Spectral properties of contact matrix: Application to proteins |
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Authors: | Email author" target="_blank">J F?SadocEmail author |
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Institution: | (1) Laboratoire de Physique des Solides, Université Paris Sud (associé au CNRS), Bat. 510, Centre d'Orsay, 91405 Orsay, France |
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Abstract: | A protein can be modelled by a set of points
representing its amino acids.
Topologically, this set of points is entirely defined by its contact matrix
(adjacency matrix in graph theory).
The contact matrix characterizing the relation between neighboring amino acids is
deduced from Voronoi or Laguerre decomposition. This method allows
contact matrices to be defined without any arbitrary cut-off that
could induce arbitrary effects.
Eigenvalues of these matrices are related
with elementary excitations in proteins. We present some
spectral properties of these matrices that
reflect global properties of proteins. The eigenvectors
indicate participation of each amino acids to the excitation modes of the proteins.
It is interesting to compare the protein modelled as a close packing of amino acids,
with a random close packing of spheres.
The main features of the protein are
those of a packing, a result that confirms the importance of the
dense packing model for proteins. Nevertheless there are some
properties, specific to the hierarchical organization
of the protein: the primary chain order, the secondary structures
and the domain structures. |
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Keywords: | |
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