Introduction: Modeling and 3D Printing of a ΦX174 Bacteriophage Capsid

By Acheron
About: My name is Aaron Berliner. I studied bioengineering, control theory, optimization theory, synthetic biology, systems biology, nanotechnology, artificial neural networks, and some microelectromechanical system …

Backstory

In 2014, I worked with Autodesk to design, build, and test a synthetic ΦX174 Bacteriophage by transforming synthesized DNA into an E. coli cell; and nobody cared. My boss, Andrew Hessel, realized that many people had a difficult time understanding what viruses were and how they could be used. And more importantly, the concept of building a virus from a digital file was alien to many non-biologists. In what can only be described a Hail Mary, I converted a protein model of a ΦX174 Bacteriophage capsid into a 3D printable geometry and printed the file on one of Autodesk's Objet Connex 500 printers in Vero Clear. That's how I spent my Saturdays. At first, I just wanted to hold my work in my hands so I could show people and seem cool. When I showed Andrew Hessel, he realized he could use the process of 3D printing the model as an analogue for how viruses could be designed and synthesized and tested. And more importantly, he could hand someone a model and say he gave them a virus.

As of November 2015, the ΦX174 Bacteriophage model has been printed well over 200 times for multiple people and organizations including the San Francisco Exploratorium, space hero Buzz Aldrin, Virgin's Richard Branson, hoards of student tour groups and Autodesk executives alike, and even California Lieutenant Governor and former Mayor of San Francisco Gavin Newsom. It can be seen in magazine articles in Bloomberg and Wired and even in Andrew Hessel's video on the cancer-killing viruses of the future. Amazingly, the print has even been acquired for exhibition by the MoMA In New York City and MODA in Atlanta. I create this instructable so that others can print their own copy of the virus (partially so I can stop making them myself) and use it as an instrument to help illustrate the process for how biology can be created digitally, whether as proteins or plastic.

Summary

The products of virology, although crucial in molecular biology and medicine, can be esoteric and difficult to appreciate. In order to provide a better way for the populace to understand the objects the objects of study in virology, a model of the PhiX174 virus was created, modified, and 3D printed.

ΦX174 Bacteriophage

Enterobacteria phage PhiX174 (< Microvirus < Microviridae) is a Group II single stranded DNA virus that primarily infects Enterobacteria such as E. coli. The PhiX174 capsid is non-enveloped and round with a T=1 icosahedral symmetry. The capsid of ~ 30 nm in diameter consists of 12 pentagonal trumpet-shaped pentomers. The virion is composed of 60 copies each of the F, G, and J proteins, and 12 copies of the H protein. The PhiX174 (also ΦX174) bacteriophage was the first DNA-based genome to be sequenced in 1977 and synthesized in 2003. The virus has been made synthetically at Autodesk, and now the viral capsid can be 3D printed.

Step 1: Modeling

A360

The model was assembled using the Molecular Maya plugin for Autodesk Maya 2015. The PDB entry 1CD3 contains structural information on the 'procapsid of bacteriophage PhiX174'. Seven distinct proteins form the asymmetric unit of this virus, and shown in surface representation. The biological assembly data was also loaded and applied to form the icosahedral symmetry of the capsid, instancing 60 copies of the asymmetric units. Resulting .OBJ/.FBX files were exported on the selected assembly from Maya. The .FBX file can be viewed in A360.

Autodesk Molecular Viewer

The Autodesk Molecular Viewer can also be used to visualize the Phi X174 capsid by simply entering 1CD3 into the 'Import Model from PDB' portal.

Step 2: 3D Printing Preprocessing

The .OBJ file was decomposed into 7 chains. Each chain was exported as an .STL file. No decimation was used on the models, and thus the files are very large (~200MB .OBJ, ~60 MB .FBX, ~131 MB .STL set).

Attachments

Step 3: 3D Printing

The .STL files were imported into the Stratasys Objet Connex500 software together as an assembly. The assembly was scaled in the x dimension to 30 mm which scales the nearly circular model to a diameter of 30 mm. The PhiX174 capsid is ~30 nm in diameter, and thus the PhiX174 model is a 10^6 scale model. Each STL in the PhiX174 assembly was assigned to a specific color created from the mixing profile between Vero White and Vero Black materials:

<ol><li>chain_1_surface chain_1 model_1 chain_1_surface chain_1 model_2 <li>Vero Blackmodel_1 model_2 model_3 model_4 model_5 model_6 model_7<li>mod.000, DM_8330_Gray35model_1 model_2 model_3 model_4 model_5 model_6 model_7<li>mod.001, DM_8320_Gray25model_1 model_2 model_3 model_4 model_5 model_6 model_7<li>mod.002, DM_8310_Gray15model_1 model_2 model_3 model_4 model_5 model_6 model_7 mod.003, Vero<li>Whitemodel_1 model_2 model_3 model_4 model_5 model_6 model_7 mod.004, Vero Blackmodel_1<li>model_2 model_3 model_4 model_5 model_6 model_7 model_8, Vero Black</ol>

There exist only 5 colors in the Vero Black/White set. Each assembly model has an approximate material usage of

  • 9 gram Vero Black
  • 12 gram Vero White
  • 22 gram Support

The model was copied to produce 20 models/build tray for mass production. The 20 models/build tray has an approximate material usage of

  • 121 gram Vero Black
  • 186 gram Vero White
  • 328 gram Support

At a cost of ($0.41/gram of material and $0.15/gram of support)*1.15, The resulting cost of each model is $13.70. The resulting cost of each build tray is $201.33. The total cost for 100 models made with 5 trays is $1006.65 which is comparable to Shapeways for a single color material print.

The printing time/tray of 20 models was ~6 hours. The printed models were cleaned by spraying with high pressure water.