Diffusion doesn't tell molecules where to go

My latest animation is about the kinetic molecular theory (sounds boring, what does it mean?) and how molecules diffuse, which is one of the core concepts that makes biology possible. There’s a lot of misconceptions around how any why diffusion actually happens, so I took the opportunity to run some computer simulations to visualize what’s going on. I hope you enjoy it and it clarifies some ideas!

On my second channel “Making BIocinematics”, I also uploaded a behind the scenes video explaining a bit how I created the simulations and graphics in the animation. Please subscribe if you’d like to see more!

I’ve decided to present my behind the scenes explanations in video format, rather than on this blog, but I’ll try to post the behind the scenes videos here too, along with references for the videos. Let me know in the YouTube comments what you’d like to see more or less of. This will help me tailor my “making of” videos to the audience that is watching them.

And here are some references for the animation. I’m still pondering better formats. As I’m sure anyone who has done science animation knows, it’s pretty tough to track exactly what references were used, when, and how, but I do think that information is important. More pipeline development required.

References

1. 27.3: The Distribution of Molecular Speeds is Given by the Maxwell-Boltzmann Distribution. Chemistry LibreTexts https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Map%3A_Physical_Chemistry_(McQuarrie_and_Simon)/27%3A_The_Kinetic_Theory_of_Gases/27.3%3A_The_Distribution_of_Molecular_Speeds_is_Given_by_the_Maxwell-Boltzmann_Distribution (2014).

2. Atmosphere of Earth. Wikipedia (2019).

3. Sanger, M. J., Brecheisen, D. M. & Hynek, B. M. Can Computer Animations Affect College Biology Students’ Conceptions about Diffusion & Osmosis? The American Biology Teacher 63, 104–109 (2001).

4. Brown, T. E., LeMay, H. E. & Bursten, B. E. Chemistry: The Central Science. (Pearson, 2005).

5. Earth Fact Sheet. https://nssdc.gsfc.nasa.gov/planetary/factsheet/earthfact.html.

6. David L. Nelson & Michael M. Cox. Lehninger Principles of Biochemistry. (2004).

7. Michell Humidity Calculator. http://www.michell.com/us/calculator/.

8. McKnight, E. J. Student misconceptions of osmosis and diffusion. 103.

9. Edmund A. Marek, Ann M. L. Cavallo & Connie Cruse Cowan. Students’ Misconceptions about Diffusion: How Can They Be Eliminated? The American Biology Teacher 56, 74–77 (1994).

Osteocalcin and Bone Mineral

April's Molecule of the Month at the Protein Data Bank features proteins that bind to biominerals. This is osteocalcin binding to calcium ions, a major component of the calcium-phosphate lattice that makes up hydroxyapatite. Hydroxyapatite is essentially "bone mineral", which helps gives bones strength and rigidity.

The glowing spheres are the calcium ions that osteocalcin is currently binding.

This illustration was the first one where I brought molecular data directly into Houdini, the new 3D application that I have been learning over the past few months. Houdini requires very different workflows from other 3D applications, so learning how to manipulate data for this illustration was interesting and insightful, and I believe processes like this will allow me to create some pretty interesting content in the future.

The green balls here are the important calcium ions. It didn’t take too many nodes to generate this, which is nice.

Houdini can natively read PDB data files like the one I downloaded for osteocalcin, however beyond some helpful data organization, it doesn't have any tools for displaying different molecular representations, so everything from space-filling representations (like the one above) to surface meshes to backbones must be created from scratch. Fortunately Houdini is a great tool for building tools, so I'll be spending some time developing an internal toolkit to show molecules in different visual styles.

A single hydroxyapatite unit: Ca in green, PO4 in yellow/red, and OH in red/white

The crystal data for the bone mineral was in a different format (CIF), so I used UCSF Chimera to export a new PDB file and get the measurements that allowed me to expand a single atomic "cell" to the full crystal field of repeated units.

Thanks for reading,

Stuart

Measles Virus Nucleocapsid

In continuing my illustration series following the Molecule of the Month over at the Protein Data Bank (1), this month I created an image showing the nucleocapsid of the measles virus.

Measles Virus Nucleocapsid - March Molecule of the Month

I'm sure you've heard of measles before. In fact, it seems to be a bit of an ongoing newsworthy item now and again. Measles is caused by a virus that is extremely contagious and can be deadly (2). Fortunately, we have a widely available vaccine (typically administered together with protection against mumps, rubella, and sometimes varicella (3)) to prevent the spread of this illness.

This image doesn't show the entire virus, instead it focuses on the genetic material (RNA in red) and the protein coat (grey) that protects the viral genes from our bodies' natural defenses (4) and also plays a role in helping the virus make copies of itself through transcription and RNA replication (5).

Making of

I spent a long time looking at the proteins amazingly illustrated by David Goodsell on the RCSB website, and wondering how I might create an illustration of my own. I liked the idea of the long repetitive pattern of the nucleocapsid. When I did some more research, I realized that a long flexible tail was omitted from the structural data (4) and the close-up illustration of the nucleocapsid. Working with my recent method (explained in this YouTube tutorial) I decided to append the flexible tail to the existing data and create something (hopefully) striking. Although the tail originates toward the hollow space in the center of the complex, there is evidence that the tail feeds itself back toward the outside (there's also space limitations with stuffing it all inside), resulting in an external coat of long flexible fibers (6,7).

PDB 4UFT

Once I had that piece in place, it became clear that I could create something quite menacing, using visual inspiration from the Sentinels in The Matrix (which is 20 years old this month!) (8). This approach did have some technical and visual challenges to work out.

A bunch of simulations all stacked up

Instead of making 2,516 copies (9) of the nucleoprotein and simulating all of them individually, I decided to simulate a lower number of copies and create static meshes that could be randomly scattered along the length of the nucleocapsid. I figured out the correct transformation offsets I would need to spiral the copies correctly, and used MASH to create a single unit of 37 proteins. Side note: Yes, although I'm learning Houdini, I did use Maya for this illustration because I already know the tools well and I have yet to figure out a pipeline for getting molecular data directly into Houdini.

37 proteins and 222 RNA nucleotides

Then I adjusted the random seed to make several more 37-monomer "units", and sent them over to ZBrush for some retoplogy to reduce the mesh density for all the background units. I also made a lower-resolution RNA spiral unit.

Tip: After retopology of thin meshes, use the 3D Gizmo and ctrl+drag the yellow center to inflate the model closer to the original volume.

Turns out the RNA is all cytosine residues… so not perfectly accurate… shhh!

 Finally, I used MASH again to spread the units along a curve, and posed the whole assembly to my liking.

I believe this is approximately the correct full length of the measles genome, and yes it should fit inside a typical measles capsid. Successful assembly!

I feel like the RNA is the most central and dangerous aspect of this virus, so I wanted all of the color in the image to come from that and have it draw the eye. Because of how the protein binds to the RNA, I didn't get as clean a view of the RNA helix as I was hoping, but I think overall the image works as intended. I hope you like it.

No connection to the Xbox Red Ring of Death

Thanks for reading,

Stuart

References (fancy!):

1.  PDB101: Molecule of the Month: Measles Virus Proteins. RCSB: PDB-101 Available at: http://pdb101.rcsb.org/motm/231. (Accessed: 12th March 2019)

2. Measles. World Health Organization (2018). Available at: https://www.who.int/news-room/fact-sheets/detail/measles. (Accessed: 15th March 2019)

3. MMR Vaccination | What You Should Know | Measles, Mumps, Rubella | CDC. Centers for Disease Control and Prevention (2018). Available at: https://www.cdc.gov/vaccines/vpd/mmr/public/index.html. (Accessed: 15th March 2019)

4. Gutsche, I. et al. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid. Science 348, 704–707 (2015).

5. Jiang, Y., Qin, Y. & Chen, M. Host–Pathogen Interactions in Measles Virus Replication and Anti-Viral Immunity. Viruses 8, (2016).

6. Jensen, M. R. et al. Intrinsic disorder in measles virus nucleocapsids. Proc. Natl. Acad. Sci. U. S. A. 108, 9839–9844 (2011).

7. Desfosses, A., Goret, G., Farias Estrozi, L., Ruigrok, R. W. H. & Gutsche, I. Nucleoprotein-RNA Orientation in the Measles Virus Nucleocapsid by Three-Dimensional Electron Microscopy. J. Virol. 85, 1391–1395 (2011).

8. The Wachowski Brothers. The Matrix. (1999).

9. Lund, G. A., Tyrrell, D. L., Bradley, R. D. & Scraba, D. G. The molecular length of measles virus RNA and the structural organization of measles nucleocapsids. J. Gen. Virol. 65 ( Pt 9), 1535–1542 (1984).

Maya Tutorial - Making of: eIF4E

Today I released a tutorial about how to use Molecular Maya’s Modeling Kit to fill in a missing region from protein data, based on the illustration I shared in my previous post. You can learn more about Molecular Maya and the modeling add-on kit here (https://clarafi.com/tools/mmaya/), but even if you don’t have the kit, there’s still a number of points about structural data and how to understand PDB reports that may be helpful.

The protein up for demonstration here is a eukaryotic translation initiation factor (English: It helps get messenger RNA to the ribosome so proteins can be made). The challenging thing about this protein is it has a long flexible “disordered” tail that is not included in the x-ray crystallography data, because flexible poorly-structured regions just don’t crystallize well, so this is a very typical scenario when trying to use Protein Data Bank (PDB) files.

Fortunately, we do know the amino acid sequence of this tail, and we can use features of the mMaya modeling kit to synthesize and simulate the missing region, allowing us to complete our protein model.

I hope this tutorial is interesting and useful. If you have questions or if you’d like to see a tutorial on another aspect of building molecular models, you can ask me in the YouTube comments, or DM me on Twitter, or any number of ways!

Thanks for reading (and watching)!

Stuart