Protein Preparation

Protein crystal structures are only the interpretation of a set of data derived from an experimental measurement.

The inconsistencies of the raw protein structure have to be removed together with adding those parts of the structure that are not available from the experiment.

Our preparation handles the following cases:

• ambivalent side chains: even highly resolved structures can not decide on the positions of oxygen and nitrogen e.g. the ASN side chains even if the plane of this amide group is determined; this holds also for the assignment of any atom in the imidazole ring of the HIS side chain.
  
  
• state of protonation: although the pK-values have been determined for every amino acid in aqueous solution, these values vary strongly due to the specific environment in the protein; thus the charge of every ionizable group has to be determined.
  
  
• positions of hydrogens: since these are not available from the experiment they have to be determined.
  
  
• solvation: only a limited number of solvent molecules will be introduced in the crystal structure; a reliable structure must contain all solvent molecules.
  
  
• hetero-groups: especially novel inhibitors may contain structural features that are beyond the scope of the molecular mechanics method; thus new additional parameters as well as the partial charges have to be determined.

Only this preparation makes it possible to use the protein structures in modeling studies. Only after this the results from optimizations or MD simulations on protein structures are valid and can be analyzed and interpreted. Only then conclusions can be drawn.