Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

May 20, Tue 2008
11:00 am, MRB 200 Conference Room

Dr. Eugene Krissinel

Senior Technical Officer, European Bioinformatics Institute,

PISA, or a story about perceptions, expectations, naivety, macromolecular complexes and their complexity in bioinformatics and crystallography

Protein crystallography is an important source of data on 3-dimensional structures of macromolecular complexes, which often are the biological units performing a particular physiological function. Up to date, more than 80% of PDB structures have been obtained by means of X-ray diffraction on macromolecular crystals, yet the identification of complex structures is not straightforward due to two main reasons. Firstly, only covalently linked structures without crystallographic symmetry are identified reliably in X-ray experiments, while monomeric units of macromolecular complexes are linked by weaker, non-covalent interactions and are often crystallographically-related. Secondly, it is generally unclear to what extent crystal packing reflects structure of a complex as it is found in native environment. In the talk, I will address these issues from the positions of chemical thermodynamics. A new approach to the identification of macromolecular assemblies in crystal packing, which reaches 90% of correct identifications, will be presented. I will also present results of docking studies on the scale of the whole PDB, where the rate of failure may be interpreted in thermodynamic context to indicate conditions under which complex structure is reflected by crystal packing. The corresponding software is available as a public web-server PISA at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html and is deployed by the PDB as a mandatory processing tool since 2007.