Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins using Frequent Subgraph Mining Method

author: Mohammad Al Hasan, Indiana University-Purdue University Indianapolis
published: Oct. 25, 2016,   recorded: August 2016,   views: 1191

Related Open Educational Resources

Related content

Report a problem or upload files

If you have found a problem with this lecture or would like to send us extra material, articles, exercises, etc., please use our ticket system to describe your request and upload the data.
Enter your e-mail into the 'Cc' field, and we will keep you updated with your request's status.
Lecture popularity: You need to login to cast your vote.


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.

Link this page

Would you like to put a link to this lecture on your homepage?
Go ahead! Copy the HTML snippet !

Write your own review or comment:

make sure you have javascript enabled or clear this field: