Feature: Another dimension in protein interaction

View of all complexes and constituent proteins in the nucleus of yeast. The proteins are labeled by gene name, green lines represent known interactions between proteins and the thickness of the line depends on the quality of evidence for an interaction.

Sitting in a darkened room, I gaze up at a giant projection of what could be an abstract artwork, or perhaps an advanced computer game. Arrayed before me is a constellation of tiny floating dots, some loosely scattered, some clustered within larger structures, and many of them bound together by a startling array of glowing lines looking for all the world like a giant space battle. But this is not art (though it’s clearly artistic), nor is this a game; this is an up close and personal view a common yeast cell.

“Imagine for a moment that you’ve come up to a yeast cell and you’ve just poked your head inside the outside membrane,” says Professor Marc Wilkins, the ‘father’ of proteomics and Director of the NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences at the University of New South Wales. Wilkins is the project lead for the technology on display, a new three dimensional visualisation tool for exploring the inner workings of cells, called The Interactorium.

Wilkins points out the various organelles within the cell – there’s the nucleus, there’s the mitochondria – and all the thousands of dots scattered around, those are the proteins. It’s all there. Then, with a couple of clicks of the mouse, Yose Widjaja – PhD student and the brains behind the coding of The Interactorium – gracefully rotates the mass of dots and lines, selects a single ‘node’, and the view zooms in to reveal the protein in detail.

Mere words and still images simply can’t do justice to the beauty and elegance of The Interactorium. For a cell – even one as ‘simple’ as a yeast cell – is a startlingly complex thing; thousands of individual proteins, each with potentially dozens of interactions. Trying to visualise all this through with a conventional database, or even a two dimensional diagram, rapidly becomes an exercise in folly. But with The Interactorium it’s all there in glorious 3D, intuitively navigable, displaying a vast amount of information in an immediately digestible form.

The Interactorium is also more than just a tool for generating pretty 3D images. Wilkins hopes it will not only enhance our understanding of the inner workings and dynamics of cells – healthy and diseased – but also aid in the development of new drugs that target specific proteins with super-surgical precision.

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