The LIM-homeodomain (LIM-HD) protein family is responsible for cell type specification in a wide variety of tissues. In these proteins the homeodomain (HD) binds to DNA and the LIM domains recruit other proteins, while the role of the C‑terminal region is yet to be fully determined. Initial work on LIM-HD proteins such as Isl1 revealed that the LIM domains could inhibit DNA-binding. It was suggested that the LIM domains of Isl1 could bind to the HD to inhibit its function and that interaction with a protein partner could relieve inhibition of DNA-binding. This hypothesis has since been essentially disregarded due to evidence that key protein partners must assemble into cell-specific complexes to facilitate DNA-binding by Isl1 under physiological conditions.

Work from our laboratory has revealed a LIM-interaction domain (LID) in the C‑terminal region of Isl1 that lies close to the HD. This LID is responsible for binding to other LIM-HDs such as Lhx3 for the formation of expanded LIM-HD complexes. We hypothesised that the LIM domains and LID in Isl1 may be able to interact. No evidence has previously been found for an intermolecular interaction between these domains in Isl1. However, this does not preclude the possibility of an intramolecular interaction. We are using multiple approaches to investigate the potential existence and nature of such an interaction, including protein engineering and expression, biophysical analysis, yeast two-hybrid competition assays, and nuclear magnetic resonance. Our results indicate that a very weak, intramolecular interaction may take place between the LIM domains and LID in Isl1 that might sterically hinder DNA-binding of the HD and regulate Isl1 function.