MSU students create hands-on experience with 3-D protein models

  • Mar 15, 2016
  • Faculty & Staff, Research, Students, Biochemistry

Three MSU Ph.D. students display their three-dimensional protein models

Three MSU Ph.D. students display their three-dimensional protein models, which were printed using a 3-D printer. Left to right, Tyler Walter; Leslie Kuhn, BMB professor; Gracielou Klinger; and Daniel Lybrand.

Graduate students in Michigan State University’s 2015 Biochemistry 803/805–Introduction to Protein Structure, Design, and Mechanism course were able to see—and even hold—the protein molecules they were studying. That’s because the molecules were printed out as 3-D objects.

The students learned how to use PyMOL, a molecular graphics software, to design a three-dimensional representation of a specific protein interaction, using structural data from the Protein Data Bank. The three-dimensional designs were then converted into 3-D models.

“This was the first time we did this,” said Leslie Kuhn, professor in the MSU College of Natural Science’s Department of Biochemistry and Molecular Biology. “We wanted to give students a chance to choose a protein system in which they could show some aspect of molecular recognition—that is, how a protein selects, via its shape and its chemistry, what its binding partners in the cell will be.”

Two different materials were used to produce the various 3-D models. One is a sand-like material that can be produced in many colors, but is somewhat brittle. The second material is a strong, highly flexible plastic, but it can be printed in only one color.

“The technology has some limitations, but I was impressed with how many different molecular representations the students were able to do with the modeling,” said Kuhn, who directs the Protein Anaysis & Design Laboratory at MSU.

“This year we’re focusing more on how to teach students about the molecular modeling software in a way that they can take what they learn and use it in their own research,” Kuhn added. “Next year, we’ll do a new 3-D model design project.”