PROTEIN DOMAIN DEFINITION BASED ON THE ENERGY DISTRIBUTION IN THE SPATIAL STRUCTURE
Berezovsky I. N., Esipova N. G., Namiot V. A. Tumanyan V. G.
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia;; Research Institute of Nuclear Physics of Moscow University, Moscow 117234, Russia
We propose an algorithm for determining the domain structure of globular
proteins. The method obviates the use of complicated geometrical criteria
with numerous fitting parameters, as it relies on the entirely physical
model van der Waals interactions, which can be represented analytically
with the distribution of electron density. Various levels of hierarchy
in the protein spatial structure are discerned by analysis of the energy
interaction between structural units of different scales. The algorithm
readily and accurately locates domains formed by continuous segments of
the protein chain as well as those comprising nonsequential segments, and
sets no limit to the number of segments included in a domain. We have analyzed
309 protein structures. The domains delineated with our approach may coincide
with reference definition at different levels of the globule hierarchy.
Along with defining the domain structure, our approach allows one to consider
the protein spatial structure in terms of the spatial distribution of the
interaction energy in order to establish the correspondence between the
hierarchy of energy distribution and the hierarchy of structural elements.
This work was supported by Russian Foundation for Basic Research grant