Infectious Pathogens

by educator, published

Infectious Pathogens by educator Jan 18, 2013
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Virus genomes are protected by an outer protein layer called a capsid or nucleocapsid. Marvel at nature's beauty and the ability to self-assemble structures at the nanometer scale. These models are for teaching and fun! Also see a set of protein domain models www.thingiverse.com/thing:43156


The capsids and nucleocapsids of viruses are only nanometers across and protect the viral genome encased within (http://en.wikipedia.org/wiki/Virus#Structure). The capsids are beautiful examples of icosahedral symmetry and are wonderful examples of self-assembly. Many nanotechnologists are now trying to replicate what nature does so well in order to deliver drugs more effectively among other things. In order to teach about virus structure and self-assembly, I took x-ray crystal structure data and models of various viruses from the VIPER database (.vdb files) (http://viperdb.scripps.edu/) and converted them to .stl files using the program, Chimera (http://www.cgl.ucsf.edu/chimera/). Instructions for converting models are below as well as a short description of each virus. When slicing the viruses, there are some errors; however, the viruses print well. Any suggestions and improvement to the .stl files is appreciated. You can read more about the structures at some of the web links listed at the end.

Dengue virus, database # 1THD
Dengue fever, is an infectious tropical disease caused by the dengue virus and transmitted by mosquito. Symptoms include fever, headache, muscle and joint pains, and a characteristic skin rash that is similar to measles. In a small proportion of cases the disease develops into the life-threatening dengue hemorrhagic fever. Dengue is a positive strand RNA virus that is part of the flavivirus family. Dengue is an enveloped virus meaning it has a nucleocapsid protecting the RNA and the nucleocapsid is surrounded by lipids (hence the name enveloped).

B19, database# 1S58
Parvovirus B19 virus is part of the parvovirus family and causes a childhood rash called fifth disease or erythema infectiosum that is commonly called slapped cheek syndrome. B19 is a non-enveloped virus whose capsid protects a single stranded linear DNA genome.

Human Papilloma virus 16, database# 1DZL
Infection by most papillomaviruses is either asymptomatic or causes small benign tumors, known as papillomas or warts (e.g. human papillomavirus HPV6 or HPV11). Papillomas caused by some types, however, such as human papillomaviruses 16 and 18, carry a risk of becoming cancerous. Human papilloma virus is a non-enveloped, double stranded, circular DNA virus.

Hepatitis B, database # 2g33

Hepatitis B is an infectious inflammatory illness of the liver caused by the hepatitis B virus (HBV). Hepatitis B virus (HBV) is a member of the Hepadnavirus family.The virus particle, (virion) consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein. These virions are 42 nM in diameter. The nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity.

Phi X 174 database number # 1CD3
Phi X 174 is a virus that infects bacteria and was the first DNA-based genome to be sequenced in 1977. This bacteriophage has a [+] circular single-stranded DNA genome. The assembly of the capsid has been successfully done in vitro and is the focus of many studies on self-assembly, drug delivery and nanotechnology.

West Nile virus, database # 2OF6
West Nile virus (WNV) is a mosquito-borne flavivirus and is found in temperate and tropical regions of the world. Image reconstructions and cryoelectron microscopy reveal a 45–50 nm nucleocapsid covered with a host-dervived membrane. This structure is similar to the dengue fever virus. West Nile is a positive strand RNA virus that is part of the Flavivirus family. West Nile is an enveloped virus meaning it has a nucleocapsid protecting the RNA and the nucleocapsid is surrounded by lipids (hence the name enveloped).

Adenovirus, database # 2C6S
Adenoviruses are medium-sized (90–100 nm), non-enveloped (without an outer lipid bilayer) icosahedral viruses with a double-stranded linear DNA genome. Adenoviruses are responsible for 5–10% of upper respiratory infections in children, and many infections in adults as well. The adenovirus is being tested as a gene therapy delivery vehicle as well as a treatment for a variety of cancers.

Convert vdb to stl file

Go to the virus structural database at http://viperdb.scripps.edu/

Download the virus structure of your choice as a .vdb file

Open the .vdb (VIPERdb) file in chimera http://www.cgl.ucsf.edu/chimera/

In order to print a virus capsid you shouldn't use the "multiscale" surfaces that appear when you open the VIPERdb file. Make a single surface for the whole virus by creating a simulated density map. Show the command line with Chimera menu Favorites / Command Line... and use

molmap #0 10 sym i222

after opening your virus model. The molmap command will make a simulated density map and show a contour surface for that map. The resolution in the example is 10 Angstroms and the protein model #0 is replicated with icosahedral symmetry (with the VIPERdb coordinate system). Switch the volume step size to 1 in the volume dialog (or use command volume #0 step 1) to see the surface at full resolution. (thank you Tom Goddard for suggestions on using chimera)

Save as stl file

Open in replicator G

Scale to appropriate size (many times very small and unseeable!). This can also make the .stl file VERY big. I have no idea why.

Upload to cloud.nettfabb.com to fix stl. Sometimes the .stl is unfixable. I do not know why.

Slice and print! During slicing, many errors do occur. However, the final model is quite printable and useable.

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Really nice work!
Any chance up putting up Zika?

Your instructions were so awesome, thank you! Used it to make a PRD1 phage :)

Thanks!!! Excellent!!

Curious to know if you tried to print with or without supports. I wonder what would happen by printing the hollow ones with supports. Will it then be possible to remove the supports from the inside of the virus?

Awesome! I'm printing the adenovirus surface and plan on using it when I pitch a theoretical gene therapy for neurodegenerative disease :D.

Just thought you should know, I work in an HPV serology lab so I printed out HPV 16 and brought it to work. Everyone loved it! Thank you for sharing these.

Just wanted to let you know I made a copy of the HepB Core and gave it to a professor at Stanford who told me the other day he uses it with his students... This is great stuff!

Very cool stuff! Thanks and keep it up!