Catching Up With David Goodsell

It’s been nine years since I wrote a post about scientific illustrator David Goodsell. That’s too long. Russ Hobbie and I cite his wonderful book The Machinery of Life in the very first section of Intermediate Physics for Medicine and Biology. A physicist wanting to learn more about biology but not wanting to wade into all the biochemical details should simply study Goodsell’s art.

As an emeritus scientist myself, I suppose it’s unfair to complain that one year ago Goodsell retired. I hope he keeps painting on the side as he enjoys the retired life, and continues to share his work with us. Below I present a few of his more recent creations, all free via a creative commons license at the RCSB Protein Data Bank website. At the risk of sounding corny, what a true gift to mankind. And what a true gift to physics students wanting to gain insight into biological size scales and microscopic structures.

Influenza Virus, 2024

I’ll start with the influenza virus, since it’s still flu season here in Michigan. 

Illustration by David S. Goodsell, RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-049 

Cross section through an influenza virion. It is surrounded by a lipid bilayer membrane (light purple) filled with hemagglutinin (purple), neuraminidase (magenta), and a few M2 proteins (small purple proteins). M1 matrix protein (blue) lines the inner side of the membrane. RNA-dependent RNA polymerase (red) is bound to the genomic RNA strands (yellow), which are protected in a helical complex with nucleoprotein (orange).

Flu viruses subtypes are often specified by nomenclature like H3N2, which means it contains type 3 hemagglutinin and type 2 neuraminidase. The flu is an RNA virus, meaning its genetic information is stored in RNA, not DNA, and in this case single-stranded RNA. The RNA-dependent RNA polymerase is an enzyme that catalyzes the replication of the RNA strands. 

The influenza virus has a diameter of about 100 nm (in other words, a tenth of a micron) 

Measles Virus Proteins, 2019

Next up is the measles virus. I show this one because measles is tragically making a comeback in the United States. Not because of some horrible mutation, but because of a hesitancy by many to get the vaccine. Fortunately, Michigan has not suffered much from the measles… yet.

Illustration by David S. Goodsell, RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-018 

Cross section through measles virus. The virus is enveloped by a lipid membrane (light magenta) studded with many hemagglutinin and fusion proteins (outermost proteins in blue), which together bind to human cells and enter them. The viral genome is a strand of RNA (yellow) protected by nucleoproteins (green). RNA-dependent RNA polymerase (bright magenta) copies the RNA once the virus infects a cell, assisted by the largely-disordered phosphoprotein (purple strands connecting the polymerase to the nucleoprotein). Matrix protein (turquoise) helps the virus bud from infected cells. Several human proteins, such as actin and integrins, are also caught in the budding virus (shown in purple). 

This painting was created for the Molecule of the Month on Measles Virus Proteins and recognized by the 2019 FASEB BioArt Awards.

Goodsell bases these paintings on data about the virus structure. If you hang out on social media too much (as I sometimes do) you hear things like “viruses don’t exist.” Apparently people who think that believe all this data is artifact.

The measles virus is roughly two times larger than the influenza virus, having a diameter of about 200 nm. Notice how the light purple lipid bilayer, with a thickness of roughly 4 nm, appears larger in the influenza virus illustration than in the measles illustration. Goodsell strives to get it right.

Bacteriophage T4 Infection, 2023 

In IPMB, Russ and I write that “some viruses, called bacteriophages, infect and destroy bacteria.” They are important in the history of molecular biology and genetics, so I thought you might enjoy seeing how this infection occurs.

Illustration by David S. Goodsell, RCSB Protein Data Bank and Scripps Research. doi: 10.2210/rcsb_pdb/goodsell-gallery-048 

Snapshots from the life cycle of bacteriophage T4. At left, a bacteriophage (red) is injecting its DNA genome (white) into an Escherichia coli cell. At center, the bacteriophage has taken over the cell, destroying the cellular DNA (purple) and forcing the cell to make many new copies of itself. At right, the bacteriophage produces a channel-forming protein (magenta) that pierces the inner cell membrane, allowing lysozyme enzymes to break down the peptidoglycan sheath (fibrous molecules shown in turquoise between the two cellular membranes) that supports the cell. The cell bursts, releasing several hundred new bacteriophages.

Unlike the flu and measles viruses, T4 is a DNA virus; it injects its DNA into bacteria. Note that there is a big difference in the spatial scale of this illustration compared to the previous two. Most viruses are on the order of a tenth of a micron in size, and E. coli bacteria are about a couple microns long. Those tiny red dots are the T4′s icsahedral head (capsid), and is about the same size as the influenza virus shown earlier. Remember, a human cell has a size on the order of 10 microns, which is giant compared even to those bacteria. You could fit about 2000 E. coli into a typical human cell.

SARS-CoV-2 mRNA Vaccine, 2020

Finally, I end with the Covid vaccine. In particular, it’s an mRNA Covid vaccine, as produced by Pfizer or Moderna.

Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-027 

Messenger RNA (mRNA) vaccines developed for the COVID-19 pandemic are composed of long strands of RNA (magenta) that encode the SARS-CoV-2 spike surface glycoprotein enclosed in lipids (blue) that deliver the RNA into cells. Several different types of lipids are used, including familiar lipids, cholesterol, ionizable lipids that interact with RNA, and lipids connected to polyethylene glycol chains (green) that help shield the vaccine from the immune system, lengthening its lifetime following administration. In this idealized illustration, all of the lipids are arranged in a simple circular bilayer that surrounds the mRNA and the PEG strands have both extended and folded conformations. 

It is interesting how much the vaccine looks like a virus. The main difference is that it only contains mRNA that codes for the spike protein—the protein that is recognized by the immune system—and not any other proteins, so it can’t make functional copies of the Covid virus. Eventually, these nanoparticles of vaccine will bind with human cells, the mRNA will enter the cell (but not the cell nucleus), and it will produce spike protein by the cell’s usual translation process. The immune system will recognize the spike protein and develop defenses against it. Elegant, life-saving science at work, beautifully illustrated by David Goodsell.

The size of the nanoparticle is about 100 nm, roughly the same size as the Covid 19 virus itself. Again, you can use that lipid bilayer (whose thickness is essentially a biological constant) as a size scale.
 

I’ll end with a wonderful video about Goodsell and his art. Enjoy!

Inside the Cell: The Molecular Art of David Goodsell

https://www.youtube.com/watch?v=Gk8cNkm5NTk