Surface receptors in cells play a vital role in enabling cells to gain information on the surrounding environment and to initiate various actions. Currently, little is known about how such receptors work, in particular, the mechanics of how the binding of a molecule to the extracellular side results in a signal being transferred to the intracellular space. The group is investigating the complex between Death Receptor 5 and its ligand TRAIL. TRAIL has recently been the focus of much attention, due to its ability to trigger apoptosis selectively in cancer cell lines and HIV infected T-cells. This project was initiated in collaboration with the Dept. of Pharmaceutical Biology of Prof. Wim Quax, where research is conducted on mutants of TRAIL. To date, activities have focused on simulations of the DR5-TRAIL complex and on studies of TRAIL and the Death Receptor separately. In addition, work on the development of molecular shaped simulation boxes has been conducted in collaboration with Dr. Henk Bekker from the Dept. of Computational Sciences. The use of a molecular shaped box can speed up simulations by a factor two, which is especially valuable for simulations of large protein complexes such as TRAIL and the DR5 that consist of a total of roughly 650 residues. Another system under investigation is bacteriorhodopsin, a photoreceptor and a presumed proton pump. Bacteriorhodopsin is the main constituent of the Purple Membrane, a naturally occurring crystalline patch with a hexagonal lattice, with bacteriorhodopsin molecules organised as trimers. A full atomic model of the purple membrane has been generated (see figure 1) and simulations have been performed to understand the mechanisms of the action of bacteriorhodopsin and to investigate the binding of calcium to the purple membrane and to the protein in particular. This work is performed in collaboration with the groups of Xavier Daura and Estebe Padros of the Universidad Autonoma de Barcelona and the group of Andrea Amadei of the University of Roma II “Tor Vergata”.
This page was last updated on August the 30th, 2016.