Student Projects

Simulation of Peptide Folding

Protein and peptide folding represents the ultimate test of our ability to model protein-protein interactions. It is also of fundamental importance in structural biology because it is a central event in the translation of genetic information into function. The project will focus on simulating the folding of a series of WW domains together with G. Lippens (Pasteur Institute, Lille). These small protein domains (~30 a.a.) are amongst the fastest known folding motifs of their size. These offer the possibility to directly simulate folding in a system with a well defined tertiary structure and one for which accurate NMR structural data is readily available. This also makes them an ideal case to compare different approaches for simulating folding. Approaches that will be investigated include replica exchange methods, which have been claimed by others to be highly efficient, as well as methods that have been developed in Groningen, such as the addition of co-solvents to promote secondary structure formation and approaches designed to computationally mimic some aspects of molecular chaperone.

Modelling the Nucleation and Growth of Amyloid Fibrils

Various disease states including Alzheimer's disease, the various spongiform encephalopathies, Parkinson's diseases and type II diabetes specific proteins are characterised by the formation of Amyloid deposits in various tissues. Amyloids form from misfolded proteins in which specific regions first aggregate then assemble into multilayer regular fibrils. Understanding of how such aggregates form is not only critical to understanding protein folding in general, but may also assist in developing rational therapeutic approaches to such diseases. Because amyloids are non-crystalline, insoluble polymeric aggregates they are difficult to study by experiment. While some information is available from techniques such as fluorescence, NMR spectroscopy fibre diffraction and protein engineering no detailed atomic model for the structure of amyloid fibril has yet been developed. The aim of this project is to use molecular dynamics simulation techniques to shed light on the structure and formation of amyloid fibrils and, in particular, to identify the minimal stable of nucleation structure required for fibril growth. The work will be part of an ongoing research effort performed in collaboration with researchers based at the University of Groningen in The Netherlands with links to researchers in Heidelberg and Cambridge. The model systems will be a peptide from transthyretin, TTR(105-115). This peptide has been shown to form deposits exhibiting the characteristics of cross-beta x-ray diffraction patterns of amyloid aggregates.

Membrane Protein Interactions

Cell membranes are self-organised supramolecular structures critical to cell function. They contain lipids and proteins as well as non-lipidic components, including peptides, and respond dynamically to a changing environment. This is achieved, in part, by having a heterogeneous composition, which allows the membrane to self-organise in response to external signals. For example, peptide aggregation within the membrane can induce pore formation, membrane fusion, or even cell lysis. Despite being critical to cell function, little is known in regard to the behaviour of proteins and peptides within lipid membranes or the mechanism by which peptides and proteins assemble into functional complexes as it is very difficult to obtain detailed structural data in a membrane environment. Fortunately, simulations have proved extremely powerful in elucidating the properties of peptides and proteins within membranes. Recently, we showed that random mixtures of lipid in water will spontaneously assemble in simulations into equilibrated bilayers and even small vesicles. We are now using this approach to directly assemble systems incorporating several different lipids and peptides. Spontaneous aggregation into an equilibrated phase is being used to circumvent slow lateral diffusion within phospholipid membranes. In particular, we are using the spontaneous assembly of lipid bilayers to drive the formation of functional complexes such as membrane pores. Membrane pores are small channels that facilitate the transport of water or ions through the bilayer. This project will focus on the assembly of antimicrobial peptides and toxins that act by inducing membrane pores. Together with P. Kuchel (University of Sydney) we will attempt to model the structural behaviour of C-type natriuretic peptide (a component of male platypus venom). The C-type natriuretic peptide is structurally related a group of antimicrobial peptides known collectively as Defensins. These induce cell death in bacteria by the creation of pores within the cell membrane and are of interest in both the food preservation and pharmaceutical industries.

A structural model for low pH mediated viral fusion

Important viral pathogens like influenza, dengue and West Nile viruses enter host cells using low pH-mediated fusion. This fusion of the viral envelope and host cell membrane is driven by virus encoded fusion proteins expressed on the virion surface. These have been separated into two classes, Class I and Class II fusion proteins, based on their architecture, with the influenza virus heamagglutinin (HA) an example of Class I proteins and the flavivirus envelope protein (E) representing Class II proteins.
Database mining of sequence and structural features of both the influenza virus HA and dengue virus E proteins for multiple viral strains shows remarkably high conservation of selected histidine residues. In the available crystal structures of pre-fusion forms of these proteins, the highly conserved histidines are found buried in similarly conserved hydrophobic pockets. However, in post-fusion crystal structures these protonated histidines are found to be hydrogen-bonded with new residue partners. We suggest that protonation of the histidines in the low pH environment of the endosome provides the free energy required to release the histidines from their hydrophobic “clamp” and drive the structural changes in the fusion protein necessary for membrane fusion through an unstable transition state to the more stable post-fusion form. Preliminary experimental data as well as simulation of fusion triggering conditions using a molecular dynamics approach have further highlighted the potential role of histidine protonation in localized unfolding of the pre-fusion form of E. A clearer understanding of the detailed molecular events driving viral fusion will provide valuable additional targets for the rational design of small molecule inhibitors as well as aiding in the construction of attenuated infectious clone mutants that could serve as future vaccine candidates.

This page was last updated on July the 10th, 2017.

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