METHODS FOR STRUCTURAL BIOLOGY

Modern research in the mechanisms underlying biological processes makes widespread use of structural information of many molecules, like DNA, ribosomes, proteins, etc. Many methodologies can be used (and are used) to extract such structural information. Most of my research in the development of methods for structural biology is centred on crystallography. Crystallography is widely, and unjustly, known to be a research subject dealing with minerals, crystals and, more generally, all matter in the solid state. This is actually a misconception. Although Crystallography was born in the eighteenth century as a subject to explain the properties of certain kind of materials, during the nineteenth and twentieth century it went through a tremendous expansion, expecially thanks to X-ray diffraction. In modern times Crystallography is applied to fields as diverse as Biology, Forensic Studies and Mineralogy.

In this page I have collected a few Crystallography topics I have actively researched.

Some technical details on Molecular Replacement
One of the most used techniques to solve a protein structure, using data from x-ray diffraction of crystals, is the molecular replacement. This technique has been explained over and over again in several papers, books, workshops and conferences. Modern implementations of molecular replacement utilise the fast rotation function, first introduced by Tony Crowther in 1972. It is very difficult to get hold of a copy of the original Crowther's article. Two good reviews of his treatment are [1] and [2]. I have tried to explain Crowther's idea and to introduce and expand all calculations in here.
BLEND
One of my latest research projects concerns the handling and processing of multiple data sets from multiple crystals. The main product of my investigations is BLEND [3], a computer program I have developed in collaboration with Gwyndaf Evans at MPL. BLEND is distributed within the CCP4 suite of programs for computational crystallography.
BLEND documentation (on CCP4 website)
BLEND tutorials (on CCP4 website)
BLEND documentation (on this website)
BLEND tutorials (on this website)
BLEND tutorial for the 2015 joint MPL-DIAMOND industry symposium on membrane proteins

REFERENCES

  1. Dodson, E. J. (1985). Proceedings of the CCP4 Study Weekend. Molecular Replacement, pp 33-45. Warrington: Daresbury Laboratory.
  2. Giacovazzo, C. (1998). Direct Phasing in Crystallography, pp 645-651. Oxford University Press.
  3. J. Foadi, P. Aller, Y. Alguel, A. Cameron, D. Axford, R.L. Owen, W. Armour, D. Waterman, S. Iwata and G. Evans (2013) Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography Acta Cryst., D69, 1617–1632

(back to james foadi's home page)