- Article -
| In Silico Biology 9, 0029 (2009); ©2009, Bioinformation Systems e.V. |
Interface of apoptotic protein complexes has distinct properties
Pralay Mitra1,2, Riddhiman Dhar2 and Debnath Pal1,2*
1 Supercomputer Education and Research Centre,
2 Bioinformatics Centre,
Indian Institute of Science, Bangalore-560012, India
* Corresponding author
Email: dpal@serc.iisc.ernet.in
Edited by E. Wingender; received August 11, 2009; revised September 17; accepted September 19, 2009; published November 26, 2009
Abstract
Apoptosis is a programmed mechanism of cell death that is a normal component of development and health of multi-cellular organisms. In this study, we ask if interface properties of apoptotic protein complexes are different from protein complexes in general. We find that although in apoptotic protein complexes the overall distribution of interface size, surface complementarity, hydrogen bonding, hydrophobicity are similar to general interface properties, apoptotic complexes tend to have more fragmented interfaces and different secondary structural preferences. The statistics on the number of interfaces where specific amino acid(s) occur with significantly enhanced frequency suggest that Arg, Met and Asp are most important functional residues. The role of Met is believed to be unique, as evidenced from the existing data on hot spot potential of residues. These findings together provide insight into the possible role of various physico-chemical attributes at the protein interface in regulation of the apoptosis process.
Keywords: apoptosis, protein-protein interaction, residue propensity, protein interface, secondary structure