AC biochemistry professor Jim Hebda has been conducting research into alpha-B crystallin proteins. This week he and his summer research students are using the new 3D printer to create physical models of some of these protein structures. Here’s Jim with a brief description:
Alpha-B Crystallin is a protein that helps to prevent the formation of cataracts in the lens of the eye. Formation of dimers (chemical compounds with two structurally similar units–figure A) and higher order structures, or oligomers, containing 24 subunits or more (figure B), has been linked to the stability of the lens and its ability to keep other proteins there from aggregating and forming light scattering particles that lead to cataracts. This physical unit will allow students to better visualize the protein and the locations of the mutations we are engineering.
The 3D printed structure below was printed on the Ultimaker 2+ from the Protein Data Bank (PDB) file 3L1G for the dimer and the cryoelectron microscopy image EMD 1776. for the oligomer.The printed proteins in A and B are approximately 3x1x1 and 2x2x2 inches, respectively. The PDB file was converted to a biological dimer using MakeMultimer.py (watcut.uwaterloo.ca). Both protein structures were converted to a 3D .stl file using Chimera (UCSF), and then prepared for printing using the Ultimaker’s print slicing software, Cura.
In each of the following figures, a computer visualization of the protein structure is on the left, and the 3D printed physical model is on the right.
A. Alpha-B Crystallin Biological Dimer
B. Alpha-B Crystallin Large Oligomer
- Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).
- “UCSF Chimera–a visualization system for exploratory research and analysis.” Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.
- Michael Palmer. MakeMultimer.py. Retrieved Jun 14, 2016 from http://watcut.uwaterloo.ca/tools/makemultimer