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. 2021 Apr 30;7:612920. doi: 10.3389/fmolb.2020.612920

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Copyright © 2021 Konagurthu, Subramanian, Allison, Abramson, Stuckey, Garcia de la Banda and Lesk.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Example dissection of an actin-binding protein into “concepts” from the inferred dictionary. (A) Secondary-structural cartoon representation of the crystal structure of the actin-binding protein actophorin from Acanthamoeba (1ahq) (Leonard et al., 1997). (B) Secondary structural assignment [using SST (Konagurthu et al., 2012); H = helix, E = strand of sheet] and the optimal dissection of the protein chain into nonoverlapping regions, using the inferred concept dictionary. This information is shown with reference to the amino-acid sequence information in a marked-up format: the dissection of 1ahq uses concepts (see the text) c_0823 (highlighted in yellow) and c_1021 (highlighted in blue). (C) Tableau representation of the folding pattern of 1ahq. The highlighted subtableaux corresponds to concepts c_0823 and c_1021. Here, only the lower-triangle part of the tableau information is shown because the full tableau is a symmetric matrix. The rows and columns are indexed by secondary structure elements in order of appearance in the polypeptide chain. Off-diagonal elements record the angles between the pairs of secondary structural elements; boldface indicates that there is a contact between the corresponding pair of secondary structural elements. (D, E) The concepts c_0823 and c_1021 are shown, together with their archetypal tableaux and corresponding secondary structural representation.