Acta Crystallographica Section D

Biological Crystallography

Volume 63, Part 1 (January 2007)


Crystallography of complexes

Proceedings of the CCP4 study weekend

[Buy print version] A printed copy of this issue is available for purchase

[Preface]
[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Nuclear receptor 1 with bound natural ligand (p. 72).

research papers


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Acta Cryst. (2007). D63, 1-8  [ doi:10.1107/S090744490603575X ]

Macromolecular recognition in the Protein Data Bank

J. Janin, F. Rodier, P. Chakrabarti and R. P. Bahadur

Synopsis: X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein-protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts.

Online 13 December 2006


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Acta Cryst. (2007). D63, 9-16  [ doi:10.1107/S0907444906047330 ]

From structure of the complex to understanding of the biology

M. G. Rossmann, F. Arisaka, A. J. Battisti, V. D. Bowman, P. R. Chipman, A. Fokine, S. Hafenstein, S. Kanamaru, V. A. Kostyuchenko, V. V. Mesyanzhinov, M. M. Shneider, M. C. Morais, P. G. Leiman, L. M. Palermo, C. R. Parrish and C. Xiao

Synopsis: The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques.

Online 13 December 2006


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Acta Cryst. (2007). D63, 17-25  [ doi:10.1107/S0907444906047044 ]

So how do you know you have a macromolecular complex?

T. R. Dafforn

Synopsis: Structures of protein complexes offer some of the most interesting insights into biological processes. In this article, the methods required to show that the complex observed is the physiological one are investigated.

Online 13 December 2006


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Acta Cryst. (2007). D63, 26-31  [ doi:10.1107/S0907444906046373 ]

Measurement of the formation of complexes in tyrosine kinase-mediated signal transduction

J. E. Ladbury

Synopsis: The use of isothermal titration calorimetry (ITC) provides a full thermodynamic characterization of an interaction in one experiment. The determination of the affinity is an important value; however, the additional layer of information provided by the change in enthalpy and entropy can help in understanding the biology. This is demonstrated with respect to tyrosine kinase-mediated signal transduction.

Online 13 December 2006


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Acta Cryst. (2007). D63, 32-41  [ doi:10.1107/S0907444906045975 ]

Solving structures of protein complexes by molecular replacement with Phaser

A. J. McCoy

Synopsis: Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described.

Online 13 December 2006


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Acta Cryst. (2007). D63, 42-49  [ doi:10.1107/S0907444906041059 ]

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

O. Dror, K. Lasker, R. Nussinov and H. Wolfson

Synopsis: A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented.

Online 13 December 2006


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Acta Cryst. (2007). D63, 50-57  [ doi:10.1107/S0907444906046762 ]

Computational analyses of the surface properties of protein-protein interfaces

J. Gruber, A. Zawaira, R. Saunders, C. P. Barrett and M. E. M. Noble

Synopsis: This paper presents a survey of techniques that explore the surface properties of protein:protein interfaces so as to inform the prediction of probable sites of protein:protein interaction on newly determined protein structures.

Online 13 December 2006


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Acta Cryst. (2007). D63, 58-61  [ doi:10.1107/S090744490604604X ]

An introduction to stereochemical restraints

P. R. Evans

Synopsis: A brief summary of the types of restraint defined in refinement dictionaries.

Online 13 December 2006


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Acta Cryst. (2007). D63, 62-71  [ doi:10.1107/S0907444906051869 ]

The use of biophysical methods increases success in obtaining liganded crystal structures

C. Chung

Synopsis: This paper highlights some of the problems that can arise when attempting to obtain crystal structures of small molecule-protein complexes and how biophysical methods can be used to define and overcome these problems. Many of the techniques mentioned are also applicable to the study of protein-protein complexes and mode-of-action analysis.

Online 13 December 2006


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Acta Cryst. (2007). D63, 72-79  [ doi:10.1107/S0907444906047020 ]

Crystallization of protein-ligand complexes

A. M. Hassell, G. An, R. K. Bledsoe, J. M. Bynum, H. L. Carter, S.-J.J. Deng, R. T. Gampe, T. E. Grisard, K. P. Madauss, R. T. Nolte, W. J. Rocque, L. Wang, K. L. Weaver, S. P. Williams, G. B. Wisely, R. Xu and L. M. Shewchuk

Synopsis: Methods presented for growing protein-ligand complexes fall into the categories of co-expression of the protein with the ligands of interest, use of the ligands during protein purification, cocrystallization and soaking the ligands into existing crystals.

Online 13 December 2006


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Acta Cryst. (2007). D63, 80-93  [ doi:10.1107/S0907444906047287 ]

Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia

S. W. Cowan-Jacob, G. Fendrich, A. Floersheimer, P. Furet, J. Liebetanz, G. Rummel, P. Rheinberger, M. Centeleghe, D. Fabbro and P. W. Manley

Synopsis: A case study showing how the determination of multiple cocrystal structures of the protein tyrosine kinase c-Abl was used to support drug discovery, resulting in a compound effective in the treatment of chronic myelogenous leukaemia.

PDB references: 2hyy, 2hz0, 2hz4, 2hzn and 2hzi

Online 13 December 2006


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Acta Cryst. (2007). D63, 94-100  [ doi:10.1107/S0907444906022657 ]

Crystallographic refinement of ligand complexes

G. J. Kleywegt

Synopsis: Methods and resources for obtaining chemically plausible starting models and restraint sets for refinement of ligand complexes are described and some of the potential pitfalls are discussed.

Online 13 December 2006


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Acta Cryst. (2007). D63, 101-107  [ doi:10.1107/S0907444906046233 ]

Ligand identification using electron-density map correlations

T. C. Terwilliger, P. D. Adams, N. W. Moriarty and J. D. Cohn

Synopsis: An automated ligand-fitting procedure is applied to (Fo - Fc)exp(i[varphi]c) difference density for 200 commonly found ligands from macromolecular structures in the Protein Data Bank to identify ligands from density maps.

Online 13 December 2006


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Acta Cryst. (2007). D63, 108-117  [ doi:10.1107/S0907444906023389 ]

Assessment of automatic ligand building in ARP/wARP

G. X. Evrard, G. G. Langer, A. Perrakis and V. S. Lamzin

Synopsis: The performance of the ligand-building module of the ARP/wARP software suite is assessed through a large-scale test on known protein-ligand complexes. The results provide a detailed benchmark and guidelines for future improvements.

Online 13 December 2006


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