Embedding peptide chains into a planar mesh

Sandi Režonja (2019) Embedding peptide chains into a planar mesh. EngD thesis.

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Abstract

Peptides are sequences of amino acids. In case of their coiled coil structural motif we can predict what bonds will form and create larger structures. We use chains made of peptides for assembly of stable periodic nets. We represent peptides as a chain structure graph in our mathematical model, which we embed into a planar net to guarantee the proper form. Relations between links given in a relation matrix decide whether or not links will self-assemble into a net. Because of the use of orthogonal link sets, relation matrices are permutation matrices. We can further limit relation matrices by applying several conditions derived from nature, stability and net shapes. For the search of periodic nets and uniqueness check we propose area restrictions. The presented lazy embedding algorithm connects one pair of links in a step and embeds them only if there is only one embedding option left.

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