The goal of this protocol is to create and 3D print structurally accurate biomolecular models using an affordable desktop 3D printer. This method is used to design 3D printable models of biomolecules, starting from the structural data and fabricate them using low-cost 3D printers. 3D printing the physical models facilitates interaction and discussion of molecular structure and function.
Interaction with the models provides an intuitive perception that greatly exceeds what is possible using a computer. To begin, first fetch the PDB structure file of the molecule of interest by entering the PDB code in UCSF Chimera. Next, thicken the diameter of the ribbon, so that it can be successfully printed.
Use the ribbon style editor menu under Tools and Depiction. Under the Scaling tab, change the height of every item to at least 0.7, according to the structure type. To obtain a sturdier model, display the hydrogen bonds.
Then change the PseudoBond style to stick, and change the radius to 0.6. Now, export the displayed representation as a 3D file. Select STL as the file type, and save the model.
Further processing is still required before printing. Repair is needed due to object overlap, which is very common in complex models. To correct this, open Autodesk NetFabb and import the STL file that was exported from Chimera.
In NetFabb, open the Extras menu and select Automatic Part Repair, then select Extended Repair, and wait while the file is processed. For small models, this will take seconds, but for large models it may take minutes. Once the model has been processed, save the result.
Right-click on the model and select Export Part and As STL, or use Project and Export Project as STL. The program adds repaired to the filename to distinguish it from the original file. The STL model can be automatically oriented using Autodesk Meshmixer, or manually oriented in simplified 3D.
Optimal orientation will lead to less part usage, and reduce failure chances when printing. For automatic orientation, open Meshmixer and import the repaired STL file. Then, select Analysis and Orientation.
Adjust the Strength Weight value to 100. Adjust the Support Volume Weight value to zero. Adjust the Support Area Weight to zero, and then click Update.
The model is then rotated to minimize the number of overhangs. To accept the resulting orientation, open the dropdown menu and export the result as a binary STL file. Open the slicing software and select the STL file.
Double-click on the model and enter the scaling factor. The default is 10 million, meaning one centimeter in the printed model is equivalent to a nanometer in the molecule. Next, scale the ribbons and stick representations to at least 300%so that they will be large enough to print.
Surfaces can be scaled as desired. Adjust the orientation of the model if desired, and then, generate the support structures for the model. Click the Support icon and select normal supports.
Specify a maximum overhang angle of 50 degrees, and pillar resolution suitable to the size of the features of your model, such as three millimeters in this example. Then click Generate Automatic Supports. These structures will hold separate and overhanging parts of the model in place during printing.
Next, edit the automatically generated supports to add missing supports and remove superfluous ones. First, use the Add Supports tool to ensure all of the overhanging features are well-supported, and no structures hang in mid-air. Second, use the Remove Supports tool to delete supports and internal cavities, such as the inside of alpha helices or binding pockets.
Now, add a printing process to prepare the model G-code for a specific printer and printing material. Edit the printing process settings as follows. Select the type of filament you will print with.
PLA is recommended. Then, add a skirt to ensure good initial flow of the material. Then, add a raft to secure the model and supports.
Use an infill of 50%for ribbon models and 20%for surface models. There are numerous other parameters that can be tuned for printing success. Consult the program documentation on the website for details.
Next, click Prepare to Print, and select the appropriate process. This will slice the model into layers, and construct a path for the printer nozzle to follow. Problems with the model that will cause a print to fail can often be spotted in the trajectory printout.
It's important to always inspect the generated trajectory, and, if necessary, rework your model. Finally, inspect the G-code trajectory for errors. Look for the absence of supports under overhangs, tall isolated structures that could be knocked over, undesired cavities, or areas that are too thin to print.
If the print trajectory appears satisfactory, save it as a G-code file. Otherwise, edit the model, orientation, or process settings, and try again. To begin, prepare the printer by loading the filament and ensuring that the bed is level.
Next, run the G-Code on the printer, either streaming it from a computer or from an SD card attached to the printer. Watch the print until the first layer has been successfully completed, and abort the process if there are any errors. Desktop 3D printers are prone to failure, and this can be discouraging for new users.
We have listed common problems and solutions in the appendix, and encourage the reader to utilize online resources to troubleshoot their printer. When the print is finished, let the model cool to room temperature, and then detach it from the build plate by gently pulling it sideways. If the raft adheres strongly to the build plate, carefully pry it off using a sharp edge.
Next, remove the support structures from the model using standard pliers. Many can be removed with standard pliers, and those that are difficult to reach or are connected to delicate structures can be removed using cutting pliers. A ribbon model of ubiquitin reveals the structure of the alpha helices and beta sheets, and the location of hydrogen bonds.
By comparison, a surface model of ubiquitin could also be made. A model of an alpha helix with atomic representation shows how amino acid residues connect with hydrogen bonds to form a helical secondary structure. A histone H3 protein model can be made in ribbon and surface representations.
These models reveal how multiple histones may interact with each other to form larger complexes. An octamer of histone proteins forms the core of a nucleosome, revealing the quaternary structure of histone subunits. The DNA that winds around the histone octamer, forming the nucleosome core particle, is printed with flexible filament, enabling it to be removed, twisted and coiled.
Lastly, a dinucleosome surface model shows how nucleosome core particles form as beads on a string. Multiple dinucleosomes may be stacked to reveal the helical structure of the chromatin fiber. Physical models of biomolecules have advantages over digital models.
They can be manipulated, pointed to, or passed between researchers and students. These actions can improve the communication of ideas, or help point out features of the molecule. Because molecular models have complex 3D geometry, they can be challenging to print, and may require some trial and error.
Our protocol will help the user overcome some of the most common issues with the process. By following this protocol, you'll be able to create a digital 3D model of a biomolecule, process the 3D file, and create a physical model using a fused filament fabrication 3D printer.
