My PhD was awarded from The University of Warwick where i worked under the supervision of Professor P.M.Rodger. The project involved molecular dynamics simulations of DNA interacting with a novel macromolecular ligand. Click here for a poster of this work presented at the FOMMS2003 conference in Colorado.

Currently, I am a Post Doctoral Research Associate in Professor Mark Sansom's group and College Lecturer in Biochemistry at Christ Church.

Current Research

A Simulation Pipeline

The overall aim of this project is to prototype high throughput biomolecular simulations to enable full exploitation of structural genomics.
Initial work focuses on bacterial outer membrane proteins (OMPs). As an intial step towards an automated simulation pipeline we have developed a semi automated method with in-built checking of simulation stability- this is currently being tested on the National Grid Service. Click here for a report. on work presented at the 'Systems Biology- will it work?' conference. BioSimGRID will be used to store the simulation data

OprF

Other work involves homology modelling of OprF (a major OMP of Pseudomonas aeruginosa)- an orthologue of OmpA. We are investigating the pore-forming ability of the N-terminal half of this protein by performing atomistic simulations of our own homology model and also of one reported by Brinkman et al. (Brinkman, F. S., Bains, M., and Hancock, R. E. W., 2002, J Bacteriol., 182:5251-5255). Our homology model, TYR residues are shown in green ==>

NalP

Nalp (PDB code 1UYN)is an autotransporter serine protease from Neisseria meningitidis. The crystal structure of the in vitro-folded translocator domain (C-terminal domain)of NalP revealed a 12-stranded beta barrel with a hydrophilic pore that contains an N-terminal alpha helix.(Oomen et al, EMBO J (2004),23, 1257-1266) I am investigating the pore activity of this protein and the role of the N-terminal domain. Simulations are underway in which the pore activity is measured in the presence and absence of the N-terminal alpha helix.