Delineation of
Continuous Domains in Proteins by Differences of Free Energy
XIE Zhi-Qun, DING Da-Fu, XU Gen-Jun*
( Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, the Chinese Academy of Sciences, Shanghai 200031,
China )
Abstract Domain is a
protein architecture under proteins’ tertiary structure,which can be identified
in most of proteins. Different combinations of domains lead to the formation of
diverse tertiary structures with diverse function for proteins. The delineation
of domains for a protein is important not only conceptually but also
practically. Unfortunately, up to now there is not an ideal means to achieve
that. This paper proposes a method for domain delineation based on the maximum
refolding free energy. The criteria are more or less objective. By using this
method, 50 proteins are analyzed. The boundaries for most proteins agree with
the data reported in literature. There are a few examples that seem more
reasonable, although they are not identical with those in literature.
Key words domains； free energy； structural parameterization； degree of isolation； identification
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