Hands-On Visualization of Molecules

Scientists have devised a new way to interact with molecules so tiny that they cannot be visualized with even the most powerful microscopes.

The new technology combines hand-held objects with complex computer displays, and is called tangible interfaces for structural molecular biology. Its creators hope to see it used for both scientific and educational research. "We want to be able to understand, communicate, and interact with complex structures in natural ways. The easier it is to hold a biological molecule in your hands, the easier it will be to figure out what it is doing in the body,” explained Prof. Art Olson, a molecular biologist at the Scripps Research Institute (La Jolla, CA, USA).

By utilizing sophisticated three-dimensional (3D)-producing printers that "print” solid objects out of thousands of layers of plastic or plaster, the group can fabricate models of DNA, proteins, and other small biologic molecules. These models can be twisted, touched, nipped, and flung from person to person. Then, using a basic digital video camera to take and track images of these objects, the researchers are able to devise an artificial environment in which the computer interfaces with the object in what is called an augmented reality.

The molecular model appears on the computer screen, twisting and turning in real time as the individual holding the object manipulates it, and software designed by the Scripps Research team enables the computer to superimpose scientific data about the molecule onto the display.

The scientists have created novel ways to build the pieces of a structure, such as a protein. They have been experimenting in constructing hybrid models, such as inserting magnets to snap together two pieces of a model. This has allowed them to show such processes as viral assembly, the 3D folding of a long amino acid chain into a small protein, and docking between two proteins.

To demonstrate self-assembly--a common mechanism whereby small objects such as viruses put themselves together from tiny identical subunits into a compact structure, similar to a 3D puzzle--the researchers put pieces of plastic that look like very complicated Legos approximately the size of a quarter into a jar and shake them up. The pieces represent protein molecules that come together to form a virus particle, and small magnets imbedded in them help direct them to reshape in the correct way. After some forceful shaking, there is an assembled model of a virion inside the jar.

By using the computer's augmented reality software, the scientists were then able to combine real-world objects with a computer-generated graphics where the computer interfaces with the object. Prof. Olsen demonstrated this by taking a model of a protein and displaying on the computer screen its electrostatics--red and blue clouds surrounding the object he is holding that show favorable and unfavorable interactions. As the two ends of the molecule are brought together in close proximity to each other, the cloud surrounding the ends changes from glowing blue to flowing red. The protein does not "like” to have these two ends so close to one another. Correspondingly, according to Prof. Olsen, such substantial interfaces could be utilized to manipulate models and predict molecular interactions.

The study was published in the March 2005 issue of the journal Structure.




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