Page 166 - Macromolecular Crystallography

CHAPTER 11

Getting a macromolecular

model: model building,

refinement, and validation

R. J. Morris, A. Perrakis, and V. S. Lamzin

11.1 Introduction
consuming measurements as well as computation-
Determination and analysis of three-dimensional ally and labour-intense interpretation.
(3D) structures is a cornerstone in modern molec- Especially during the last two decades, crystal-
ular biology. Macromolecular structure plays an lography has developed into the primary tool for
unchallenged role in the interpretation of biochem- the investigation of biological macromolecules. Sub-
ical data and constitutes a main key that can open ject to the strength of the X-ray diffraction produced
the door to unravel mysteries of the function of by fragile protein crystals and, therefore, the res-
biological macromolecules. The vast majority and olution of the crystallographic data, the method
a wide variety of chemical reactions and other pro- allows visualization of the electron densities down
cesses in living organisms is carried out by proteins. to the individual atoms and sometimes even fur-
They are typically specific, highly efficient and yet ther – approaching a resolution at which subtle, but
very versatile. The formation, development, and biochemicallymostimportant, electronicdifferences
the sustenance of a living organism are governed may be studied. This obviously had important con-
by the correct function of proteins, which in a sequences in opening up an entire new wealth of
given environment is defined by their spatial struc- possibilities for the structural investigation of pro-
ture. Therefore the investigation into macromolecu- teins and the establishment of structure–function
lar structures and the characteristics that determine relationships at truly atomic level of detail.
their function has been of particular interest over Protein molecules are generally large and are com-
the last decades, often giving rise to new and highly posed of polypeptide chains of amino acids that
detailed biological insights at the atomic level. provide amazing conformational flexibility. This is
A large number of methods have been estab- reflected not only in the way proteins are folded into
lished to address the gathering structural infor- anappropriatelyarrangedglobularbodywithaded-
mation. Some are based on the biophysical prop- icated purpose (function) but also in the way they
erties of the studied molecules, others on their undergo conformational changes upon interactions
chemical composition. A most important final step with other proteins or small molecules (ligands).
is to properly relate the structural knowledge to This conformational flexibility results in a challenge
the inferred functionality. Currently, X-ray crys- in obtaining sufficiently ordered protein crystals
tallography is the predominant technique for 3D that, being placed into an X-ray beam, would be
structure determination, owing to its now practi- able to provide diffraction data to sufficient res-
cal simplicity, ease, and high level of automation olution. An additional feature of protein crystals
as compared to the formerly tedious and time that promotes this flexibility is that the molecules

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