Poster Presentation 24th Australian Conference on Microscopy and Microanalysis 2016

Comparative protein modelling and molecular dynamics simulation of viral pathogens. (#271)

Jason A Roberts 1 2 , Bruce R Thorley 1 2 , Michael J Kuiper 3 , Peter M Smooker 1 , Andrew Hung 1
  1. School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia
  2. Victorian Infectious Diseases Reference Laboratory, Melbourne, VIC, Australia
  3. Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia

Recent advances in supercomputing technology combined with advanced software analysis tools has facilitated the in-silico reconstruction of macromolecular structures using predictive methods. Previous work by our group resulted in the first complete reconstruction and simulation of a human pathogen incorporating the encoding genomic information1. Integral to the development of this work was the standardization of a protocol for the reconstruction and examination of viruses that exhibit icosahedral symmetry incorporating the use of predictive modelling methods to replace missing structural data. A novel component of the research involved the reconstruction of large, multi-million atom, macromolecular structures with multiple repeating units. The simulation outputs could then be used for statistical purposes to indicate subtle atomic movements that show a direct correlation with b-factors derived from x-ray diffraction experiments.

  1. Roberts, J.A., Kuiper, M.J., Thorley, B.R., Smooker P.M., Hung. A., Investigation of a predicted N-terminal amphipathic α-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion. Journal of Molecular Graphics and Modelling, 38, September: 165-173.