Lab. of Computer and Structural Analysis of Bioploymers, V. A.. Engelhardt Institute of Molecular Biology, Moscow, Russia
We have proposed an automatic recognition method for delineation regions of
high energetic stability in globular proteins. This approach is based on
numerical estimations of non-covalent interactions energy as input data for
the objective method of domain structure determination, which has been
developed earlier.
Here, we have extended the objective method to have the possibility to
define of multi-segment discontinuous domains. The high-energetically patterns
have been obtained by application of this procedure to the significant set of
3D-structures from PDB database. These "energetical domains" are generally in
agreement with domain structure determined by other authors on the basis of the
inter/intradomain contacts number estimation. While we consider more
sophisticated criteria, the resultant domains show some peculiarities
comparatively to common structural domains. The differences concern several
aspects, mainly: (i) some variations in domain boundaries; (ii) particular
segments belong to other domains, then defined by structural approach.
This consideration is practically uninfluenced from the number and
disposition of local structures with high or low count of contacts ( for
example, secondary structures ), because, using energetic approach one can
analyse not only the number of contacts, but the efficiency of interactions
between different types of atoms. We suggest that our approach is more
complete, because it allow more adequately interpret interrelation between a
physical - chemical properties, domain structures, thermodynamics of proteins
and its function.