CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments

Abstract

Integrative computational modeling is currently the method of choice for studying the detailed mesoscale molecular structure of cellular environments. However, current methods are highly compute intensive and require extensive and diverse domain knowledge. We have developed an interactive mesoscale illustration method, cellPAINT, that allows non-expert users to create mesoscale models that integrate a variety of biological data. CellPAINT uses the approach of popular digital painting software, providing users with a palette of “brushes” to paint molecules and infrastructure into a mesoscale scene, and coloring tools and visual filters to customize the rendering. CellPAINT also incorporates a variety of mesoscale properties, such as an interactive temperature slider that controls diffusive motion and interaction of proteins within membranes. The current release allows creation of scenes with an HIV virion, blood plasma, and a simplified T-cell.

Visualizing protein structures — tools and trends

“…Whereas the overwhelming part of protein visualization so far may have focused on displaying existing models, the future may focus more intensely on methods to visually create complex molecular landscapes from scratch. Novel technology may be instrumental to this task [70][71][72][73].…”

Integrative Modeling and Visualization of Exosomes

“…In addition, we included miRNA in an argonaute2-miRNA complex, since there is some controversy about presence of miRNA in plasma (Gallo et al 2012, Arroyo et al 2011. Structures for blood plasma components were based on previous work with cellPAINT (Gardner et al 2018) and low density lipoprotein structure was based on a cryo-electron study (entry EMD-5239 at http://www.emdatabank.org).…”

“…In the current work, the abundance of mRNA and miRNA was arbitrarily set to the average value of the soluble proteins and one DNA strand was included per vesicle. Similarly to previous work (Gardner et al 2018), concentrations of blood plasma components were based on proteomic studies (Chan et al 2004).…”

“…CellPAINT allows users to create similar illustrations using an interface akin to a paint program, providing a menu of molecules and membranes that may be added into a crosssectional view of a cellular scene (Gardner et al 2018). As with the painting, only a thin slice of the scene is visible, with a bright foreground layer and several background layers progressively obscured with distance-dependent depth cueing to black.…”

“…We began with traditional scientific illustration to create visualizations for dissemination, outreach, and education, focusing on defined portions of living cells and their interactions with viruses (Goodsell, Franzen, et al 2018). We have recently extended this work by developing cellPAINT, a digital painting program that assists in the creation of these types of subcellular landscape illustrations (Gardner et al 2018). Building on this work, we are currently developing tools to create and visualize accurate 3D models of the molecular structure of cellular compartments and entire cells (Johnson et al 2015).…”