Modelling COVID-19 Spike Protein Interactions on CSIRO’s Bracewell GPU Cluster

Dr Michael Kuiper1, Dr Tim Ho2

1CSIRO, Docklands, Australia
2CSIRO, Clayton, Australia

The coronavirus SARS-CoV-2 (COVID-19) attaches to human cell through its spike (S) protein receptor binding domain (RBD) to ACE2 proteins to begin the infectious process.

We used molecular dynamics to model the RBD binding to ACE2 protein to better understand the key interactions between residues. Additionally, we built a larger spike model, complete with its glycosylation pattern to help our researchers visualize effects of mutations and better understand interactions of other host proteins, such as the protease furin, which is important for viral infectivity.

CSIRO’s Bracewell GPU cluster was key to quickly initiating and performing this work. Having rapid access allows for quick prototyping and troubleshooting with the simulations. Earlier on in the pandemic little structural information was available. However, as the worldwide research effort gained pace, we were able to incorporate new findings into our developing models. As a new dominant strain was being recorded, (D614G) we were able to incorporate this into our models and, with experimental validation from the Australian Center for Disease Prevention (ACDP), able to assess the effects of the mutation. Fortunately, this strain does not appear to resist vaccine responses, however, work by others indicates it is a more efficient spreader.


Dr Michael Kuiper is a computational research scientist at CSIRO’s Dat61 specialising in bio-molecular simulations and visualisation. He contributes to many varied collaborative projects enabling researchers in biological science to utilise high-performance computing (HPC) and has a keen interest in using Virtual Reality to visualize molecular complexes. Currently he is focused on COVID-19 research as well as microbial plastics degradation and antimicrobial resistance. Michael previously worked at other HPC centres including the VLSCI and has spent time in Antarctica studying antifreeze proteins in fish with the United States Antarctic Program.

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