Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins using Frequent Subgraph Mining Method
published: Oct. 25, 2016, recorded: August 2016, views: 1191
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Studying the interface region of a protein complex pavesthe way for understanding its dynamics and functionalities.Existing works study a protein interface region by the com-position of its residues, by the geometry of the interfaceresidues, or by directly aligning interface regions. Very fewworks use graphs as the tool for modeling the interface re-gions. In this work, we use interface residues for formingnetworks from a set of protein structures, and then ﬁnd sub-graphs that are frequent in those networks. For ﬁnding suchsubgraphs, we use a scalable frequent subgraph mining al-gorithm, which can mine frequent sub-network patterns ofa speciﬁc size. We then discover the functional motif alongthe interface region of a given protein from those mined sub-graphs. In our experiment, we use PDB structures from twodimeric protein complexes: HIV-1 protease (329 structures)and triosephosphate isomerase (TIM) (86 structures). Theproposed frequent subgraph based approach discovers thegraphs representing the dimerization lock which is formed atthe base of the structure, in 323 of the 329 HIV-1 proteasestructures. Similarly, for 86 TIM structures, the approachdiscovers the dimerization lock formation in 50 structures.Our method captures the locking mechanism at the dimericinterface by taking into account the spatial positioning ofthe interfacial residues through graphs.
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