Rendering protein structures inside cells at the atomic level with Unreal Engine

Abstract

While the recent development of cryogenic electron tomography (CryoET) makes it possible to identify various macromolecules inside cells and determine their structure at near-atomic resolution, it remains challenging to visualize the complex cellular environment at the atomic level. One of the main hurdles in cell visualization is to render the millions of molecules in real time computationally. Here, using a video game engine, we demonstrate the capability of rendering massive biological macromolecules at the atomic level within their native environment. To facilitate the visualization, we also provide tools that help the interactive navigation inside the cells, as well as software that converts protein structures identified using CryoET to a scene that can be explored with the game engine.

Figure 1.

UE5 rendering of a salmonella minicell infected by P22 bacteriophages. (a) Overview of the scene. (b) Slice view of a reference tomogram from. (c) View outside the bacteria, showing viruses attached to the bacteria outer membrane and pilus extending out of it. (d) View inside the bacteria, showing virus DNA being transcribed and translated by the bacteria.

Figure 2.

UE5 rendering of parts of the Golgi apparatus and the chloroplast from a Chlamydomonas cell. (a) Overview of the scene. (b) Slice view of reference tomograms from^,. (c) View inside the lumen of the thylakoid membranes, showing the photosystems and light harvesting complexes. (d) View of the chloroplast stroma, showing ATP synthase, RubisCO and ribosomes.

Figure 3.

Converting real CryoET data to a UE5 scene. (a) Slice view of a tomogram of NL63 from. (b) Subtomogram averages of the spike proteins at different conformations mapped back to the tomogram, rendered in UCSF Chimera. (c) Atomic models of the same spike protein particles mapped to their corresponding positions in a UE5 scene. (d) Zoomed-in view of the UE5 scene.

Figure 4.

Annotation of macromolecular objects in the interactive game mode using UE5. (a) Annotation of a tRNA (highlighted in cyan outline) inside a ribosome. (b) Annotation of the DNA inside the portal of P22 virus, after some portal and capsid proteins were removed in the interactive mode.

Figure 5.

Rendering of 3D 360° videos. (a) Camera setup for each frame: top – fixed camera positions, bottom – rotating camera positions. (b) The panromantic view of the left (top) and right (bottom) eye view of one frame of the scene in Figure 1. A short 3D 360° video of the scene can currently be found at youtu.be/nqrMXAaOKYw