2021 CellPAINT Contest

In collaboration with the RCSB Protein Data Bank, we are doing a contest to create images with CellPAINT in two categories:

“Science of Vaccines” and “50 Years of PDB”

MORE INFORMATION AT PDB-101 —  enter by May 1 !!!

We have added several new molecules to CellPAINT2.0 for creating illustrations of mRNA vaccines like the ones being used to fight SARS-CoV-2. You can get a standalone version of the new program “CellPAINT2D_VaccineContest” at SourceForge, or use the web version on the main CellPAINT page.

This page includes information on where to find the new molecules in the program.

You can also add other molecules to CellPAINT using “Create Ingredient” to fetch structures from the PDB. Take a look at the tutorial page to learn how!

New molecules for mRNA vaccine illustrations

mRNA Vaccine Palette:

  1. A membrane that can be used for vaccine particles or vaccines fusing with the cell membrane. Draw these clockwise if you want to create a closed vesicle. If you draw it in the opposite direction, all of the membrane-bound molecules will be on the wrong side.
  2. Two types of PEGylated lipid–an extended one and a compact one.
  3. messenger RNA

Endoplasmic Reticulum Palette:

  1. A membrane for the ER. Draw this clockwise in order to have all the membrane-bound proteins on the proper side.
  2. Ribosome with signal recognition particle. See below for instructions about changing colors.
  3. Ribosome bound to membrane translocon. See below for instructions about changing colors.
  4. Unstructured protein, which can be used for the nascent protein coming from the ribosome.
  5. Spike protein monomers, oriented so that they will face inside the ER.
  6. Spike protein trimers

Coronavirus Palette:

  1. Spike protein trimers, which will orient correctly on the cell surface.

Human Cell Palette:

  1. Signal recognition particle

The mRNA Vaccine Palette also includes several lipids that may be used if you want to dive into the details of the vaccine particle. (A) Compact and (B) extended conformations of PEGylated lipid may be added to the surface of vesicles.  (C) Ionizable lipids and (D) cholesterol — for both of these, there are three brushes: one draws it on the outside leaflet of the membrane, one draws it in the inner leaflet, and one treats it as a soluble molecule. There are many conceptions for the actual structure of these vaccine particles, so feel free to explore your hypotheses about it.

We are currently experimenting with ways to allow several colors in a single molecule. The two ribosome brushes in the mRNA Vaccine palette can currently have two colors. You can control which color you’re changing with the “Color Chain” checkbox. If it is not checked, the sliders will change the color of the ribosome, if it is checked, the sliders will change the color of the translocon or SRP.