Chemistry Pre-Med Student Prints 3D Models of Protein Molecule Structures

Posted on 10/17/2016 7:32:15 PM

This summer, Lewis Dominguez, a junior chemistry pre-med student working with professor Jana Villemain, set out to learn what it takes to generate 3D-printed physical models of protein molecules from 3D digital model files. 

Protein molecules, complex macromolecules composed of linked amino acids, are known as the workhorses of the cell and have diverse jobs from catalyzing reactions to regulating gene expression related to their 3D structure.

They are much too small to observe their structural detail, even with the most powerful microscopes. Therefore, 3D digital models using computer software are commonly used to visualize and study proteins with known structures determined by X-ray crystallography and NMR (nuclear magnetic resonance) techniques. 

Lewis Dominguez at the 3D printerWith the advent of 3D printing, the information contained in 3D digital model files can now be converted to physical models composed of plastic via a 3D printer. Starting with a MakerBot-Replicator-2 3D printer on loan from the IUP Math Department, Lewis undertook to learn the nuts and bolts of 3D printing making a simple object using the printer. Then, he set out to print models of interesting protein molecule structures that provide examples of protein structural elements commonly studied in biochemistry or biochemistry-related courses in biology and chemistry.

3D model files of proteins highlighted on the Protein Databank’s Molecule of the Month and many more are readily available for download on the publicly available National Institutes of Health 3D print exchange, complete with linked literature references describing the protein’s 3D structure and biochemical properties.

So far, Lewis has generated several 3D models displaying different structural aspects of a cellular signaling protein complexed with caffeine, known as a G-protein Coupled Receptor. These GPCR receptors have been long-time targets of many current pharmaceutical drugs, although their 3D structure was first determined in 2008 and was awarded a Nobel prize.

“3D protein structure models such as these (have) the power to connect biochemical concepts of structure and function with hands-on examination of the protein structure by students” said Villemain. The effects of changes in the amino acid sequence on the protein structure can be viewed by comparing two protein models side-by-side. The effects can be further correlated to changes in the protein’s function. Lewis is also working with Professor Charles Lake to generate structures on a more advanced printer in the Department of Chemistry, the MakerBot 5th generation, which is also equipped with a digitizer to convert the 3D object shapes into a digital file for 3D printing.

Now that 3D printers are more widely accessible to undergraduate students in the life sciences, students are more capable of generating a 3D molecule model in conjunction with a class or research project for themselves. Free, well-established resources, such as the NIH Print Exchange and modeling software, are available to work with the information required for 3D printing a protein or biomolecule model.

Lewis intends to share what he has learned regarding 3D printing proteins and other biomolecules by presenting an overview of the process, titled “Plastic Proteins: Practical Guide to 3D Printing of Protein and other Biological Model Structures for Undergraduates,” in November at the PA Stem conference to be held at Millersville University. Professor Villemain and Lewis also have plans to offer a workshop on 3D printing proteins for interested students in the life sciences at IUP in the near future.  

Department of Chemistry