Graph Coverings for Investigating Non Local Structures in Proteins, Music and Poems

• Published in: Sci Vol. 3; no. 4; p. 39
• Main Authors: Planat, Michel, Aschheim, Raymond, Amaral, Marcelo M., Fang, Fang, Irwin, Klee
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.11.2021
• Subjects: Amino acids; Artificial intelligence; finitely generated groups; Generators; graph coverings; Immune system; Language; Mathematics; Music; musical forms; Mutation; Poetry; protein structure; Proteins; SARS-Cov-2; Severe acute respiratory syndrome coronavirus 2
• ISSN: 2413-4155; 2413-4155
• DOI: 10.3390/sci3040039

We explore the structural similarities in three different languages, first in the protein language whose primary letters are the amino acids, second in the musical language whose primary letters are the notes, and third in the poetry language whose primary letters are the alphabet. For proteins, the non local (secondary) letters are the types of foldings in space (α-helices, β-sheets, etc.); for music, one is dealing with clear-cut repetition units called musical forms and for poems the structure consists of grammatical forms (names, verbs, etc.). We show in this paper that the mathematics of such secondary structures relies on finitely presented groups fp on r letters, where r counts the number of types of such secondary non local segments. The number of conjugacy classes of a given index (also the number of graph coverings over a base graph) of a group fp is found to be close to the number of conjugacy classes of the same index in the free group Fr−1 on r−1 generators. In a concrete way, we explore the group structure of a variant of the SARS-Cov-2 spike protein and the group structure of apolipoprotein-H, passing from the primary code with amino acids to the secondary structure organizing the foldings. Then, we look at the musical forms employed in the classical and contemporary periods. Finally, we investigate in much detail the group structure of a small poem in prose by Charles Baudelaire and that of the Bateau Ivre by Arthur Rimbaud.