ABSTRACT
The method for two-dimensional representation of protein surfaces, based on the analogy with geographic map, and the algorithm for the search of the most favourable regions of izologous intermolecular interactions are proposed. It is assumed that the most favourable izologous interaction corresponds to an izologous contact of subunits which maximally dehydrates surface hydrophobic groups. The subunits are approximated by ellipsoids of revolution. The hydrophobic groups are assumed to be dehydrated if their C beta-atoms are inside the surface regions of the contacting ellipsoids inaccessible for contact with the sphere representing a water molecule. Using the proposed methods it is shown that for all izologous structures, known to atomic resolution, general shape of the molecule and distribution of hydrophobic groups on its surface: 1) provide a rough intersubunit recognition during assembly (deviation of the center of the experimentally localized contact region from the center of one of two-three regions obtained by us does not exceed 6--7 A); 2) choose only a few most favourable mutual orientations of the contacting regions; 3) can determine the pathway of the assembly.
Subject(s)
Proteins , Macromolecular Substances , Mathematics , Models, Molecular , Protein Binding , Protein Conformation , Surface PropertiesABSTRACT
The calculation of the structure of haemoglobin alpha--beta-dimer is performed. Calculation is divided into two steps: at the first step highly hydrophobic regions of the subunit surfaces which can provide the stability of the complex are found; at the second--the fitting of this surface regions is carried out. The calculation has resulted in finding three most stable structures. R. m. s. deviation of the positions of C beta-atoms of one of these structures from those in the native one is 3.5 A.
