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Structure and Function of the Proteasome

Supervisor:

Audience:

Completed on:

Tools used:

Prof. Derek Ng¹

Life science students, educated lay-audience

Apr. 2017

UCSF Chimera, MAXON Cinema4D, Pixologic ZBrush, Adobe Photoshop, Adobe Illustrator

This molecular biology illustration was created to clarify on the mechanism of protein breakdown by our cells' recycling nanomachine - the proteasome. Elucidation of this multistep process has been a monumental effort from the structural biology and biochemistry research communities, but the complexity of the process is difficult to communicate to nonspecialized or lay audience. This piece was designed and created to directly resolve such communication challenges. Molecular models were sourced from RCSB Protein Data Bank using Chimera, and rendered through a combination of Cinema4D 3D rendering and digital illustration.

¹Biomedical Communications, University of Toronto

 
Process Work

1. Rationale

As I studied proteasomes in academic research in the past, the mechanistic and functional aspects of this protein complex have fascinated me. In this project, I aimed to consolidate current research understanding of the mechanism behind proteasome activity, and represent this in a visual language suitable for an educated lay audience.

Beck F. et al 2012

2. Data Collection

A literature search was conducted to find appropriate proteasomal structure sets which captured multiple states of proteasomes in the midst of their enzymatic activities. The associated 3D structures associated with this literature (ref) were found on Protein Data Bank (PDB) and imported into UCSF Chimera for modifications, such as missing subunits. The modified models were either used as illustration reference, or further processed in Pixologic ZBrush and rendered in Cinema4D.

Unverdorben, P. et al 2014

3. Layout Design

The final deliverable piece for this project was to be printable as a tabloid double-page spread, 11'' x 17''. For establishing layout, factors like narrative flow and balance between textual description and visuals were taken into consideration. Specifically, due to the sheer complexity of the proteasomal structure, a large section of the layout was dedicated to that aspect.

4. Colour and Style

Due to the multimeric multistep nature of the proteasome's enzymatic activity, a colour swatch spanning several distinct hues was established. This provided an additional benefit of creating a visual linkage between the proteasomal structure section and the proteasomal mechanism section. A realistic rendering style was used for the proteasomal structure to enhance its visual impact, and by contrast a flatter rendering style was used for the proteasome mechanism to enhance readability.

 
References

Glickman, M.H., and A. Ciechanover. "The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction." Physiological Reviews 82, no. 2 (2002): 373-428.

Groll, M., and R. Huber. "Inhibitors of the eukaryotic 20S proteasome core particle: a structural approach." Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1695, no. 1-3 (2004): 33-44.

Matyskiela, M.E., G.C. Lander, and Andreas Martin. "Conformational switching of the 26S proteasome enables substrate degradation." Nature Structural & Molecular Biology 20, no. 7 (2013): 781-88

Protein Data Bank PDBID: 4CR2, 4CR3, 4CR4

Protein Data Bank PDBID: 5GJR

Sato, Y., A. Yoshikawa, A. Yamagata, H. Mimura, M. Yamashita, K. Ookata, O. Nureki, K. Iwai, M. Komada, and S. Fukai. "Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains." Nature 455, no. 7211 (2008): 358-62.

Unverdorben, P., F. Beck, P. Sledz, A. Schweitzer, G. Pfeifer, J.m. Plitzko, W. Baumeister, and F. Foerster. "Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome." (2014).

© 2018 Jerry Gu. All Rights Reserved. 

Please do not reproduce or redistribute without permission.

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