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Article
Visualizing Amino Acid Substitutions in a Physicochemical Vector Space
bioRxiv
  • Louis R Nemzer, Nova Southeastern University
Document Type
Article
Publication Date
7-16-2021
Keywords
  • Bioinformatics
Disciplines
Abstract

A three-dimensional representation of the twenty proteinogenic amino acids in a physicochemical space is presented. Vectors corresponding to amino acid substitutions are classified based on whether they are accessible via a single-nucleotide mutation. It is shown that the standard genetic code establishes a “choice architecture” that permits nearly independent tuning of the properties related with size and those related with hydrophobicity. This work sheds light on the metarules of evolvability that may have shaped the standard genetic code to increase the probability that adaptive point mutations will be generated. An illustration of the usefulness of visualizing amino acid substitutions in a 3D physicochemical space is shown using data collected from the SARS-CoV-2 receptor binding domain. The substitutions most responsible for antibody escape are almost always inaccessible via single nucleotide mutation, and also change multiple properties concurrently. The results of this research can extend our understanding of certain hereditary disorders caused by point mutations, as well as guide the development of rational protein and vaccine design.

Comments

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.

Creative Commons License
Creative Commons Attribution-No Derivative Works 4.0 International
DOI
10.1101/2021.07.15.452549
Citation Information
Louis R Nemzer. "Visualizing Amino Acid Substitutions in a Physicochemical Vector Space" bioRxiv (2021) p. 1 - 23
Available at: http://works.bepress.com/lnemzer/60/