3D-Printed Enzyme – Proof of Concept

Introduction

I had theorized in my previous post that it was possible to easily 3D print an enzyme structure given a Protein Data Bank (PBD) file. Now, a month and many iterations later, I was finally able to print restriction enzyme Fok1 [PDB ID:1fok], bound to a strand of DNA. I had not anticipated the problems of 3D-printing such a complex structure when I first started this expedition, I now have a very robust and simple way of printing these structures.

Result

The printed model, Fok1 [PDB ID:1fok], is in Sculpteo’s white plastic, and is approximately 4.8cm x 4.0cm x 4.3cm. It has a slight coarse and grainy texture, but still retains tiny details like arrowheads on the model. One factor that surprised me is the model’s flexibility. Whereas my previous printed models were rigid, this printed protein strand has spring like behavior in certain areas and can withstand some serious stretching.

Method Summary

My goal was to optimize simplicity in the PDB-to-3D-model methodology. This means, I wanted minimal manual adjustment of vertices to the PDB render. On top of that, I wanted to print a ribbon style model, which was more challenging to print than a mesh based model, due to its thin components.

I started by rendering the Fok1 [PBD ID:1fok] in Chimera. Chimera conveniently can export the model in a STL format, perfect for 3D printing. Before exporting, I thickened the model to meet minimum thinness requirements. Finally, I uploaded the STL to Sculpteo to print.

Method Details

1. Import PBD file into Chimera, via either a fetching of the file from PDB or a custom PDB file.
2. Select the chains containing DNA or substrate and hide the atom and bond models. The atom and bond models typically are too thin to be printed, without more finessing.

1. Select the remaining ribbon model and adjust the ribbon model attributes in Tools>Depiction>Ribbon Style Editor. The ribbon model, as is, is too thin to be printed. All attributes need to be thickened. The following is the setting I used for my Fok1 model.

1. Export the scene to an STL and then upload the model to Sculpteo for printing. Sculpteo offers a beautiful, almost-real-time printability check of the model, for fast design feedback turnaround times.

Caveats

The major problems I encountered was having structures too thin to be printed. I initially tried to print with Shapeways. However, the first ~10 iterations didn’t even pass their manual checking stage. Printing a wirely protein structure is definitely pushing the boundaries of 3D printing capabilities. I eventually decided to switch to Sculpteo because of their significantly faster turnaround times. Sculpteo was awesome and definitely delivered.