Pyruvate dehydrogenase kinase 4 (PDK4), a mammalian mitochondrial
serine kinase has emerged as an interesting candidate for diabetes
therapy. Due to the high prevalence of this disease especially
type 2 diabetes (T2D) and the health complications associated with it, there is extensive effort to find the appropriate treatment. Understanding the regulation of PDK4 activity would therefore contribute significantly to the development of therapeutic agents. This research outlines the utilization of bioinformatics tools such as Interweaver, ClustalW and
Protein Structure Visualizer, in order to predict
proteins that potentially interact with PDK4 and possibly regulate its activity. Interweaver database identified 96
proteins that have possible interaction sites for PDK4.
Protein p100/p49, containing a death domain that is known to have a role in suppressing apoptosis, was identified as a potential partner for PDK4. The alignment between p100/p49 primary sequence and that of PDK4 using ClustalW demonstrated sequence similarity between the two
proteins. Swiss PDB Viewer then located the positions of the
amino acids that are in the hypothetical protein binding motif of p100/p49 within the 3D structure of hPDK4. These
amino acids were found to be located in the region of PDK4 which is known to bind
protein substrates of PDK4 and may be accessible to other
proteins as well. These findings were very interesting as PDK4 has not previously been associated with apoptosis and this could be the link between apoptosis and
insulin resistance. Cell biology studies were then performed to verify the relationship between PDK4 and apoptosis. In this regard, HeLa and HepG2 cells were treated with apoptosis-inducing agents such as TNFα,
C2-ceramide, and
linoleic acid. These cells were then monitored for apoptosis and PDK4
mRNA expression using
a DNA laddering assay as well as Real Time PCR. The results showed that these factors induced apoptosis in a concentration dependent manner and suppressed PDK4
mRNA levels. These findings suggested a relationship between PDK4 and apoptosis.