Strong traces model of self-assembly polypeptide structures

MaRDI QIDQ2975293zbMATH OpenFDO

Authors Gašper Fijavž, Tomaž Pisanski, Jernej Rus

Publication date 11 April 2017

Full work available at URL https://arxiv.org/abs/1308.4024

zbMATH Keywords

parallel strong tracespolypeptide nanostructure design

Mathematics Subject Classification ID

Planar graphs; geometric and topological aspects of graph theory (05C10) Applications of graph theory (05C90) Chemical graph theory (05C92) Mathematical biology in general (92B99)

Abstract: A novel self-assembly strategy for polypeptide nanostructure design was presented in [Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments, Nature Chemical Biology 9 (2013) 362--366]. The first mathematical model (polypeptide nanostructure can naturally be presented as a skeleton graph of a polyhedron) from [Stable traces as a model for self-assembly of polypeptide nanoscale polyhedrons, MATCH Commun. Math. Comput. Chem. 70 (2013) 317-330] introduced stable traces as the appropriate mathematical description, yet we find them deficient in modeling graphs with either very small (less or equal to 2) or large (greater or equal to 6) degree vertices. We introduce strong traces which remedy both of the above mentioned drawbacks. We show that every connected graph admits a strong trace by studying a connection between strong traces and graph embeddings. Further we also characterize graphs which admit parallel (resp. antiparallel) strong traces.

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