CellPAINT: Turnkey Illustration of Molecular Cell Biology

Abstract

CellPAINT is an interactive digital tool that allows non-expert users to create illustrations of the molecular structure of cells and viruses. We present a new release with several key enhancements, including the ability to generate custom ingredients from structure information in the Protein Data Bank, and interaction, grouping, and locking functions that streamline the creation of assemblies and illustration of large, complex scenes. An example of CellPAINT as a tool for hypothesis generation in the interpretation of cryoelectron tomograms is presented. CellPAINT is freely available at http://ccsb.scripps.edu/cellpaint.

Keywords: biomolecular assembly; cellular structure; computational biology; cryo-electron tomography; molecular illustration.

Figure 1

Coronavirus illustration. (A) Integrative illustration of SARS-CoV-2 (magenta) fusing with an endosomal membrane (green) and releasing its genomic RNA (purple) into the cytoplasm (blue), created with traditional painting techniques. (B) Selected entries to the 2020 CellPAINT Coronavirus Contest at the RCSB Protein Data Bank.

Figure 2

CellPAINT user interface. Here, the user is illustrating a scene using the default ingredients for a simple eukaryotic cell, blood plasma, and coronavirus. A new ingredient is being created for ACE2 based on atomic coordinates fetched from the Protein Data Bank.

Figure 3

Definition of colliders. (A) 2D polygon collider defined from the image contour. (B) Eigenvector and eigenvalue calculated from the polygon vertices. (C) Main proxy collider chosen from the eigenvector.

Figure 4

Fiber generation and constraints. DNA structure from PDB ID 196D is used as an example. (A) Subunit is aligned by the user along the horizontal axis and a repetition/spacing distance is defined, using sliders in the user interface. (B) Two subunits are separated to illustrate the colliders and the joints in use. A rectangular main collider defines the steric properties of each subunit and is the anchor for the persistence length spring joint (blue). The two circular colliders at each end of the subunit serve as anchors for the hinge joint in magenta and do not see the colliders on the neighboring subunit. The hinge line length (magenta) will be constrained to be zero, the spring line length (blue) is always proportional to the spacing times N, the neighbors index defining the number of segments. (C) The DNA fiber with proper spacing, illustrating the second role of the circle collider (arrow) that fills the gap for acute angle between subunit. (D) Circular DNA showing the role of the spring joints in maintaining a persistence length.

Figure 5

Colliders in CellPAINT. (A) Definition of membrane thickness and surface offset (displacement along the Y-axis between the center of the protein and the center of the membrane). (B) The main collider of a surface ingredient in red. (C) The membrane collider of the same ingredient in yellow. We define an exterior collider box made of the contour points at the exterior side of the membrane, and an interior collider box made of the contour points at the interior side of the membrane. Two additional circle colliders further anchor the railing system that will constrain the rigid body to remain embedded the membrane. (D) Examples of colliders illustrating the different types of collision, as displayed within the Unity editor with protein-protein collision in red, membrane-protein collision in yellow and membrane-membrane collision in green.

Figure 6

Lock option and collider simplification. (A) A coronavirus drawn using the default ingredients in CellPAINT (left), with an overlay that shows all of the colliders used during brushing (right). (B) After locking the ingredients in the virus, a simple 2D polygon collider is calculated, which then excludes other ingredients in the scene, such as the surrounding blood plasma proteins shown here.

Figure 7

Interactive hypothesis testing with cryo-ET sections. (A) Mitochondrion with cristae, endoplasmic reticulum and actin bundle. Densities circled in red are examples of densities interpreted using CellPAINT. (B) Interpretation with mitochondrial outer membrane in purple, inner membrane in pink and ER in navy blue. ATP synthase in tan, mitochondrial ribosome in plum, cytochrome c in hot pink, soluble cytoplasmic ribosomes in orange, membrane-bound ribosomes in light blue, and actin in yellow. (C) Mitochondrion adjacent to endoplasmic reticulum. (D) Interpretation with SAM50 complex in light green, TOM40 complex in aquamarine, and TIM22 complex in dark green. (E) Mitochondrion-mitochondrion interface. Brackets in red indicate measured distances between OMMs of the observed mitochondrial interface, where the furthest distance is 34 nm (left bracket) and closest distance is 18 nm (right bracket). (F) Interpretation with MFN1/2 “extended” in red and “folded” in salmon. The break in the lower membrane is an example of a region where the membrane is not perpendicular to the plane of the slice. Scale bars 100 nm.

Figure 8

Images of coronavirus biology created using “Group” and “Lock.” (A) Coronavirus particles budding into an endosome, with cytoplasm at top in blue. (B) Idealized conception of coronavirus mRNA vaccine, with spike-coding mRNA in purple, and pegylated lipid in green, surrounded by blood plasma. The process of creating these two images is described in the text.

Figure 9

Tiling approach to cellular illustration. Three composite tiles (left) are used as brushes to create an illustration of an erythrocyte cell surface, with hemoglobin at the bottom and blood plasma at the top.

Figure 10

Comparison of a cross-section of HIV-1 in blood plasma created in (A) the 3D approach used in CellPAINT-3D and (B) the 2.5D approach used in CellPAINT. Each has advantages and disadvantages: for example, the packing of molecules is more physically accurate in 3D, but molecules are easier to recognize in 2.5D (for example, try identifying antibodies in each image).