Visualizing alpha-helical peptides in R with helixvis

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Authors Raoul R. Wadhwa, Vigneshwar Subramanian, Regina Stevens-Truss
Journal/Conference Name J. Open Source Software
Paper Category
Paper Abstract Studying the interactions of short peptides is conceptually non-trivial, even when the peptide’s primary and secondary structures are known. The difficulty is often a result of the three-dimensional spatial complexity present in protein secondary structure. Here, we focus on α-helical secondary structure. Two-dimensional visualizations, specifically helical wheels (Figure 1, left panel) and wenxiang diagrams (Figure 1, right panel), are used by biochemists to study α-helices. Helical wheels provide a bird’s eye view of a helical peptide with the amino acids forming a perfect circle, and allow for rapid identification of the peptide’s hydrophobic faces (Schiffer & Edmundson, 1967), helping solve a common challenge in biochemistry research. In contrast, wenxiang diagrams incorporate residue order by making residue distance from the center directly proportional to residue position in the peptide (Chou, Zhang, & Maggiora, 1997). However, this makes the identification of hydrophobic faces less intuitive. Together, these two forms of visualization allow researchers to more clearly understand the underlying structure of α-helical peptides. Given the existence of databases listing thousands of peptides, all of which need to be visualized for manual inspection prior to wet-lab experiments, there is a need for software that allows for rapid programmatic construction of large numbers of publication-quality helical wheels and wenxiang diagrams.
Date of publication 2018
Code Programming Language R
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