivocal (Kayastha, 1992, J Theor Biol 158, 133). Also, enzyme--enzyme interactions among soluble enzymes have gained considerable popularity, where metabolite channelling is stated to be controversial. Section 13 on Recombinant Protein Technology is very thin. One of the greatest technological advances has been the introduction of protein engineering, which has a major impact on the study of protein structure, stability, and function. Discussion on such an important area has been limited to a few paragraphs. Labelling in some of the figures has been reduced to the extent that it has lost clarity. In conclusion, for those who have time to read rather than just to extract some information, this book is extremely well written and exceptionally readable. Leaving aside certain practical details of techniques on protein purification, this book may outdate some of the earlier recommended books for teaching, for example, Protein Purification by Scopes (Springer, 1982). This book is recommended for undergraduate to graduate students and anyone who is interested in proteins. Arvind M Kayastha

BIOCHEMICAL EDUCATION 22(2) 1994

This book is small in size but great in explaining simple topological terms like linking number, twist, writhe, supercoiled structures, knots, catenanes and topoisomerases. DNA Topology includes references, index, list of abbreviations and a glossary. It is a member of the qn Focus" series written concisely and clearly. It is recommended for everyone interested in DNA structure and function. The strategy of the book is to progress from the primary structure through the secondary structure of D N A to tertiary structure, including topological problems providing new insight into the biological function of DNA topology. The description of an alternative supercoiling is especially interesting. Knots and catenanes which seem to be esoteric structures involve complex mathematical concepts. These structures exist in nature and their generation by recombination enzymes yielded important mechanistic information concerning the enzymes themselves. An essential class of interconverting enzymes is also dealt with, these are the DNA topoisomerases which catalyze the conversion of tertiary structures. Beside the biological function, the potential of topoisomerases as drug target is also discussed. Biological consequences of DNA topology involve compaction, genome organization both in prokaryotes and eukaryotes. A new, so-called twin supercoiled domain model of topoisomerases has been introduced by the authors, which might be involved in transcription. Authors also review the influence of D N A topology in gene expression, DNA replication and examples are given for recombination reactions highlighting the aspects relevant to DNA topology. There is one point I would disagree with: the authors believe that the chromosome organization in prokaryotic cell is less clearly defined than that of the eukaryotic genome. I think that it is the process of chromosome condensation which is not understood. There is a wide gap between the nucleosomal arrangement and metaphase chromosomes of eukaryotic cells with several steps of condensation which are completely unknown so far. A new problem arose after reading DNA Topology, which is by no means the responsibility of the authors. In discussing the structural organization of DNA it used to be convenient to refer to different structural levels such as basic structures: primary, secondary, tertiary structure or topology and higher structural levels (from nucleosomal arrangement to chromosomal organization see Biochem Educ 14, 50-59, 1986). As the authors of DNA Topology define it: their principal purpose is to focus on higher order of structural features of DNA, namely supercoiling, knotting and catenation. How then do they define chromosomal organization? In this book it seems to be genome organization. Sanger's book synonymous with Principles of Nucleic Acid Structure (1984) mentions several forms of higher organization of D N A including simple aggregation, bead-like structures coiling up into toroids, nucleosomes, the hypothetical super-superhelix (solenoid), lamellar microcrystals and the organization of chromatin in chromosomes. There are other interpretations which also indicate that contrary to the unambiguous structural levels of protein organization (primary, secondary, tertiary, quaternary structures) the structural levels of DNA (beyond the secondary structure) are not clearly defined. In conclusion it would be worthwhile to come to an agreement and to unify the terms of different structural levels of DNA. G Banfalvi