Early this semester, my research mentor Dr. Swigonova explained to me the process for creating the 3D digital protein model that would eventually be 3D printed for use in teaching settings. I don’t consider myself the most competent user of technology but I was pretty confident that I could manage this new software, called Chimera. The next several weeks were spent in what can best be described as a prolonged battle with an unresponsive piece of software that resisted many of my initial attempts to conquer it. This is nothing against the program – now that I’ve figured it out, it’s incredible – but I underestimated the learning curve a bit. The lowest point was when I spent a good two hours painstakingly creating artificial bonds in the software that would act as stabilizing structures in the printed model and then, in a burst of satisfaction at having finally completed it, quickly exited out of the software without saving it.  After a brief period of despair, I reopened the model – and it only took me an hour the second time!

The lesson here is not a platitude about failure, but about an unanticipated challenge for me in the research process which was acclimating to technology that I was unfamiliar with before. Between biology and chemistry labs and plenty of experience in humanities research, I thought I would be well-prepared for this new area of research but I quickly discovered that 3D modelling was not in my already established toolkit. It was a good reminder for me to be prepared, when embarking on any new research project, to learn any number of new skills. It took about a month of working with the software to get confident with it and get to the point where I could focus more on the research itself rather than wrangling with my computer. Now, I can work with it mostly without deleting everything – though I am by no means an expert – and I’m excited to have a new skill for application in future research projects.

After all this talk about the software, I have to show you something for it. Funnily enough, the preparation of the model in digital form is probably the least time-consuming part of the process. To the right, you can see what the model looks like in its digital form – this is a ribbon model of the glucose transporter (GLUT) in its open conformation. You can see the glucose bonded inside – one of the things we were interested in showing is the bonding complex, which is why the amino acid side chains are extended here and shown bonded to the sugar in black. The yellow bonds are artificial structural supports, included to make the physical model more stable for handling. 

Below on the left is what the molecule looks like right after it is printed – pretty different, right? Most of this is scaffolding, which allows us to print the complicated helices and hydrogen bonds. Careful clipping and scraping allows us to extricate the structure from its plastic mesh, and we get the much neater looking product shown to the right

After this, it’s time to paint the model to make it look a bit more like the digital representation, with color coded bonds and atoms. We start with a layer of spray paint, and then move on to the painstaking process of hand-painting each hydrogen bond and each atom of the extended amino acid chains. In addition to the ribbon models, we also make surface models – to the left is the spray-painted surface model with the bound glucose painted black.

I haven’t quite finished the detailed painting of the ribbon model yet and will be continuing to work on it for the last few weeks of the semester, and I can’t wait to finally see the finished product realized! I’m also looking forward to continuing to work with Dr. Swigonova next semester and starting construction of a model of a sodium-glucose linked transporter (SGLT) to go along with the GLUT model as they are both major proteins involved in cellular uptake of glucose.