VR helps researchers understand molecular processes
14 September 2012
The University of Sheffield’s Krebs Institute Structural Biology Group (SBG) has recently installed an ActiveWall virtual reality (VR) system and is using Virtalis’ own VR software enabler for PyMOL* (a widely used 3D molecular visualisation application) both to visualise and interact with molecular data in spectacular stereoscopic 3D.
SBG’s focus is to study the atomic structure of biological macromolecules, and by understanding these structures, the group hopes to elucidate the relationship between structure and function. Four complementary techniques are used to explore cells and molecules in atomic detail: X-ray protein crystallography, nuclear magnetic resonance spectroscopy (NMR), cryo-electron microscopy (cryoEM), and bioinformatics. Dr. Patrick Baker, a researcher in protein crystallography within the group, takes up the story:
“The proteins in our cells are really molecular machines. They are also very tiny, being typically just two to ten nanometres across. Yet within that small size, each protein molecule comprises between 1,500 and 20,000 individual atoms. Studying such complex structures can be mind boggling at times and, historically, we needed large polystyrene or wooden models to represent the structures.
“Twenty years ago, it took between one and five years to determine a structure. Now, we can have that structure within a week of creating the crystal. Structural biologists have long been at the forefront of what computers can do, owing to the enormous demands placed on them by molecular graphics. The advent of stereoscopic 3D viewing has been a further leap forward, because we can see so much more of the structure without becoming confused.”
The Virtalis ActiveWall immersive, interactive 3D visualisation system draws on active stereo technology and features a custom screen, specialist computer, custom software and powerful projectors. Movements within the ActiveWall environment are tracked using a special system, which alters the perspective of the visuals according to the user’s position and orientation within the scene; this provides a natural and accurate sense of relationship and scale.
A hand-held controller allows the immersive experience to be further enhanced, allowing the user to navigate through the virtual world, pick and manipulate component parts in real-time and make decisions on the fly. Dr Baker again:
“Our ActiveWall allows us to share our results with colleagues, work with industrial collaborators and, of course, teach. Previously, I’ve used a 3D monitor, but the ActiveWall gives insights you couldn’t get with the monitor, as it was too zoomed in. Now I can walk right up to the screen to examine an area in detail and the rest of the molecule remains visible.
“It is an excellent teaching aid; we are using it to help students understand complex molecular structures. Also, this is a great collaborative working tool. We can get a group of about a dozen non-specialists all looking at the same thing, enabling productive discussions about the various structures.
“We’re working with chemists to design molecules that can bind to, and inhibit, essential proteins in bacteria as leads to new anti-infectious agents to combat increasing drug resistance. We collaborate with pharmaceutical companies on understanding the relationship between structure and function as we move towards personalised medicine.
“Once we start looking at such interactions there is another leap in complexity and we really need that third dimension.”
The SBG is using its Virtalis ActiveWall and the PyMOL 3D/VR-enabler to analyse proteins from the bacteria Burkholderia pseudomalleii, a soil-borne organism that is the causative agent of the tropical disease Melliodosis.
Working with colleagues in Thai, Malaysian and Singaporean Universities, the Group is investigating the bacteria’s proteins, the functions of which are unknown. They discovered that one - Burkholderia lethal factor 1 (BLF1) - has a very similar 3D shape to the cytotoxic necrotising factor of E.coli, indicating that it, too, is a potent toxin.
It transpired that although both these toxins shared the same mechanism, their cellular targets were different. BLF1 targets protein translation, killing the host cell. Understanding the molecular structure and function of this toxin may lead to ways to counter pathogenicity and ameliorate the symptoms of the disease. Even more exciting, the toxic effect of this protein could perhaps be harnessed as a drug to kill rapidly dividing cells, as found in many cancers.
*Virtalis developed a VR software enabler for the PyMOL 3D molecular visualisation application through work conducted for Dr James F. Hinton, professor of chemistry and biochemistry at the University of Arkansas, which hosts the US Centre for Protein Function and Structure.
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