Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

Proline-Tyrosine Ring Interactions in Black Widow Dragline Silk Revealed by Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulations

Selective one-dimensional 13C-13C spin-diffusion solid-state nuclear magnetic resonance (SSNMR) provides evidence for CH/π ring packing interactions between Pro and Tyr residues in 13C-enriched Latrodectus hesperus dragline silk. The secondary structure of Pro-containing motifs in dragline spider silks consistently points to an elastin-like type II β-turn conformation based on 13C chemical shift analysis. 13C-13C spin diffusion measurements as a function of mixing times allow for the measurement of spatial proximity between the Pro and Tyr rings to be ∼0.5-1 nm, supporting strong Pro-Tyr ring interactions that likely occur through a CH/π mechanism. These results are supported by molecular dynamics (MD) simulations and analysis and reveals new insights into the secondary structure and Pro-Tyr ring stacking interactions for one of nature's toughest biomaterials.

Silk Assembly against Hydrophobic Surfaces─Modeling and Imaging of Formation of Nanofibrils

A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, β-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of ∼7 nm and a width of ∼11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.

Rapid molecular diversification and homogenization of clustered major ampullate silk genes in Argiope garden spiders

The evolutionary diversification of orb-web weaving spiders is closely tied to the mechanical performance of dragline silk. This proteinaceous fiber provides the primary structural framework of orb web architecture, and its extraordinary toughness allows these structures to absorb the high energy of aerial prey impact. The dominant model of dragline silk molecular structure involves the combined function of two highly repetitive, spider-specific, silk genes (spidroins)-MaSp1 and MaSp2. Recent genomic studies, however, have suggested this framework is overly simplistic, and our understanding of how MaSp genes evolve is limited. Here we present a comprehensive analysis of MaSp structural and evolutionary diversity across species of Argiope (garden spiders). This genomic analysis reveals the largest catalog of MaSp genes found in any spider, driven largely by an expansion of MaSp2 genes. The rapid diversification of Argiope MaSp genes, located primarily in a single genomic cluster, is associated with profound changes in silk gene structure. MaSp2 genes, in particular, have evolved complex hierarchically organized repeat units (ensemble repeats) delineated by novel introns that exhibit remarkable evolutionary dynamics. These repetitive introns have arisen independently within the genus, are highly homogenized within a gene, but diverge rapidly between genes. In some cases, these iterated introns are organized in an alternating structure in which every other intron is nearly identical in sequence. We hypothesize that this intron structure has evolved to facilitate homogenization of the coding sequence. We also find evidence of intergenic gene conversion and identify a more diverse array of stereotypical amino acid repeats than previously recognized. Overall, the extreme diversification found among MaSp genes requires changes in the structure-function model of dragline silk performance that focuses on the differential use and interaction among various MaSp paralogs as well as the impact of ensemble repeat structure and different amino acid motifs on mechanical behavior.

Recombinant Spider Silk Fiber with High Dimensional Stability in Water and Its NMR Characterization

Spider dragline silk has unique characteristics of strength and extensibility, including supercontraction. When we use it as a biomaterial or material for textiles, it is important to suppress the effect of water on the fiber by as much as possible in order to maintain dimensional stability. In order to produce spider silk with a highly hydrophobic character, based on the sequence of ADF-3 silk, we produced recombinant silk (RSSP(VLI)) where all QQ sequences were replaced by VL, while single Q was replaced by I. The artificial RSSP(VLI) fiber was prepared using formic acid as the spinning solvent and methanol as the coagulant solvent. The dimensional stability and water absorption experiments of the fiber were performed for eight kinds of silk fiber. RSSP(VLI) fiber showed high dimensional stability, which is suitable for textiles. A remarkable decrease in the motion of the fiber in water was made evident by ¹³C solid-state NMR. This study using ¹³C solid-state NMR is the first trial to put spider silk to practical use and provide information regarding the molecular design of new recombinant spider silk materials with high dimensional stability in water, allowing recombinant spider silk proteins to be used in next-generation biomaterials and materials for textiles.

Protein secondary structure in spider silk nanofibrils

Nanofibrils play a pivotal role in spider silk and are responsible for many of the impressive properties of this unique natural material. However, little is known about the internal structure of these protein fibrils. We carry out polarized Raman and polarized Fourier-transform infrared spectroscopies on native spider silk nanofibrils and determine the concentrations of six distinct protein secondary structures, including β-sheets, and two types of helical structures, for which we also determine orientation distributions. Our advancements in peak assignments are in full agreement with the published silk vibrational spectroscopy literature. We further corroborate our findings with X-ray diffraction and magic-angle spinning nuclear magnetic resonance experiments. Based on the latter and on polypeptide Raman spectra, we assess the role of key amino acids in different secondary structures. For the recluse spider we develop a highly detailed structural model, featuring seven levels of structural hierarchy. The approaches we develop are directly applicable to other proteinaceous materials.

Secondary fibril structure is a key component of the mechanical properties of protein materials like silk, yet, limited information is known about the internal structure of these protein fibrils. Here, the authors report on the use of polarised Raman and FTIR spectroscopy to study silk materials and identify six distinct secondary structures.

Recombinant Spider Silk: Promises and Bottlenecks

Spider silk threads have exceptional mechanical properties such as toughness, elasticity and low density, which reach maximum values compared to other fibre materials. They are superior even compared to Kevlar and steel. These extraordinary properties stem from long length and specific protein structures. Spider silk proteins can consist of more than 20,000 amino acids. Polypeptide stretches account for more than 90% of the whole protein, and these domains can be repeated more than a hundred times. Each repeat unit has a specific function resulting in the final properties of the silk. These properties make them attractive for innovative material development for medical or technical products as well as cosmetics. However, with livestock breeding of spiders it is not possible to reach high volumes of silk due to the cannibalistic behaviour of these animals. In order to obtain spider silk proteins (spidroins) on a large scale, recombinant production is attempted in various expression systems such as plants, bacteria, yeasts, insects, silkworms, mammalian cells and animals. For viable large-scale production, cost-effective and efficient production systems are needed. This review describes the different types of spider silk, their proteins and structures and discusses the production of these difficult-to-express proteins in different host organisms with an emphasis on plant systems.

Systemic and Local Silk-Based Drug Delivery Systems for Cancer Therapy

For years, surgery, radiotherapy, and chemotherapy have been the gold standards to treat cancer, although continuing research has sought a more effective approach. While advances can be seen in the development of anticancer drugs, the tools that can improve their delivery remain a challenge. As anticancer drugs can affect the entire body, the control of their distribution is desirable to prevent systemic toxicity. The application of a suitable drug delivery platform may resolve this problem. Among other materials, silks offer many advantageous properties, including biodegradability, biocompatibility, and the possibility of obtaining a variety of morphological structures. These characteristics allow the exploration of silk for biomedical applications and as a platform for drug delivery. We have reviewed silk structures that can be used for local and systemic drug delivery for use in cancer therapy. After a short description of the most studied silks, we discuss the advantages of using silk for drug delivery. The tables summarize the descriptions of silk structures for the local and systemic transport of anticancer drugs. The most popular techniques for silk particle preparation are presented. Further prospects for using silk as a drug carrier are considered. The application of various silk biomaterials can improve cancer treatment by the controllable delivery of chemotherapeutics, immunotherapeutics, photosensitizers, hormones, nucleotherapeutics, targeted therapeutics (e.g., kinase inhibitors), and inorganic nanoparticles, among others.

Doing What Spiders Cannot-A Road Map to Supreme Artificial Silk Fibers

Fabricating artificial spider silk fibers in bulk scale has been a major goal in materials science for centuries. Two main routes have emerged for making such fibers. One method uses biomimetics in which the spider silk proteins (spidroins) are produced under nativelike conditions and then spun into fibers in a process that captures the natural, complex molecular mechanisms. However, these fibers do not yet match the mechanical properties of native silk fibers, potentially due to the small size of the designed spidroin used. The second route builds on biotechnological progress that enables production of large spidroins that can be spun into fibers by using organic solvents. With this approach, fibers that equal the native material in terms of mechanical properties can be manufactured, but the yields are too low for economically sustainable production. Hence, the need for new ideas is urgent. Herein, we introduce a structural-biology-based approach for engineering artificial spidroins that circumvents the laws with which spidroins, being secretory proteins, have to comply in order to avoid membrane insertion and provide a road map to the production of biomimetic silk fibers with improved mechanical properties.

Meta-analysis reveals materiomic relationships in major ampullate silk across the spider phylogeny

Spider major ampullate (MA) silk, with its combination of strength and extensibility, outperforms any synthetic equivalents. There is thus much interest in understanding its underlying materiome. While the expression of the different silk proteins (spidroins) appears an integral component of silk performance, our understanding of the nature of the relationship between the spidroins, their constituent amino acids and MA silk mechanics is ambiguous. To provide clarity on these relationships across spider species, we performed a meta-analysis using phylogenetic comparative methods. These showed that glycine and proline, both of which are indicators of differential spidroin expression, had effects on MA silk mechanics across the phylogeny. We also found serine to correlate with silk mechanics, probably via its presence within the carboxyl and amino-terminal domains of the spidroins. From our analyses, we concluded that the spidroin expression shifts across the phylogeny from predominantly MaSp1 in the MA silks of ancestral spiders to predominantly MaSp2 in the more derived spiders' silks. This trend was accompanied by an enhanced ultimate strain and decreased Young's modulus in the silks. Our meta-analysis enabled us to decipher between real and apparent influences on MA silk properties, providing significant insights into spider silk and web coevolution and enhancing our capacity to create spider silk-like materials.

Structure and Dynamics of Spider Silk Studied with Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulation

This review will introduce very recent studies using solid-state nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulation on the structure and dynamics of spider dragline silks conducted by the author's research group. Spider dragline silks possess extraordinary mechanical properties by combining high tensile strength with outstanding elongation before breaking, and therefore continue to attract attention of researchers in biology, biochemistry, biophysics, analytical chemistry, polymer technology, textile technology, and tissue engineering. However, the inherently non-crystalline structure means that X-ray diffraction and electron diffraction methods provide only limited information because it is difficult to study the molecular structure of the amorphous region. The most detailed picture of the structure and dynamics of the silks in the solid state experimentally have come from solid-state NMR measurements coupled with stable isotope labeling of the silks and the related silk peptides. In addition, combination of solid-state NMR and MD simulation was very powerful analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution. In this review, the author will emphasize how solid-state NMR and MD simulation have contributed to a better understanding of the structure and dynamics in the spider dragline silks.

Dynamic Responsive Formation of Nanostructured Fibers in a Hydrogel Network: A Molecular Dynamics Study

In an effort to study natural fiber formation, such as, e.g., spider silk, we present a model, which is capable of forming biomimetic fibrillar nanostructure from a hydrogel micellar network. The latter consists of interacting atomic groups which form cores of micelles, and of flexible chains forming the shells of the micelles. Micelles are connected in a compact network by linearly stretched chains. The structural elements of the network can be transformed during deformation from micellar into fibrillary type and their evolution is found to depend significantly on strain rate. Our model suggests a set of conditions suitable for the formation of nanostructured fibrillar network. It demonstrates that a fibrillar structure is only formed upon sufficiently fast stretching while, in contrast, the micellar gel structure is preserved, if the material is pulled slowly. We illustrate this key aspect by a minimalistic model of only four chains as part of the whole network, which provides a detailed view on the mechanism of fibril formation. We conclude that such a simplified structure has similar functionality and is probably responsible for the formation of nano-structured molecular fibrils in natural materials.

Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate

Spider silk is a biomaterial with exceptional mechanical toughness, and there is great interest in developing biomimetic methods to produce engineered spider silk-based materials. However, the mechanisms that regulate the conversion of spider silk proteins (spidroins) from highly soluble dope into silk are not completely understood. The N-terminal domain (NT) of Euprosthenops australis dragline silk protein undergoes conformational and quaternary-structure changes from a monomer at a pH above 7 to a homodimer at lower pH values. Conversion from the monomer to the dimer requires the protonation of three conserved glutamic acid residues, resulting in a low-pH `locked' dimer stabilized by symmetric electrostatic interactions at the poles of the dimer. The detailed molecular events during this transition are still unresolved. Here, a 2.1 Å resolution crystal structure of an NT T61A mutant in an alternative, asymmetric, dimer form in which the electrostatic interactions at one of the poles are dramatically different from those in symmetrical dimers is presented. A similar asymmetric dimer structure from dragline silk of Nephila clavipes has previously been described. It is suggested that asymmetric dimers represent a conserved intermediate state in spider silk formation, and a revised `lock-and-trigger' mechanism for spider silk formation is presented.

Conformational change of 13C-labeled 47-mer model peptides of Nephila clavipes dragline silk in poly(vinyl alcohol) film by stretching studied by 13C solid-state NMR and molecular dynamics simulation

For determination of the conformation of irregular sequences in glycine-rich region of the Nephila clavipes spider dragline silk, the combination of ¹³C selectively labeled model peptides for the typical primary structure and their ¹³C solid-state NMR observations is very useful (T. Asakura et al. Macromolecules. 51 (2018) 3608-3619). However, spiders produce the fiber through the stretching process in nature and therefore, it is difficult to study conformational change by stretching as mimic using the model peptides because these are generally in the powder form. In this paper, ¹³C selectively labeled three model peptides, (Glu)₄(Ala)₆GlyGly¹²Ala¹³Gly¹⁴GlnGlyGlyTyrGlyGlyLeuGlySerGlnGly²⁵Ala²⁶Gly²⁷ArgGly-GlyLeuGlyGlyGlnGly³⁵Ala³⁶Gly³⁷(Ala)₆(Glu)₄ with three underlined ¹³C labeled blocks and their poly(vinyl alcohol) blend films were prepared and the conformational changes of these peptides were monitored by stretching of the films using ¹³C solid-state NMR. In addition, the molecular dynamics simulation was done to evaluate change in the conformation of the sequence by stretching theoretically. The fractions of β-sheet of Ala³⁶ and Gly³⁷ residues in glycine-rich region adjacent to the C-terminal (Ala)₆ sequence increased significantly by stretching compared with those of other ¹³C labeled Ala and Gly residues.

DNP NMR spectroscopy reveals new structures, residues and interactions in wild spider silks

DNP solid state NMR spectroscopy allows non-targeted analysis of wild spider silk in unprecedented detail at natural abundance, revealing hitherto unreported features across several species. A >50-fold signal enhancement for each silk, enables the detection of novel H-bonding networks and arginine conformations, and the post-translational modified amino acid, hydroxyproline.

Experimental Methods for Characterizing the Secondary Structure and Thermal Properties of Silk Proteins

Silk proteins are biopolymers produced by spinning organisms that have been studied extensively for applications in materials engineering, regenerative medicine, and devices due to their high tensile strength and extensibility. This remarkable combination of mechanical properties arises from their unique semi-crystalline secondary structure and block copolymer features. The secondary structure of silks is highly sensitive to processing, and can be manipulated to achieve a wide array of material profiles. Studying the secondary structure of silks is therefore critical to understanding the relationship between structure and function, the strength and stability of silk-based materials, and the natural fiber synthesis process employed by spinning organisms. However, silks present unique challenges to structural characterization due to high-molecular-weight protein chains, repetitive sequences, and heterogeneity in intra- and interchain domain sizes. Here, experimental techniques used to study the secondary structure of silks, the information attainable from these techniques, and the limitations associated with them are reviewed. Ultimately, the appropriate utilization of a suite of techniques discussed here will enable detailed characterization of silk-based materials, from studying fundamental processing-structure-function relationships to developing commercially useful quality control assessments.

Structural Comparison of Various Silkworm Silks: An Insight into the Structure-Property Relationship

Silkworm silk has attracted considerable attention in recent years due to its excellent mechanical properties, biocompatibility, and promising applications in biomedical sector. However, a clear understanding of the molecular structure and the relationship between the excellent mechanical properties and the silk protein sequences are still lacking. This study carries out a thorough comparative structural analysis of silk fibers of four silkworm species ( Bombyx mori, Antheraea pernyi, Samia cynthia ricini, and Antheraea assamensis). A combination of characterization techniques including scanning electron microscopy, mechanical test, synchrotron X-ray diffraction, Fourier transform infrared spectroscopy (FTIR), and NMR spectroscopy was applied to investigate the morphologies, mechanical properties, amino acid compositions, nanoscale organizations, and molecular structures of various silkworm silks. Furthermore, the structure-property relationship is discussed by correlating the molecular structural features of silks with their mechanical properties. The results show that a high content of β-sheet structures and a high crystallinity would result in a high Young's modulus for silkworm silk fibers. Additionally, a low content of β-sheet structures would result in a high extensibility.

Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation

Change from rectangular arrangement to staggered arrangement of (Ala)₆ by heat treatment.