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From 2013.igem.org

Silk protein

The spider silk protein is a fibrous protein. It does not have a folded state on its own; it is able to assemble (multimerize) with multiple identical proteins to form the silk. The protein consists of roughly 3 motifs, each featuring a particular secondary structure in the assembly (table 1) (ref 11 paper recomb biomaterials).

Depending on the processing of the silk proteins, it can have a degree of these secondary structures, defining its properties (table 1).

Amino acid sequence	Secondary structure	Properties
AAAAAAAA	β-sheet	Tensile strenght, rigidity, hydrophobicity
GPG(AG)QQ / GPG(SGG)QQ / GPGGX	β-spiral / β-turn	Extensibility, elasticity
GGX	310 helix	Link, alignment, flexibility

Table 1, Spider silk protein motifs

In order to make the silk material a large amount of these proteins are required. The protein has a very repetitive nature (fig. 2), with these motifs (table 1) recurring within the protein. This is difficult to produce, because it requires presence of the same tRNAs in a large amount. This can be solved with codon optimization. See ‘Codon optimization’ (link) at the modelling section for the explanation of this approach.