| Honours; Masters; PhD | The mechanism of activation of cytokine receptors: |
| | The activation of cell surface receptors such as the growth hormone receptor and the epidermal growth factor receptor is a critical step in cell regulation. Molecular dynamics simulation techniques will be used to characterize the conformational changes within the extracellular and transmembrane domains that accompany the binding of the cytokine (growth hormone1 or epidermal growth factor) to its receptor thereby shedding light on the mechanism of action of cytokine receptors in general. |
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| Honours; Masters; PhD | From model systems to true biological membranes |
| | Lipid molecules are fundamental components of biological membranes. Not only do they play a role in the compartmentalization of cells and organelles but, also participate in fundamental processes such as cell division and intracellular trafficking. The aim of this project is to develop detailed models representing the membranes of specific cell types. |
| Images: |
| Vesical_fusion
Snapshots from a simulation of the fusion of two small phospholipid vesicles in near atomic resolution (see Marrink and Mark 2003, JACS, 125, 11144). |
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| Honors; Masters; PhD | Force fields for drug-like molecules |
| | A critical consideration when modelling biomolecular systems is the description of the interactions. The aim of this project is to develop and validate an automated force field topology builder (ATB; http://compbio.biosci.uq.edu.au/atb/). The ATB provides force field descriptions for drug-like molecules for use in studying the ligand-macromolecule interactions with applications in drug design and X-ray refinement. |
| Keywords: | molecular modelling; Atomic force fields; drug design |
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| Honours; Masters; PhD | Understanding the mechanism of action of antimicrobial peptides |
| | Cytolytic antimicrobial peptides form an integral part of the innate immune system of many vertebrates including man. These antimicrobial peptides act by binding to and disrupting bacterial cell membrane. They are highly specific and increasingly recognized as a potential source of novel antibiotic agents. A major limitation in the further development of AMPs in a therapeutic setting is that the mechanism by which these peptides discriminate between different classes of membranes is still poorly understood. The aim of this project is to use computer simulation techniques elucidate the mechanism of action of cytolytic peptides at an atomic level. Specifically to study their binding to the outer membrane of specific pathogenic bacteria and determine the key structural and physico-chemical properties that allows them to distinguish between the pathogenic intruder and host cells. |
| Keywords: | Molecular simulation, antimicrobial agents, GROMOS, GROMACS |
