NAME: Mikhail Isupov

AFFILIATION: University of Exeter, UK

CONTACT: M.Isupov@exeter.ac.uk

 

TITLE: "Tricks of Molecular Replacement; Try, Analyse and Try Again"

ABSTRACT: A common approach in difficult MR cases is the use of a protein oligomer as a search model. A conserved oligomer - a dimer, a trimer, a hexamer etc. is identified by comparison of structures of several related proteins. The oligomer is often a better search model then a protein monomer provided that the molecular contacts are extensive and the relative position of monomers is conserved within a family.

 

When a MR solution can not be found even with such an oligomeric model one needs to analyse the crystal packing, native Patterson synthesis and self-rotation function together with the biophysical information of the oligomeric state of the target protein. The self-rotation function can suggest the molecular symmetry of the target structure and orientation of its NCS axes. Molecular symmetry axes of the oligomeric search model have to be parallel to NCS axes or to coincide with the crystal axes. This restricts possible orientations and in some cases positions of the search model thus reducing the search space in MR. Alignment of the molecular symmetry axes of the search model with NCS axes of the crystal was crucial for successful MR solution in several specific cases. Details of some of these cases will be presented.

 

Trimming of the search model, rigid body refinement in P1 and partial model refinement for subsequent use in MR are often useful in difficult cases and will be briefly discussed.