Integrative illustration of a JCVI-syn3A minimal cell

Abstract

Data from genomics, proteomics, structural biology and cryo-electron microscopy are integrated into a structural illustration of a cross section through an entire JCVI-syn3.0 minimal cell. The illustration is designed with several goals: to inspire excitement in science, to depict the underlying scientific results accurately, and to be feasible in traditional media. Design choices to achieve these goals include reduction of visual complexity with simplified representations, use of orthographic projection to retain scale relationships, and an approach to color that highlights functional compartments of the cell. Given that this simple cell provides an attractive laboratory for exploring the central processes needed for life, several functional narratives are included in the illustration, including division of the cell and the first depiction of an entire cellular proteome. The illustration lays the foundation for 3D molecular modeling of this cell.

From complex data to clear insights: visualizing molecular dynamics trajectories

“…, (Miao et al, 2017, described DNA nanostructure visualization across multiple abstractions with smooth transitions between levels of abstraction to provide continuous visualisation across scales. Goodsell worked on integrative illustrations for the coronavirus, the minimal cell JCVI-syn3.0 and the microdomain of Caulobacter crescentus (Goodsell et al, 2020;Goodsell, 2022;Goodsell and Lasker, 2023). The main idea is to simplify visual complexity by employing streamlined representations, utilizing orthographic projection to preserve scaling relationships, and employing a color scheme that emphasizes the functional compartments of the molecular system.…”

Integrative visualization of the molecular structure of a cellular microdomain

“…First, we have used traditional scientific illustration methods to create depictions of cross-sections through many types of cells, primarily for use in scientific dissemination, education, and outreach (Goodsell, 1991(Goodsell, , 2021. Second, when technically possible, we have created 3D computational models of these cells, for example, in recent models of whole mycoplasma and minimal genome cells (Goodsell, 2022;Maritan et al, 2022). Increasingly, we are using the Number/ foreground c Reference PopZ 6 8200 0.5 28.5 (Bowman et al, 2008;Ebersbach et al, 2008) Membrane clients Podj 2 700 0.9 8.8 (Hinz et al, 2003;Viollier et al, 2002) PleC illustration effort as a prelude to full 3D modeling, as a tool to enumerate the many types of structures and interactions that need to be modeled.…”

“…As in previous illustrative work, the Caulobacter illustration employs intentional artistic license to improve the readability of the image (Goodsell, 2009(Goodsell, , 2022. The image depicts all macromolecules using simplified shapes, all drawn in canonical views for easy recognition.…”

Design X Bioinformatics: a community-driven initiative to connect bioinformatics and design

“…The article includes detailed discussions of design decisions, narrative and structural choices, modelling, renderings, and applications. In this way, David Goodsell offers both novices and visualization experts exclusive insights into how one of the most prolific life scientists and artists makes his design decisions [ 9 ].…”

“… Integrative illustration of a JCVI-syn3A minimal cell: the artistic conception of a cross-section through a dividing cell. Small molecules, ions, and water have been omitted for clarity (©2022 Goodsell, CC BY 4.0 [ 9 ]). …”