You can 3D Print Your Own Protein! Here's One Way How
3D PRINT SHOP at EMORY UNIVERSITY
Location: 2nd floor, Cox Hall, the computer tech lab
Directions: Go up the stairs to Cox Hall, to the floor above the cafeteria. There will be a sign for the computer / tech lab. Upon entering the second floor, it’s the first door on your left. After entering the center, go all the way to the back past the desks / computers and take a right. You will run into the 3D print shop.
Printers: Anyone can print objects on one of the five 3D printers available: 4 PLA plastic printers (two Taz, a Makerbot and one other) and 1 resin printer. PLA is a biodegradable plastic. Resin can be printed in finer detail than PLA. All you need is a .stl file. I’ll go over where to get those in the next sections.
Printing an object and cleaning up the model: When printing an object, the printer prints supports underneath parts of the object that are in mid-air. These supports must be broken off and removed after printing with clippers / tweezers. The staff in the print-shop will help you orient your protein to have minimal supports. Some supports may be printed in the interior of the object, if it is a hollow ribbon structure. Try to remove as many of these as you can. I recommending printing on the PLA printers, as removing resin supports is more challenging. For a video of the GFP ribbon model being printed, see this video here. Each PLA print costs $2.00, regardless of size, and each resin print costs $4.00.
Chose a protein structure that you want to 3D print from one of the following sources:
a. NIH 3D Print Exchange here
b. Thing-i-verse, 3D print library, here
c. Protein Databank (PDB) here
Using one of these sources, chose a protein structure – not a small molecule – try to choose a protein that is not gigantic and is a monomer. The NIH 3D print exchange and Thing-i-verse give downloads of their objects directly as .stl files, however, their database is limited. If you are interested in a protein that is not in these databases, you can acquire it from the Protein Databank, which has the structures of all known proteins. The Protein Databank structures are downloadable as .pdb files, which can be converted into .stl files.
Specific directions from each of these sources is given below.
CHOOSING A PROTEIN: TYPE OF PRINT, SURFACE OR RIBBONS
It is up to you whether you want to choose a surface model or a ribbon model to print – depending on what aspect of the protein you want to highlight and whether or not that particular aspect is visible in either kind of model. Both surface and ribbon models can be downloaded from the NIH and Thing-i-verse. However, if you want to do ribbon models, see extra note on ribbons below.
Note on Ribbon Models: Ribbon models are more difficult to print, as they are more delicate. In order to print a ribbon model, I recommend using the ribbons format of the GFP model that I printed from the NIH database here. However, there is only one of these types of ribbons on NIH. The other types of ribbons available I have not tested. However, there is a method to convert any .pdb file into the thicker GFP ribbons, if you want to do that, which I’ve listed below.
SOURCE 1-2: NIH 3D PRINT EXCHANGE and THING-I-VERSE
From the home page of the NIH 3D print exchange, hit “Discover” and you’ll get to their library of 3D structures or click the link given, which takes you to this page.
Click on a model you’re interested in. Hitting “download” under the photo will give you a wide range of options. Download the .stl format of the type of model you want.
One can search Thing-i-verse and download objects in .stl format in a similar manner. Just click the item, and “download this thing!” to get your .stl file.
SOURCE 3: PROTEIN DATABANK, HOW TO CONVERT .PDB file into .STL (RIBBONS / SURFACE)
Downloading from the Protein Databank
The majority of you may need to choose protein from the Protein Databank. For best success, chose smaller proteins under 80 kDa. After finding your protein of interest, click the title, click “download files” and download PDB File (Text). NOTE: Make sure that you download the structure of a protein monomer. Often times, when these proteins are crystallized, they are crystallized as two or three proteins together. Such structures are more difficult to build models out of. Finding a proper monomer structure may take some trial and error.
Converting your .pdb file into ribbons that can be printed in .STL format
You’ll need to download UCSF Chimera here. Open your .pdb file. The thicknesses (and heights) of ribbon geometry components can be easily adjusted in Chimera by clicking Tools > Depiction > Ribbon Style Editor. Making the "height" and the arrows, which interconnect the various parts thicker and more robust, will ensure it's easier to print and won't fall apart when removing support structures (see screenshots).
To convert your .pdb file into a surface model .stl you’ll need to download 2 programs: Pymol and Meshlab.
Pymol: Download the .pdb file from the Protein Databank (listed above). Download the program Pymol here. Download “from students and educators” and fill out the forms for download. Once downloaded, open your .pdb file.
Meshlab: Meshlab can be downloaded from the site here for either Mac or Windows.
Getting a surface model: Open Pymol. Open your .pdb file. In the right-hand window, click the “S” (show) and click “surface.” Wait while it loads the surface format. It takes a few minutes.
Open the VRML 2 file in Meshlab by going into File --> Import Mesh. Save the file as a .stl by hitting File --> Export Mesh As --> hit the drop down menu and chose .STL.
You now have a .STL surface model!
PRINTING THE MODEL AT THE PRINT SHOP
On the day of your time slot, arrive at the print shop (see direction above) with your .STL file on a flash drive. They will set you up on a printer, have you sign a waiver so you can use the tools to trim the supports after printing, and have you pay a $2.00 print fee on your Eagle Card for PLA prints. Make sure you have money on your Eagle Card! Money can be added to it on OPUS.
Scale: Request the 3D printing staff to scale your model to be 8-10 cm on one side, either tall or wide, so that it is a decent size to be handled.
Pick up your protein the following day and trim the supports. If the print fails, you will not be charged.