Bringing Structure to Biology
The amazing spider silk
Spider silk is an incredibly strong and versatile material, both sturdy - it is five times stronger by weight than steel - and elastic - it can be stretched 2-4 times its original length without breaking. Spider silk threads usually measure just a few microns in diameter, making them even thinner than a human hair, yet they are waterproof and able to keep their strength below -40°C.
Spiders use their silk for a variety of functions, the most well-known being weaving webs for catching prey or wrapping their prey in silk to immobilize their catch. Other uses of silk may include a safety rope connecting the spider to its web, in case the spider should fall, but also building shelters, creating a silk sac for their eggs, or even parachuting when the spider uses the wind to venture in a new area in search of other food sources (flying spiders!).
Spider silk loses its stickiness after about a day due to exposure to air and dust. To save energy, the spider eats its own web before making a new one, so the protein used for the silk threads is recycled.
Fibroin: the spider silk protein
Spider silk belongs to the scleroprotein group (fibrous proteins), which also includes keratin, collagen, and elastin. It is made up of elongated filamentous chains of the fibroin protein. Fibroin is highly water-insoluble, therefore contributing to making the spider silk waterproof. Unlike globular proteins, fibroin doesn’t denature easily, and can keep its structure and properties even in the toughest temperature and pressure conditions.
The spider silk protein represented on our March 2021 artwork is inspired from the PDB ID 2KHM, the sole available structure for fibroin-3 from Araneus diadematus, also known as European garden spider.
Fibroin-3’s amino acid composition is somewhat unusual: 50% of the amino acid sequence consists solely of glycine and alanine residues, the remaining components being mostly glutamine, proline and serine, and all the other amino acid types account for less than 10% of the sequence.
Fibroin-3 is a 636 amino acid protein, predicted to be disordered for most of its N-terminal part (1-525). The available structure, 2KHM, covers the C-terminal part (513-636) so called “non-repetitive domain”. Solved by NMR, it is possible to observe some of the disordered region in the N-terminus.
PDB ID 2KHM shows 20% of the protein, including a short span of the disordered N-terminal region (yellow) as well as the ordered non-repetitive domain (blue). All 20 models of this NMR solution structure are shown superimposed.
The protein is composed of two identical subunits and the fold involves a parallel dimeric 5-helix bundle, in which helix 4, the longest one, is the main dimerization site. Thanks to a right-handed twist between helices 4 in both monomers, a hydrophobic patch is created, accounting primarily for the stabilization of the dimer. This structure also contains a single cysteine residue in each monomer, and the two are involved in an intermolecular disulfide bond located at the N-terminal end of helix 4. Helix 1 of one monomer and helix 5 of the second monomer interact in a clamp-like manner. Two salt bridges fix helices 1 and 2 at one side of helix 4, using the only charged residues of the entire protein sequence, namely an arginine (R43) with an aspartic acid (D93), and another arginine (R52) with a glutamic acid (E101).
Dimer of the ordered “non-repetitive domain” of PDB ID 2KHM. Helix 4, at the dimer interface, is highlighted in yellow. Salt bridges are indicated in red (positively charged residues) and blue (negatively charged residue) pairs. The disulfide bond formed by the sole cysteine residue of each monomer is shown in orange.
From protein to fiber
The N-terminal domain of fibroin-3 is known to be important for the mechanical properties of the fiber and is believed to form repetitive elements in the backbone of spider silk.
The spider silk fluid inside the spider’s body is a liquid solution where the fibroin molecules retain a certain order, resulting in crystalline properties. It is believed that during their passage through the spinneret, the spider’s silk-spinning organ, the fibroin molecules align, and partial crystallization occurs parallel to the fiber’s axis. This is made possible through the self-assembly of the fibroin molecules, where their repetitive sequences contain polyalanine regions that cross-link together via hydrogen bonds to form pleated beta sheets, conferring the high strength of the silk. It is therefore not a coincidence that 50% of fibroin’s amino acid content is alanine and glycine, as they are the smallest amino acids so are able to pack together tightly. The crystalline regions are also very hydrophobic, allowing the loss of water during the solidification of spider silk.
From the silk fluid to silk fiber: fibroin molecules align along to the fiber’s axis.
Applications of spider silk
Humans have been making use of spider silk for thousands of years. The ancient Greeks used cobwebs to stop wounds from bleeding and today people of the Solomon Islands still use silk as fish nets.
Spider silk, by its incredible mechanical properties and the non-polluting way in which it is produced, is of great interest to materials chemists. The production of spider silk is environmentally friendly, since it’s made by spiders at ambient temperature and pressure and is drawn from water. In addition, the spider silk is completely biodegradable. New ultra-strong fibers based on the spider silk protein could be developed, and the potential applications of natural or synthetic spider silk in the materials industry are numerous.
However, the production of spider silk is not as simple as it seems. Spiders cannot be farmed like silkworms, since they are cannibals and will tend to eat each other if in proximity. The silk produced is very fine, so 400 spiders would be needed to produce less than a m2 of cloth. The silk also hardens when exposed to air which makes it difficult to work with.
An alternative approach would then be to make synthetic spider silk, but this method also brings its own challenges. As the silk is insoluble in water, one would need to adapt the composition of silk proteins to alter its properties. Another challenge will be to develop an artificial method of spinning silk, and handling of the highly viscous silk fluid. A better knowledge about silk structure is therefore needed before we can aim for the chemical synthesis of spider silk.
About the artwork
“My print represents proteins 2khm & 5d2s. One is silk moth and cocoons, the other is spider silk. My research has led me to compose a drawing which features the many different natural aspects which lead to the production of silk. After attending a lecture on combining proteins and art to scientific and creative advantage I investigated the complex beautiful structures of silk proteins. I used the Protein Data Bank website to observe and understand these structures using the resource's virtual 3D models and factual records. I chose to use the mulberry tree branch as a basis for my drawing as this a crucial part of sericulture and was also appreciated for its beauty in many Chinese artifacts since the discovery of weavable silk. My intent was for my drawing to resemble a traditional Chinese silk painting in its composition and use of black ink. In order to represent the multiple life stages of the Bombyx mori I chose to depict the larva, cocoons and silk moth. My drawing was created digitally using the app 'Adobe Draw', I used the touch sensitive screen of my iPhone to draw the lines with my finger. In order to print the drawing onto fabric I initially used a transfer method which involved printing onto acetate and using pressure to transfer the ink onto the silk. This method was ineffective as the thin lines on the drawing became blurred on a transfer, instead I put the silk directly into the printer to produce a clearer image. After the silk was stretched into a card frame I embroidered into some of the lines with black thread to create the illusion that the silk fibres are hanging out of the drawing. “
Zoe Coleman, a student from the Stephen Perse Foundation.
View the artwork in the virtual 2020 PDB Art exhibition.
Structure mentioned in this article
Structure of the C-terminal non-repetitive domain of the spider dragline silk protein ADF-3: 2KHM
Images created using PyMOL, BioRender and Adobe Photoshop.