Modelling of the 3-D structure of IFN-alpha-k and characterization of its surface molecular properties

The 3-D structure of IFN-alpha-k (one of the alpha-interferon family) was constructed and optimized by molecular modelling starting from the X-ray structure of IFN-beta. The molecular surface of the optimized 3-D structure of IFN-alpha-k was then evaluated and characterized for its hydrophobicity/hydrophilicity. The structure of IFN-alpha-k was completed with its first segment (23 amino acid residues) called signal peptide. The 3-D structure of this segment was predicted to be in helical form bonded to the core by one loop. It was found that the complete structure of IFN-alpha-k can exist in at least two main conformations as far as the orientation of the signal peptide is concerned, i.e. in the open form (in which the signal peptide is directed outward of the 'body' of the molecule) and the closed form (where the signal peptide is aligned with the body). The relative stability of these forms strongly depends on the stabilization by the environment (e.g. by solvation) due to the prevailing hydrophilicity of the body and hydrophobic character of the signal peptide.