Physical models of biomolecules can facilitate an understanding of their structure-function for the researcher, aid in communication between researchers, and serve as an educational tool in pedagogical endeavors. Here, we provide detailed guidance for the 3D printing of accurate models of biomolecules using fused filament fabrication desktop 3D printers.
The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology.
A thorough understanding of the function and activity of a biomolecule requires the determination of its three-dimensional (3D) structure. This is routinely achieved using X-ray crystallography, NMR, or electron microscopy. 3D structures can be understood through the perception of models, or accurate objects resembling the structures that they represent1. Historically, the construction of physical 3D models was necessary for investigators to validate, explore, and communicate the resulting hypotheses regarding function of biomolecules. These models, such as Watson-Crick's DNA double helix and Pauling's alpha helix, provided unique insight into structure-function relationships and were pivotal to our early understanding of nucleic acid and protein structure-function2,3,4. Although complex protein and nucleic acid models can be created, the time and cost of building a physical model was eventually outweighed by the relative ease of computer-aided molecular visualization.
The development of 3D printing, also known as additive manufacturing, has again enabled the construction of physical models of biomolecules5. 3D printing is the process of fabricating a physical, 3D object from a digital file through the sequential addition of layers of a material(s). A variety of mechanisms are used in this process. Until recently, the machines used to produce physical models of biomolecules were too expensive to be widely used. However, in the last decade, 3D printing technology, fused filament fabrication (FFF) in particular, has advanced significantly, making it accessible for consumer use6. FFF printers are now commonly available in high schools, libraries, universities, and laboratories. The greater affordability and accessibility of 3D printing technology has made it possible to convert digital 3D biomolecular models into accurate, physical 3D biomolecular models7,8,9. Such models include not only simple representations of single biomolecules, but also complex macromolecular assemblies, such as the ribosome and virus capsid structures. However, the process of printing individual biomolecules and macromolecular assemblies poses several challenges, particularly when using thermoplastic extrusion methods. In particular, representations of biomolecules often have complex geometries that are difficult for printers to produce, and creating and processing digital models that will print successfully requires skill with molecular modelling, 3D modelling, and 3D printer software.
The 3D workflow for printing a biomolecule broadly occurs in four steps: (1) preparing a biomolecular model from its coordinate file for 3D printing; (2) importing the biomolecular model into a "slicing" software to segment the model for the printer and to generate a support structure that will physically prop up the biomolecular model; (3) selecting the correct filament and printing the 3D model; and (4) post-production processing steps, including removing support material from the model (Figures 1 and 2). The first step in this process, computationally manipulating the coordinate file of the biomolecule, is critical. At this stage, the user may build model reinforcements in the form of struts, as well as remove structures that are extraneous to what the user chooses to display. In addition, the choice of representation is made at this stage: whether to display all or part of the biomolecule as a surface representation, ribbons, and/or individual atoms. Once the necessary additions and/or subtractions of content are made and the representation is selected, the structure is saved as a 3D model file. Next, the file is opened in a second software program to convert the model into a 3D print file that can be printed, layer by layer, into a plastic replica of the biomolecule.
The goal of our protocol is to make the fabrication of molecular models accessible to the large numbers of users who have access to FFF printers but not to more expensive 3D printing technologies. Here, we provide a guide for the 3D printing of biomolecules from 3D molecular data, with methods that are optimized for FFF printing. We detail how to maximize the printability of complex biomolecular structures and ensure the simple post-processing of physical models. The properties of several common printing materials or filaments are compared, and recommendations on their use to create flexible prints are provided. Finally, we showcase a series of examples of 3D-printed biomolecular models that demonstrate the use of different molecular representations.
Physical 3D models of biomolecules provide a powerful complement to more common computer-based methods of visualization. The additional properties of a physical 3D representation contribute to the intuitive understanding of biomolecular structure. The construction of physical 3D models of biomolecules can facilitate their study through the use of a medium that takes advantage of well-developed modes of human sensation. 3D models serve not only as an aid to the researcher, but may be used to facilitate pedagogical activities and can increase the achievement of learning outcomes13,14,15. Magnets can be added to plastic models to allow for assembly and disassembly, as shown with a model of polypeptides16. Also, 3D-printed objects can be used in research, both in the manufacturing of lab equipment17, as well as to make microfluidic devices for cells18 and models of crystals19 or neurons20. The manipulation of physical models can serve to promote collaborative discussions that can inspire new insights.
Recent developments in 3D printing technologies and reductions in the cost of printers enables the creation of complex, physical 3D models of biomolecules by an individual user. Although FFF printing technology is more common and less expensive than other methods, it poses a number of limitations. The 3D printing process is time consuming, and mechanical failures do occur. FFF printers can usually only print one material per part, restricting the display of color information. The resolution of models made on FFF printers is low, around 100 µm per layer. We advise the reader to work with these limitations and to develop an approach for their printer and biomolecule(s) of interest. We have presented the processes required for a user to develop a custom 3D representation of their biomolecule of interest that is accurate, informative, and printable. As with any new technology, there are often "growing pains" that must be overcome during its usage. We provide several examples where problems may be encountered in the process of 3D printing biomolecules (see supplement 6).
Finally, through this article, it is our objective to contribute to the growth of a community of users engaged in the 3D printing of biomolecules. Importantly, the NIH has established a database for the public to share 3D models and the methods used to print them10. We strongly encourage participation in this unique resource (see supplement 7 for instructions on how to upload a 3D model print and background information to the NIH 3D Print Exchange).
The authors have nothing to disclose.
The authors are grateful for the support of Deis3D, the Brandeis 3D Printing Club, and members of Brandeis Library/LTS/Makerlab. This work was funded in part by a grant awarded to Pomeranz Krummel by the NSF, Award No. 1157892; an ESIT grant of the BMBF, awarded to the University of Tübingen; and US Federal funds from the National Institutes of Health, Department of Health and Human Services, under Contract No. GS35F0373X. Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera was developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).
<strong>Filament</strong> | |||
PLA 3D Printing Filament (1.0 kg Roll) | Quantum3D Printing | http://quantum3dprinting.com/ | Very good quality PLA filament, strongly recomended |
NinjaFlex Flexible 3D Printing Filament | Ninjatek | https://ninjatek.com/ | High quality flexible filament |
PLA Filaments PrimaValue & PrimaSelect | 3DPrima | http://3dprima.com/ | High quality European supplier of filament |
<strong>Printers</strong> | |||
Prusa I3 MK2 3D Printer | Prusa Research | http://www.prusa3d.com/ | A popular 3D printer |
MakerGear M2 Revision E (M2e) | MakerGear | http://www.makergear.com/ | Closed source, very high quality printer |
Ultimaker 2 | Ultimaker | https://ultimaker.com/ | Very reliable, easy to use printer, highest rating on 3Dhubs.com |
Flashforge Creator Pro | Flashforge | http://www.flashforge-usa.com | Reliable, dual extrusion printer, highest rating on 3Dhubs.com |
<strong>Software</strong> | |||
Simplify3D Slicer | Simplify3D | https://www.simplify3d.com/ | Excellent slicing software |
Netfabb | Autodesk | http://www.autodesk.com/education/free-software/netfabb | Mesh repair software, available free of cost for educational purposes |
Chimera | University of California, San Francisco | https://www.cgl.ucsf.edu/chimera/ | Chimera molecular vizualizer |
Meshmixer | Autodesk | http://www.meshmixer.com/ | Used for orienting models, but has other features |