New biomolecular model helps study, design protein structures and interactions

August 27, 2012
Soft and transparent protein models

Kawakami’s molecular  models will enable researchers to quickly and collaboratively see, touch, and test ideas about molecular interactions and the behavior of proteins (credit: Masaru Kawakami/Review of Scientific Instruments)

A new soft, transparent, and squishy silicone biomolecular model that biology researchers and chemists can hold in their hands has been developed by Masaru Kawakami, Ph.D., a biophysicist researcher at JAIST (Japan Advanced Institute of Science and Technology).

For the complex world of molecular proteins — where tens of thousands of atoms can comprise a single protein — it has several advantages over traditional computer and solid models.

The new model is mostly transparent and easy to manipulate, which should help researchers more intuitively understand protein structures, positions, and interactions.

The models will also enable researchers to quickly and collaboratively see, touch, and test ideas about molecular interactions and the behavior of proteins.

These insights are keys to innovation in drug design because they help generate discussion about what a particular molecular surface might be like and how a protein is shaped and structured.

“Because my new model is soft, users can deform the model and experience ligand binding or protein-protein association, which has never been possible with other physical molecule models,” said Kawakami. “I believe my model would be an effective discussion tool for the classroom or laboratory to stimulate inspired learning.”

Demonstration of a new molecular model of sperm whale myoglobin. (a) A photograph of the myoglobin model. The rugged molecular surface and the inner main chain structure can be viewed through the silicone resin body. (b) The myoglobin model immersed in a container of water. (c) “Hands-on” simulation of heme binding to myoglobin28. (Credit: Masaru Kawakamia/Review of Scientific Instruments)


A schematic diagram of the fabrication of a soft and transparent physical protein model. (a) 3D data from a main chain (left) and surface (right) of a protein molecule are edited using PDB Viewer software and exported as a VRML file. (b) The structural data are edited using CAD software. The main chain structure is fixed to the surface structure with a mechanical support, and the surface structure is formed like an eggshell. The surface and main chain data are superimposed, and the surface shell is cut into a few pieces, depending on the complexity of the molecular shape. (c) The superimposed data are then printed out using ZPrinter, and each part is hardened by impregnation with super glue or silicone resin. (d) The shell is closed and sealed with a silicone RTV sealant and a transparent silicone resin is then poured into the cavity and cured at 80 ◦C for 2 h. (e) The shell and mechanical supports are released. (f) The silicone resin is thinly applied to the model surface and poured into the holes, which were from the mechanical supports. (g) If necessary, the surface of the model is thinly painted using an airbrush according to physicochemical properties. (Credit: Masaru Kawakami/Review of Scientific Instruments)