Evolutionary Drivers of Protein Shape

Shannon, Gareth; Marples, Callum R.; Toofanny, Rudesh D.; Williams, Philip M.

Abstract

Diffusional motion within the crowded environment of the cell is known to be crucial to cellular function as it drives the interactions of proteins. However, the relationships between protein diffusion, shape and interaction, and the evolutionary selection mechanisms that arise as a consequence, have not been investigated. Here, we study the dynamics of triaxial ellipsoids of equivalent steric volume to proteins at different aspect ratios and volume fractions using a combination of Brownian molecular dynamics and geometric packing. In general, proteins are found to have a shape, approximately Golden in aspect ratio, that give rise to the highest critical volume fraction resisting gelation, corresponding to the fastest long-time self-diffusion in the cell. The ellipsoidal shape also directs random collisions between proteins away from sites that would promote aggregation and loss of function to more rapidly evolving nonsticky regions on the surface, and further provides a greater tolerance to mutation.

Citation

Shannon, G., Marples, C. R., Toofanny, R. D., & Williams, P. M. (2019). Evolutionary Drivers of Protein Shape. Scientific Reports, 9(1), https://doi.org/10.1038/s41598-019-47337-8

• Journal Article Type: Article
• Acceptance Date: Jul 15, 2019
• Online Publication Date: Aug 15, 2019
• Publication Date: Aug 15, 2019
• Deposit Date: Aug 19, 2019
• Publicly Available Date: Aug 20, 2019
• Journal: Scientific Reports
• Print ISSN: 2045-2322
• Electronic ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 9
• Issue: 1
• Article Number: 11873
• DOI: https://doi.org/10.1038/s41598-019-47337-8
• Public URL: https://nottingham-repository.worktribe.com/output/2309041
• Publisher URL: https://www.nature.com/articles/s41598-019-47337-8
• Additional Information: Received: 2 January 2019; Accepted: 15 July 2019; First Online: 15 August 2019; : The authors declare no competing interests.