Topology plays a central role in the structure of a protein. Network
theoretical methods are being increasingly applied to investigate protein topology. In
this paper, amino acid contact energy networks (AACENs) are constructed for
globular, transmembrane and toroidal proteins. The effects of topology on proteins
are investigated by the differences of various network parameters among three kinds
of protein topologies. Globular proteins are found to have the highest network
density, average closeness and system vulnerability, while toroidal proteins have the
lowest values of these parameters. Transmembrane proteins are found to have
significantly higher assortativity values than globular and toroidal proteins.
AACENs are constructed and compared for proteins with different secondary
structure compositions, whose influences on biological functions are discussed in terms of topological
descriptors. By extracting sub-networks only including interfacial residues between different chains, it
may provide a simple but straightforward method to identify hot spots of toroidal proteins. This network
study would offer new insight into overall topology and structural organization of different types of
Keywords: Amino acid network, contact energy, protein topology, secondary structure, symmetry, toroidal proteins.
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