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Trends in Biochemical Sciences

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A bauhaus for biologists

Paul Harrison and Mark Gerstein
Trends in Biochemical Sciences 2001, 26:204-205

Dept of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06250, USA

Text only, PDF
Publications by
Mark Gerstein | Paul Harrison

An Introduction to Protein Architecture: The Structural Biology of Proteins

edited by Arthur M. Lesk

Oxford UniversityPress, 2000. $45.00

(347 pages)

ISBN 0 19 850474 8

Architectural styles of buildings come and go, whereas the architecture of modern-day proteins has been with us for eons. In An Introduction to Protein Architecture, Arthur Lesk presents an insightful survey of this most fundamental topic. It is particularly timely for a new text on this subject as the current availability of extensive web-based information resources for protein sequences and structures modifies the traditional role for the textbook.

Arthur Lesk is one of the pioneers of the analysis of protein structure and its evolution. He was also one of the original developers of computerized molecular graphics for proteins in the early 1980s. So, needless to say, this book is brilliantly illustrated with an extensive array of large, clear stereo diagrams for the structures or motifs that are described in the text. Moreover, we believe that the use of stereo figures is essential for truly visualizing the complex 3D geometry of proteins. Indeed, this is a substantially graphical textbook (about half of the total page count, discounting the structural atlas appendix, consists of figures). Presented in an uncomplicated, easy-to-read style and logically structured, the text is seldom wordy. There are brief sections describing the basic building blocks of protein structure, followed by discussions about how different proteins can be classified, with emphasis on web databases. The general discussions of protein evolution and protein motions are particularly good. Detailed studies, which stand well on their own, of immune system proteins, serine proteases and NAD-binding domains in dehydrogenases, are presented. In particular, an up-to-date introduction to structural immunology provides much information on the conformations of antibodies (with a discussion of canonical loop structures), major histocompatibility complex proteins and T-cell receptors, as well as the conformations of their interacting complexes. There is some reference at appropriate points to methods of protein structure prediction (although there could be more about topics such as fold recognition or secondary structure prediction). A nice summary is provided of the biannual CASP (Critical Assessment of Techniques for Protein Structure Prediction) competition for assessment of prediction methods, and there is also a strong section on homology modeling.

This textbook tackles well the problem of interfacing with internet information resources. Extensive reference is made to web-based catalogs of protein structure and search tools for protein structure and sequence. The author has designed a special sort of exercise called the 'weblem'. For this, the student is asked to use web tools to solve simple tasks that aid our understanding of the links between protein structure, sequence analysis and protein structure prediction.

There are (inevitably) some omissions in the subject matter in this book. In particular, some detailed discussion of protein–nucleic acid binding and the structural motifs involved would be welcome. Also, a section on the structure of membrane proteins would be desirable (although there is a very good opening chapter specifically describing the photosynthetic reaction center). Finally, although genomics and structural genomics are certainly mentioned, more emphasis could have been devoted to how 'global' genomic surveys of large numbers of structures are changing our view of what is typical and atypical in protein architecture.

These points aside, this text, written by a leading expert in the field, is to be highly recommended for anyone wishing to learn about protein architecture in the context of the current structure of bioinformatics information resources.


© 2001 Elsevier Science Ltd. All rights reserved.

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