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Research digital skills training 2021

Visualising protein interaction

Professor Juliet Gerrard, Michael Barnett, PhD Candidate, School of Biological Sciences; David Doak, Norwich University of Arts, UK; Nick Young, Bianca Haux , Centre for eResearch
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Background

Auckland molecular research at the School of Biological Sciences aims to build capability in the use of virtual reality technology for molecular visualisation, i.e. to create an experience which enables the user to actually climb inside a molecule and walk around it. For this particular project, the Centre for eResearch (CeR) has been working with Professor Juliet Gerrard and  PhD Candidate Michael Barnett from the School of Biological Science’s to visualise the protein bonding of Human Peroxiredoxin 3, the second most common protein in the human body behind Haemoglobin.

Simulation

In a solution of PRX3 monomers (single units), the monomers will bond together to form dimers (paired units). These dimers then bond together to form rings, and the rings bond together to form a filament. This entire process has been simulated using the game engine Unity and  works in te Vive by Nick Young and Bianca Haux from CeR, in collaboration with Dr David Doak from Norwich University of the Arts, UK.

 

Self assembly of peroxiredoxi

Peroxiredoxins (Prxs, EC 1.11.1.15; pronounced per-oxy- red-ox-in) are a ubiquitous family of highly abundant antioxidant enzymes that protect all cells from free radical damage. They have an intriguing repertoire of self-assembled structures which helps modulate their activity inside cells and also provides an exciting scaffolding opportunity in vitro for nanotechnology applications.

This visualisation shows the assembly of monomers into dimers, dimers into rings, and rings into nanotubes. the user can teleport with either touchpad, and you can adjust the pH by grabbing the handle above one of your controllers with the opposite controller (using the trigger on the underside) and moving it left or right. The pH controls the degree of assembly. You can pick up a monomer, dimer or ring, and can break it into its smaller components by pulling it apart with two hands or shaking it while holding it (if it’s a dimer or a ring). The rings can be re-ordered, or re-pair monomers by simply moving them closer – as monomers/dimers/rings will aim to pair with the closest object of the same type. The project is an open source at https://github.com/uoa-eresearch/prx_fishtank

Further refinement on user experience

The CeR specialists have further done some refinements in order to improve the user experience by adding the following features:

Haptic/tactile feedback to indicate attraction forces feedback.
Added special effects to demonstrate more intermolecular and intramolecular events such as the accretion of free radicals within the peroxiredoxin rings.
Added user interface improvements to allow the users to navigate the program easier.
Added keyboard controls for demo controller for the purpose of allowing for smoother demonstration experience.
Tractor beam function to allow for extra ease of interaction with the molecules to improve the stationary experience while using the app.
Added sound effects to enhance the immersion and emphasis on the events within the application/simulation.
Improvements to the quality of life of the application such as small value tweaks and graphics tweaks to visually improve the app.

Other miscellaneous

There has been a “party mode” added which can be played as a competitive game while at the same time being educating.

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