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                           JOINT SEMINAR
                       STRUCTURAL BIOINFORMATICS AND
                 COMPUTATIONAL MATERIALS SCIENCE CENTER
                              College of Science
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 PISA, or a story about perceptions, expectations, naivety, macromolecular
  compounds and their complexity in bioinformatics and crystallography

                        Eugene Krissinel, PhD
 European Bioinformatics Institute, Cambridge, United Kingdom

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 
problematic 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 crystallographi-
cally 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 perspective of chemical 
thermodynamics. A new approach to the identification of macromolecular 
assemblies in crystal packings, 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.


                        Friday, May 16, 2008
                                 2:30 pm
                     Room 318, Innovation Hall, Fairfax Campus