Tag Archives: chemistry

Implications of Dual Color Printing on Virology

By: Harsimran Kalsi

What are viruses and why are they important?

Virology is a field of science that is principally concerned with studying viruses. Viruses are infective biological agents that only reproduce inside the cells of a living host. Viruses are too small to be observed through light microscopy, and typically consist of an intricate protein coat (also known as the “capsid”) which surrounds and contains a strand of nucleic acid (genetic material that encodes the info a virus needs to reproduce).

Viruses are important because they cause some of the most lethal diseases in the world. HIV, Ebola, Rabies, Smallpox, and Influenza are just a few of the deadliest viruses in history. The 1918 flu pandemic alone infected over 500 million people and claimed the lives of 3-5% of the world’s population at that time (“The 1918 Influenza Pandemic”). The pathogenicity of viruses isn’t always human specific either, many viruses can target certain species with particular ecological niches. Understanding how viruses function is crucial in combating these prolific pathogens. What’s more, to understand a virus’s functionality, one must understand its fundamental biochemical composition.

How does structure implicate function?

Viruses share many of the defining characteristics of life and even appear to be as alive as cells in some cases (such as the bacteriophage). However, because viruses cannot survive on their own (without a host) and because they have no self-sustaining methods of metabolism to procure and process energy, they are technically considered to be non-living entities.

Viruses are amazing for several reasons. One reason is because they are incredibly advanced works of natural nanotechnology. The complex protein structures that form the capsid and the receptors on the capsid, can bind with each other in interesting ways. An icosahedral virus structure for example (such as Rhinovirus) are composed of twenty equilateral triangular subunits that all geometrically fit together. Furthermore, a complex virus structure (such as a Bacteriophage) appears almost like a spider with various appendages.

Bacteriophage from fineartamerica.com

The Bacteriophage (also known as a “phage” is a good example of a virus whose structure directly implicates function, and whose behavior makes it seem almost alive. Bacteriophages will infect and replicate within Bacteria and Archaea specifically. Phages are incredibly diverse and can be found anywhere that bacteria are found. Phages will use their spider leg like appendages to attach to bacterial cells (“docking” at very specific receptors on the bacterial cell surface), then the phage “injects” its genetic information into the bacteria where it is incorporated and transcribed. The bacterial cell now translates the genetic information into more phages which are now located within the cell. As a result, the bacterial cell itself has become a factory that produces 100,000s of new phages, until it eventually explodes in an extravagant cellular display. These new phages then go on to continue this process known as a lytic cycle.

What if we could know more about how phages bind to receptors on the surface of bacterial cells? What if we knew the structure of the receptor proteins that the phage binds to? Could we perhaps design allosteric inhibitors that prevent phages from binding to more cells? What if we knew more about the structure of the phages delivery system of genetic information? Could we then use a similar method of targeted delivery with artificial therapies to certain cell types?

In comes 3D printing

The benefit to 3D printing virus structures is that it can promote a better understanding of how certain viruses function. This increased understanding can in turn lead to several future innovations.

Virus structures are biochemically determined, broadly speaking, through a process called x-ray crystallography and diffraction. This process allows scientists to visualize an electron density map of protein/virus structures, and thus, construct a computer model of the proteins. The electron density maps allow scientists to construct the amino acid sequence that is the backbone structure of the protein.

These computer models can then be formatted to be 3D printed in many ways. Different printers and materials will lead to different outcomes. Additionally, certain protein subunits or parts may be of interest and can be printed without the rest of the protein structure. As a result, one can highlight things like active sites, receptor binding domains, and cofactors within active sites.

Recently, in collaboration with Dr. Dave Hall and Angela Vanden Elzen, I was able to 3D print a dual color virus structure for Human Papillomavirus (HPV) and Adenovirus. Dual color printing is a unique kind of 3d printing where two colors are incorporated together into a single print. Based on my research, this was the first time that a virus structure was 3d printed in two colors using a 3d printer, under the cost of $100,000. The files were posted onto Thingiverse for the rest of the community to utilize, access them here.

Method of Dual Color Printing Viruses

Initially, to print dual color virus structures, I tried to create my own stl.’s of viruses using a process similar to Dr. Hall’s (as he describes here https://www.thingiverse.com/thing:43144). The key difference, however, was that I was trying to modify the virus structure in Pymol so that different protein subunits could be differentiated from one another. The differentiation at first was through coloring, and the eventual goal was to differentiate them as .stl files. The reasoning seemed pretty straightforward, if we could code into Pymol and differentiate different protein units by color, then theoretically there must be some way we can also code an .stl differentiation into the subunits we colored.

This proved to be a relatively arduous task. Various issues arose as I tried to implement this approach. As a result, I decided to temporarily shift my focus to printing viruses a little more straightforward.

To print the dual color virus structure, I obtained the stl. versions of the viruses from Dr. Hall’s Thingiverse profile (found here). I then loaded the files into a program called, Meshmixer.

 

 

 

 

 

 

 

 

 

 

 

Within Meshmixer, I was able to mark all of the protrusions located on HPV and Adenovirus’s capids, such that they were all separate .stls. Meanwhile, the non-protrusion or “base” part of the capsid remained its own .stl.

 

 

 

 

 

 

 

I used the “Plane Cut” tool in tandem with the “Separate Shells” tool, to differentiate each protrusion and eventually combine each into one cohesive .stl. At this point, I uploaded the combined protrusions .stl to Cura along with the virus base .stl.

 

 

 

 

I then selected (right clicked) the protrusions .stl and specified that it should be printed with the second extruder. After this, selected both files, right clicked, and merged the files.

 

 

 

 

Acknowledgements

This project could not have been completed without the assistance and mentorship of Angela Vanden Elzen and Dr. Dave Hall.

References:

“The 1918 Influenza Pandemic”. Virus.Stanford.Edu, 2018, https://virus.stanford.edu/uda/. Accessed 31 May 2018.

Instrumental Analysis with 3D Printers

Gravitational potential well

For the last 3 years, Professor Deanna Donohoue has included 3D printers with her instrumental analysis chemistry course. In addition to 3D printers, students use other innovative tools such as Arduinos. For the 3D printing portion, students receive training and access to the space and are instructed to print a chemistry-related object from the Journal of Chemical Educationthe NIH 3D print exchange, or a general 3D object repository like Thingiverse.

After completing a print, students answer the following questions:

  • How can we use 3D printers with other instruments or instrument development?
  • Draw a black box model of the 3D printer. Include the computer and steps involved on the computer.
  • Find an application of 3D printing that you think is interesting.
  • Find a scientific publication which uses an instrument made with a 3D printer, or has parts from a 3D printer.

The students are encouraged to think of the printers as they would any other laboratory tool or equipment. This approach as a scientific instrument gives the students beneficial insight and understanding when it comes to troubleshooting. Professor Donohoue described these printers as exciting tools to allow for citizen science as well as creating inexpensive custom tools that allow for previously cost-prohibitive field work.

Carbon nanotube

Cuvette stand

3D Printing and Science: Designing and Printing Biomolecular Models

Adenovirus

Adenovirus from the Infectious Pathogens collection in Lux.

3D Models of viruses, proteins, and other biomolecular objects have many awesome uses. They can be used for conducting research and figuring out problems and processes. They can also be used for teaching students what these objects look like on a magnified scale to obtain an understanding of how they’re made and how they interact.

There are many excellent resources that instruct how to create these models, 3D print them, and use them in classroom settings. Here are a few:

  • The article, “3D Printing of Biomolecular Models for Research and Pedagogy,” by De Veiga Beltrame, et al, describes the benefits of using these models, and provides “a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy.” In addition to the article,  they’ve produced a supplementary video.
  • NIH 3D Print Exchange contains 3D printable files of many, many scientific models and equipment, and tools.
  • UCSF Chimera an Extensible Molecular Modeling System: According to their website, Chimera is a “program for interactive visualization and analysis of molecular structures and related data.” It also includes documentation to help get started.
  • Dr. Dave Hall from Lawrence University’s Biochemistry department has created collections of infectious pathogens and protein domains that can be downloaded and printed, and includes instructions on how to create these models with each collection.
  • Just for fun (and science), the game Foldit not only teaches about protein structures and behaviors, but also provides its players with an opportunity to contribute to scientific research through gameplay!

3D Printing in Classes Winter Term

The makerspace has been getting a lot of use with coursework this term. In addition to the classes below, a handful of students have been working on really interesting independent studies (more details to come). Below are some photos from some of the classes that have used the makerspace equipment this term.

Students in Professor Hall’s Biochemistry class learn about proteins with 3D printed models and the app, PyMol. Photo by Liz Boutelle.

Professor Deanna Donohoue’s Instrumental Analysis class looks at the 3D printed SpecPhone. Photo by Liz Boutelle.

Professor John Shimon’s Photography class made exhibit letters with the electronic cutter. Photo from the LUMakerspace Twitter.

Professor John Shimon’s New Media in Art class learns about the 3D scanner and 3D printer. Photo by Liz Boutelle.