- Email: [email protected]
Macromolecule crystallization
TTEC June 2000
4/5/00
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Page 275
BOOK REVIEW
Macromolecule crystallization Crystallization of Nucleic Acids and Proteins: A Practical Approach (2nd edn), edited by A. Ducruix and R. Giegé, 1999, Oxford University Press. UK£29.95 pbk (xiii + 435 pages) ISBN 0 199 63678 8 The ever-increasing flood of genomic data has, in one important respect, improved the quality of life for structural biologists. We can now find targets for study in biologically important areas with relative ease. However, obtaining useful crystals of proteins and nucleic acids still remains a large barrier to highthroughput, X-ray crystallography. In the second edition of Crystallization of Nucleic Acids and Proteins: A Practical Approach, the authors give examples and strategies of ways to improve the chances of obtaining RNA, DNA or protein crystals that diffract to high resolution. Taken as a whole, the chapters, which cover topics ranging from cloning and sample purification to crystal handling and the physics of crystallization, demonstrate that the crystallization of biological macromolecules is moving from a type of alchemy to a true science with a theoretical framework on which to build. Three chapters in particular make this volume worth having in the laboratory. Chapter 3 outlines the genetic engineering of crystallization targets and concludes with protocols for preparing selenomethionyl protein crystals for multiwavelength anomalous dispersion (MAD) phasing. MAD phasing of structure factors is likely to become the most widely used method for solving new macromolecule structures. Thus, the authors’ coverage of the many ways of incorporating selenomethionine into proteins, and how to handle these proteins, is essential reading for those new to this approach. Chapter 4 illustrates the effective use of statistical tools and experimental designs for optimizing crystal growth. In particular, ideas of what not to TIBTECH JUNE 2000 (Vol. 18)
expect from various factorial and response surface designs are given. For example, different designs are appropriate for finding the first crystals and for optimizing crystallization. Finally, different light-scattering techniques are outlined in Chapter 11, covering the physics of crystal nucleation
and growth. This chapter in particular shows a promising direction for systematically improving crystallogenesis. The manipulation of crystals is covered in a similar way to the previous edition, but some new methods and results are included. For example, the chapter on crystallization in gels reviews recent work describing what occurs in the gel over time (Chapter 6). Chapter 12, which covers two-dimensional crystallization on planar lipid films, is new to this edition, although the widespread use of this approach will require more-reproducible results. In the case of membrane proteins, discussed in Chapter 9,
it seems that the technology for crystallizing these difficult samples is much the same as it was in the early 1990s. For example, the table listing crystal forms of membrane proteins has only doubled in size since the first edition, and shows little variation in the conditions used. There is still plenty to be done to make membrane-protein crystallization a generally promising approach for structural biologists. The technologies for nucleicacid crystallization have developed substantially in the past few years, but the chapter dealing with these samples (Chapter 8) is not up-to-date and sometimes lacks attention to detail. The authors do not mention the heavy-atom derivatives used to solve the structures of transfer RNA, hammerhead ribozymes or the group I intron P4–P6 domain. From these structures, the lanthanides and osmium (III) hexammines are likely to be a good place to start for solving larger RNA structures. Recent work taking advantage of proteins to improve RNA crystal diffraction quality should have been included in this book1. All of the chapters provide protocols and strategy sketches that crystallographers will find useful in the wet laboratory and that should improve the productivity of their experiments. However, this book must be complemented with other works2 and recent literature in order to adequately describe the state-ofthe-art in crystallizing nucleic acids and proteins.
References 1 Ferré-D’Amare, A.R. et al. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567–574 2 McPherson, A. (1999) Crystallization of Biological Macromolecules, Cold Spring Harbor Laboratory Press
Jamie Cate Biology Faculty, Massachusetts Institute of Technology, Whitehead Institute, Cambridge, MA 02142, USA. (E-mail: [email protected])
0167-7799/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.
275
4/5/00
11:18 am
Page 275
BOOK REVIEW
Macromolecule crystallization Crystallization of Nucleic Acids and Proteins: A Practical Approach (2nd edn), edited by A. Ducruix and R. Giegé, 1999, Oxford University Press. UK£29.95 pbk (xiii + 435 pages) ISBN 0 199 63678 8 The ever-increasing flood of genomic data has, in one important respect, improved the quality of life for structural biologists. We can now find targets for study in biologically important areas with relative ease. However, obtaining useful crystals of proteins and nucleic acids still remains a large barrier to highthroughput, X-ray crystallography. In the second edition of Crystallization of Nucleic Acids and Proteins: A Practical Approach, the authors give examples and strategies of ways to improve the chances of obtaining RNA, DNA or protein crystals that diffract to high resolution. Taken as a whole, the chapters, which cover topics ranging from cloning and sample purification to crystal handling and the physics of crystallization, demonstrate that the crystallization of biological macromolecules is moving from a type of alchemy to a true science with a theoretical framework on which to build. Three chapters in particular make this volume worth having in the laboratory. Chapter 3 outlines the genetic engineering of crystallization targets and concludes with protocols for preparing selenomethionyl protein crystals for multiwavelength anomalous dispersion (MAD) phasing. MAD phasing of structure factors is likely to become the most widely used method for solving new macromolecule structures. Thus, the authors’ coverage of the many ways of incorporating selenomethionine into proteins, and how to handle these proteins, is essential reading for those new to this approach. Chapter 4 illustrates the effective use of statistical tools and experimental designs for optimizing crystal growth. In particular, ideas of what not to TIBTECH JUNE 2000 (Vol. 18)
expect from various factorial and response surface designs are given. For example, different designs are appropriate for finding the first crystals and for optimizing crystallization. Finally, different light-scattering techniques are outlined in Chapter 11, covering the physics of crystal nucleation
and growth. This chapter in particular shows a promising direction for systematically improving crystallogenesis. The manipulation of crystals is covered in a similar way to the previous edition, but some new methods and results are included. For example, the chapter on crystallization in gels reviews recent work describing what occurs in the gel over time (Chapter 6). Chapter 12, which covers two-dimensional crystallization on planar lipid films, is new to this edition, although the widespread use of this approach will require more-reproducible results. In the case of membrane proteins, discussed in Chapter 9,
it seems that the technology for crystallizing these difficult samples is much the same as it was in the early 1990s. For example, the table listing crystal forms of membrane proteins has only doubled in size since the first edition, and shows little variation in the conditions used. There is still plenty to be done to make membrane-protein crystallization a generally promising approach for structural biologists. The technologies for nucleicacid crystallization have developed substantially in the past few years, but the chapter dealing with these samples (Chapter 8) is not up-to-date and sometimes lacks attention to detail. The authors do not mention the heavy-atom derivatives used to solve the structures of transfer RNA, hammerhead ribozymes or the group I intron P4–P6 domain. From these structures, the lanthanides and osmium (III) hexammines are likely to be a good place to start for solving larger RNA structures. Recent work taking advantage of proteins to improve RNA crystal diffraction quality should have been included in this book1. All of the chapters provide protocols and strategy sketches that crystallographers will find useful in the wet laboratory and that should improve the productivity of their experiments. However, this book must be complemented with other works2 and recent literature in order to adequately describe the state-ofthe-art in crystallizing nucleic acids and proteins.
References 1 Ferré-D’Amare, A.R. et al. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567–574 2 McPherson, A. (1999) Crystallization of Biological Macromolecules, Cold Spring Harbor Laboratory Press
Jamie Cate Biology Faculty, Massachusetts Institute of Technology, Whitehead Institute, Cambridge, MA 02142, USA. (E-mail: [email protected])
0167-7799/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.
275