Novel method to detect a motif of local structures in different protein conformations |
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Authors: | Wako H; Yamato T |
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Affiliation: | School of Social Sciences, Waseda University, Tokyo, Japan. |
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Abstract: | In order to detect a motif of local structures in different protein
conformations, the Delaunay tessellation is applied to protein structures
represented by C(alpha) atoms only. By the Delaunay tessellation the
interior space of the protein is uniquely divided up into Delaunay
tetrahedra whose vertices are the C(alpha) atom positions. Some edges of
the tetrahedra are virtual bonds connecting adjacent residues' C(alpha)
atoms along the polypeptide chain and others indicate interactions between
residues nearest neighbouring in space. The rules are proposed to assign a
code, i.e., a string of digits, to each tetrahedron to characterize the
local structure constructed by the vertex residues of one relevant
tetrahedron and four surrounding it. Many sets comprised of the local
structures with the same code are obtained from 293 proteins, each of which
has relatively low sequence similarity with the others. The local
structures in each set are similar enough to each other to represent a
motif. Some of them are parts of secondary or supersecondary structures,
and others are irregular, but definite structures. The method proposed here
can find motifs of local structures in the Protein Data Bank much more
easily and rapidly than other conventional methods, because they are
represented by codes. The motifs detected in this method can provide more
detailed information about specific interactions between residues in the
local structures, because the edges of the Delaunay tetrahedra are regarded
to express interactions between residues nearest neighbouring in space.
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