Page 108 - Macromolecular Crystallography

CHAPTER 7

Molecular replacement techniques

for high-throughput structure

determination

Marc Delarue

7.1 Introduction possible set of phases to initialize refinement and
reconstruction in the best possible conditions.
In the context of structural genomics projects, there
As more and more structures are deposited in the
are two main routes to consider for solving effi-
Protein Data Bank (PDB) (Berman et al., 2000), the
ciently and rapidly the three-dimensional (3D) struc-
chances of finding a (remote) homolog structure in
ture of the target gene products by crystallography.
the PDB have become higher and, therefore, molec-
The first is the Multiple-wavelength Anomalous
ular replacement techniques are increasingly useful.
Diffraction (MAD) technique (reviewed in Chapter 8
This is reflected, for instance, in the number of hits
of this volume), which necessitates growing SeMet-
one gets by doing a search for the keywords ‘molec-
substituted protein crystals. The second is molecular
ular replacement’ in one of the leading journals in
replacement (MR), which requires X-ray data for the
the protein crystallography community, for example
native protein as well as the structure of a related
homolog.
MR is an ensemble of techniques that aims to
placeandorientateanapproximatemolecularmodel
in the unit cell of the crystal being studied. This 450
will provide the starting phases needed to calcu- 400
late the initial electron density map from which the 350
protein model can be built, either manually by iter- 300
ative use of reconstruction with molecular graphics 250
packages (Jones et al., 1991) followed by refinement Number of articles 200
(Murshudov et al., 1997), or automatically if diffrac- 150
tion data up to 2.3 Ångstroms or better are available
100
(ARP/wARP (Perrakis et al., 2001), Solve/Resolve
50
(Terwilliger, 2003)).
In this article, we will not focus on recent devel- 0 1990 1992 1994 1996 1998 2000 2002 2004
opments in refinement techniques, which benefited Year
recently from better statistical treatments such as
Figure 7.1 Histogram of the number of articles in Acta
maximum likelihood targets for refinement (Adams
Crystallographica D containing ‘Molecular Replacement’ in the
et al., 1999), but rather will describe in detail some title or abstract, year by year. The score for 2004 is a projection
of the newest developments in MR to get the best based on the first 6 months.

97