Topological Complexity in Protein Structures

• Main Author: Heller, Gabriella
• Format: Others
• Published: Scholarship @ Claremont 2014
• Subjects: knot theory; proteins; topology; non-planar graphs; Other Applied Mathematics; Other Physical Sciences and Mathematics
• Online Access: http://scholarship.claremont.edu/pomona_theses/118; http://scholarship.claremont.edu/cgi/viewcontent.cgi?article=1121&context=pomona_theses

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.