Genus trace reveals the topological complexity and domain structure of biomolecules.

ABSTRACT: The structure of bonds in biomolecules, such as base pairs in RNA chains or native interactions in proteins, can be presented in the form of a chord diagram. A given biomolecule is then characterized by the genus of an auxiliary two-dimensional surface associated to such a diagram. In this work we introduce the notion of the genus trace, which describes dependence of genus on the choice of a subchain of a given backbone chain. We find that the genus trace encodes interesting physical and biological information about a given biomolecule and its three dimensional structural complexity; in particular it gives a way to quantify how much more complicated a biomolecule is than its nested secondary structure alone would indicate. We illustrate this statement in many examples, involving both RNA a

SUBMITTER: Zajac S 

PROVIDER: S-EPMC6277428 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature