Daniel Parton

High efficiency simulations of biological systems

I am a fourth (final) year DPhil student, funded by a 4-year CASE award from the BBSRC and Fujitsu Laboratories of Europe. My research is focused on the dynamics and lateral organisation of proteins and lipids in large membrane systems, primarily using coarse-grained molecular dynamics (CG MD) simulations. I have investigated how the aggregation of generalised transmembrane proteins is modulated by a range of properties, such as hydrophobic mismatch, membrane curvature (via simulation of large vesicle systems) and protein shape/class. Other studies concern the organisation of proteins in membranes displaying ordered and disordered phases. Some of these simulations have been particularly challenging computationally, requiring the use of supercomputers in France (Jade via a HPC-Europa2 grant) and the UK (HECToR via an EPSRC grant). Previous work has included studies of the interactions of the antimicrobial peptide maculatin 1.1 with lipid membrane systems, via multi-scale molecular dynamics simulations.

I have also contributed to development of the MDAnalysis Python library, which is used for the analysis of molecular dynamics trajectories.

I previously studied Chemistry (MSci) at the University of Bristol, including a 50-week medicinal chemistry placement at GlaxoSmithKline.

Publications

• D. L. Parton, E. V. Akhmatskaya, M. S. Sansom; Water permeation through a disordered maculatin pore; In press (2011)

• D. L. Parton*, J. W. Klingelhoefer*, M. S. Sansom; Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature and protein class; Biophys. J. (2011) 101:691-699
  * Authors contributed equally.

• P. A. Procopiou, C. Browning, J. M. Buckley, K. L. Clark, L. Fechner, P. M. Gore, A. P. Hancock, S. T. Hodgson, D. S. Holmes, M. Kranz, B. E. Looker, K. M. Morriss, D. L. Parton, L. J. Russell, R. J. Slack, S. L. Sollis, S. Vile, C. J. Watts; The Discovery of Phthalazinone-Based Human H(1) and H(3) Single-Ligand Antagonists Suitable for Intranasal Administration for the Treatment of Allergic Rhinitis; J. Med. Chem. (2011), 54:2183-2195

• P. J. Bond, D. L. Parton, J. F. Clark, M. S. Sansom; Coarse-Grained Simulations of the Membrane-Active Antimicrobial Peptide Maculatin 1.1; Biophys. J. (2008), 95:3802-3815

Conference Talks and Posters

• Biophysical Society Annual Meeting, 4-9 March 2011, Baltimore, MD, USA. Poster

• Computational Molecular Science 2010, 27-30 June 2010, Cirencester, UK. Poster: Lateral Organization in Proteinaceous Lipid Membranes

• BSC-IRB Conference: Expanding the Frontiers of Molecular Dynamics Simulations, Nov 2009, Barcelona, Spain. Poster: Membrane Lysis Mechanisms of the Antimicrobial Peptide, Maculatin 1.1
  - Same poster won the GSK Award at the Department of Biochemistry's Annual Retreat

• Biomolecular Simulation (CCPB), 6-8 Jan 2009, York, UK. Presentation: Investigations of the Membrane-Permeabilizing Action of the Antimicrobial Peptide, Maculatin 1.1

• Membrane Protein Assembly: Theory and Experiment (CECAM), 3-6 Sep 2008, EPFL, Lausanne, Switzerland. Poster: Investigating the membrane lysing action of the antimicrobial peptide maculatin 1.1

Other

• Recent research featured on front cover of Oxford Biochemistry magazine, "Phenotype", Trinity term 2011