Graduation Year

Spring 2014

Document Type

Campus Only Senior Thesis

Degree Name

Bachelor of Arts

Department

Mathematics

Second Department

Chemistry

Reader 1

Erica Flapan

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© 2014 Gabriella Heller

Abstract

For DNA molecules, topological complexity occurs exclusively as the result of knotting or linking of the polynucleotide backbone. By contrast, while a few knots and links have been found within the polypeptide backbones of some protein structures, non-planarity can also result from the connectivity between a polypeptide chain and attached metal structures. In this thesis, we survey the known types of knots, links, and non-planar graphs in protein structures with and without including such bonds between proteins and metals. Then we present new examples of protein structures containing M\"obius ladders and other non-planar graphs as a result of these bound metal atoms. Finally, we propose hypothetical structures illustrating specific disulfide connectivities that would result in the key ring link, the Whitehead link and the 5_1 knot, the latter two of which have thus far not been identified within protein structures.

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