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1.  Materiomics: biological protein materials, from nano to macro 
Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics – discovering Nature’s complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature’s materials have been hindered by our lack of fundamental understanding of these materials’ intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties. Recent advances in analytical tools and experimental methods allow a holistic view of such a hierarchical biological material system. The integration of these approaches and amalgamation of material properties at all scale levels to develop a complete description of a material system falls within the emerging field of materiomics. Materiomics is the result of the convergence of engineering and materials science with experimental and computational biology in the context of natural and synthetic materials. Through materiomics, fundamental advances in our understanding of structure–property–process relations of biological systems contribute to the mechanistic understanding of certain diseases and facilitate the development of novel biological, biologically inspired, and completely synthetic materials for applications in medicine (biomaterials), nanotechnology, and engineering.
doi:10.2147/NSA.S9037
PMCID: PMC3781696  PMID: 24198478
biological materials; hierarchies; multiscale; materiomics; deformation; failure; functional material properties; protein; peptide; universality; diversity
2.  High-performance spider webs: integrating biomechanics, ecology and behaviour 
Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence spider web evolution along different structural pathways, and (ii) how silks function in an ecological context, which may identify novel silk applications. An integrative, mechanistic approach to understanding silk and web function, as well as the selective pressures driving their evolution, will help uncover the potential impacts of environmental change and species invasions (of both spiders and prey) on spider success. Integrating these fields will also allow us to take advantage of the remarkable properties of spider silks, expanding the range of possible silk applications from single threads to two- and three-dimensional thread networks.
doi:10.1098/rsif.2010.0454
PMCID: PMC3061126  PMID: 21036911
biomaterials; biomimetics; dragline silk; ecology; evolution; orb-web spider
3.  Hierarchical flexural strength of enamel: transition from brittle to damage-tolerant behaviour 
Hard, biological materials are generally hierarchically structured from the nano- to the macro-scale in a somewhat self-similar manner consisting of mineral units surrounded by a soft protein shell. Considerable efforts are underway to mimic such materials because of their structurally optimized mechanical functionality of being hard and stiff as well as damage-tolerant. However, it is unclear how different hierarchical levels interact to achieve this performance. In this study, we consider dental enamel as a representative, biological hierarchical structure and determine its flexural strength and elastic modulus at three levels of hierarchy using focused ion beam (FIB) prepared cantilevers of micrometre size. The results are compared and analysed using a theoretical model proposed by Jäger and Fratzl and developed by Gao and co-workers. Both properties decrease with increasing hierarchical dimension along with a switch in mechanical behaviour from linear-elastic to elastic-inelastic. We found Gao's model matched the results very well.
doi:10.1098/rsif.2011.0498
PMCID: PMC3350718  PMID: 22031729
hierarchical structures; mechanical properties; biological materials; dental enamel
4.  The elaborate structure of spider silk 
Prion  2008;2(4):154-161.
Biomaterials, having evolved over millions of years, often exceed man-made materials in their properties. Spider silk is one outstanding fibrous biomaterial which consists almost entirely of large proteins. Silk fibers have tensile strengths comparable to steel and some silks are nearly as elastic as rubber on a weight to weight basis. In combining these two properties, silks reveal a toughness that is two to three times that of synthetic fibers like Nylon or Kevlar. Spider silk is also antimicrobial, hypoallergenic and completely biodegradable.
This article focuses on the structure-function relationship of the characterized highly repetitive spider silk spidroins and their conformational conversion from solution into fibers. Such knowedge is of crucial importance to understanding the intrinsic properties of spider silk and to get insight into the sophisticated assembly processes of silk proteins. This review further outlines recent progress in recombinant production of spider silk proteins and their assembly into distinct polymer materials as a basis for novel products.
PMCID: PMC2658765  PMID: 19221522
biomimetics; biotechnology; protein folding; protein assembly; spinning
5.  A protocol for the production of recombinant spider silk-like proteins for artificial fiber spinning 
Nature protocols  2009;4(3):341-355.
The extreme strength and elasticity of spider silks originate from the modular nature of their repetitive proteins. To exploit such materials and mimic spider silks, comprehensive strategies to produce and spin recombinant fibrous proteins are necessary. This protocol describes silk gene design and cloning, protein expression in bacteria, recombinant protein purification and fiber formation. With an improved gene construction and cloning scheme, this technique is adaptable for the production of any repetitive fibrous proteins, and ensures the exact reproduction of native repeat sequences, analogs or chimeric versions. The proteins are solubilized in 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) at 25–30% (wt/vol) for extrusion into fibers. This protocol, routinely used to spin single micrometer-size fibers from several recombinant silk-like proteins from different spider species, is a powerful tool to generate protein libraries with corresponding fibers for structure–function relationship investigations in protein-based biomaterials. This protocol may be completed in 40 d.
doi:10.1038/nprot.2008.250
PMCID: PMC2720753  PMID: 19229199
6.  Protein-protein nanoimprinting of silk fibroin films 
Control of the interface between biological tissue and high technology materials is paramount for the development of future applications in biomedicine, especially in the case of implantable integrated devices for signal transduction.[1]-[3] Such work requires careful materials design to develop devices that can efficiently perform technological functions while retaining biocompatibility and biological integration. Silk fibroin protein from the Bombyx mori silkworm has come of considerable interest in this context, owing to its attractive mechanical,[4]-[7] biological, [8][9] and optical properties.[10][11] Recent work has shown adaptation of common micro- and nano-fabrication tools to silk films,[12]-[18] as well as silk protein secondary structure patterning techniques,[19] leading to biocompatible and degradable electronic and photonic devices which can simultaneously act as a carrier and stabilizer for protein pharmaceuticals and other bioactive reagents.[20]-[23] In particular, silk based nanoscale photonic devices face the challenge of sub-wavelength resolution fabrication on a soft polymeric substrate.[15][24] Previous work introduced the possibility of direct, rapid nanoimprinting in silk for the fabrication of photonic structures by leveraging the material properties of this protein.[25]
doi:10.1002/adma.201204678
PMCID: PMC3752341  PMID: 23483712
silk; biopolymer; protein; nanoimprinting; fabrication
7.  Increasing silk fibre strength through heterogeneity of bundled fibrils 
Can naturally arising disorder in biological materials be beneficial? Materials scientists are continuously attempting to replicate the exemplary performance of materials such as spider silk, with detailed techniques and assembly procedures. At the same time, a spider does not precisely machine silk—imaging indicates that its fibrils are heterogeneous and irregular in cross section. While past investigations either focused on the building material (e.g. the molecular scale protein sequence and behaviour) or on the ultimate structural component (e.g. silk threads and spider webs), the bundled structure of fibrils that compose spider threads has been frequently overlooked. Herein, I exploit a molecular dynamics-based coarse-grain model to construct a fully three-dimensional fibril bundle, with a length on the order of micrometres. I probe the mechanical behaviour of bundled silk fibrils with variable density of heterogenic protrusions or globules, ranging from ideally homogeneous to a saturated distribution. Subject to stretching, the model indicates that cooperativity is enhanced by contact through low-force deformation and shear ‘locking’ between globules, increasing shear stress transfer by up to 200 per cent. In effect, introduction of a random and disordered structure can serve to improve mechanical performance. Moreover, addition of globules allows a tuning of free volume, and thus the wettability of silk (with implications for supercontraction). These findings support the ability of silk to maintain near-molecular-level strength at the scale of silk threads, and the mechanism could be easily adopted as a strategy for synthetic fibres.
doi:10.1098/rsif.2013.0148
PMCID: PMC3627094  PMID: 23486175
computational mechanics; spider silk; fibre bundles; strength; shear transfer; free volume
8.  Elucidating Metabolic Pathways for Amino Acid Incorporation Into Dragline Spider Silk using 13C Enrichment and Solid State NMR 
Spider silk has been evolutionarily optimized for contextual mechanical performance over the last 400 million years. Despite precisely balanced mechanical properties, which have yet to be reproduced, the underlying molecular architecture of major ampullate spider silk can be simplified being viewed as a versatile block copolymer. Four primary amino acid motifs: polyalanine, (GA)n, GPGXX, and GGX (X = G,A,S,Q,L,Y) will be considered in this study. Although synthetic mimetics of many of these amino acid motifs have been produced in several biological systems, the source of spider silk’s mechanical integrity remains elusive. Mechanical robustness may be a product not only of the amino acid structure but also of the tertiary structure of the silk. Historically, solid state Nuclear Magnetic Resonance (ssNMR) has been used to reveal the crystalline structure of the polyalanine motif; however, limitations in amino acid labeling techniques have obscured the structures of the GGX and GPGXX motifs thought to be responsible for the structural mobility of spider silk. We describe the use of metabolic pathways to label tyrosine for the first time as well as to improve the labeling efficiency of proline. These improved labeling techniques will allow the previously unknown tertiary structures of major ampullate silk to be probed.
doi:10.1016/j.cbpa.2011.02.010
PMCID: PMC3624022  PMID: 21334448
9.  Chromosome Mapping of Dragline Silk Genes in the Genomes of Widow Spiders (Araneae, Theridiidae) 
PLoS ONE  2010;5(9):e12804.
With its incredible strength and toughness, spider dragline silk is widely lauded for its impressive material properties. Dragline silk is composed of two structural proteins, MaSp1 and MaSp2, which are encoded by members of the spidroin gene family. While previous studies have characterized the genes that encode the constituent proteins of spider silks, nothing is known about the physical location of these genes. We determined karyotypes and sex chromosome organization for the widow spiders, Latrodectus hesperus and L. geometricus (Araneae, Theridiidae). We then used fluorescence in situ hybridization to map the genomic locations of the genes for the silk proteins that compose the remarkable spider dragline. These genes included three loci for the MaSp1 protein and the single locus for the MaSp2 protein. In addition, we mapped a MaSp1 pseudogene. All the MaSp1 gene copies and pseudogene localized to a single chromosomal region while MaSp2 was located on a different chromosome of L. hesperus. Using probes derived from L. hesperus, we comparatively mapped all three MaSp1 loci to a single region of a L. geometricus chromosome. As with L. hesperus, MaSp2 was found on a separate L. geometricus chromosome, thus again unlinked to the MaSp1 loci. These results indicate orthology of the corresponding chromosomal regions in the two widow genomes. Moreover, the occurrence of multiple MaSp1 loci in a conserved gene cluster across species suggests that MaSp1 proliferated by tandem duplication in a common ancestor of L. geometricus and L. hesperus. Unequal crossover events during recombination could have given rise to the gene copies and could also maintain sequence similarity among gene copies over time. Further comparative mapping with taxa of increasing divergence from Latrodectus will pinpoint when the MaSp1 duplication events occurred and the phylogenetic distribution of silk gene linkage patterns.
doi:10.1371/journal.pone.0012804
PMCID: PMC2943472  PMID: 20877726
10.  Nanostructure and molecular mechanics of spider dragline silk protein assemblies 
Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.
doi:10.1098/rsif.2010.0149
PMCID: PMC2988266  PMID: 20519206
biological material; molecular modelling; materiomics; spider silk; deformation; failure
11.  New Opportunities for an Ancient Material 
Science (New York, N.Y.)  2010;329(5991):528-531.
Spiders and silkworms generate silk protein fibers that embody strength and beauty. Orb webs are fascinating feats of bioengineering in nature, displaying magnificent architectures while providing essential survival utility for spiders. The unusual combination of high strength and extensibility is a characteristic unavailable to date in synthetic materials yet is attained in nature with a relatively simple protein processed from water. This biological template suggests new directions to emulate in the pursuit of new high-performance, multifunctional materials generated with a green chemistry and processing approach. These bio-inspired and high-technology materials can lead to multifunctional material platforms that integrate with living systems for medical materials and a host of other applications.
doi:10.1126/science.1188936
PMCID: PMC3136811  PMID: 20671180
12.  Structural hierarchies define toughness and defect-tolerance despite simple and mechanically inferior brittle building blocks 
Scientific Reports  2011;1:35.
Mineralized biological materials such as bone, sea sponges or diatoms provide load-bearing and armor functions and universally feature structural hierarchies from nano to macro. Here we report a systematic investigation of the effect of hierarchical structures on toughness and defect-tolerance based on a single and mechanically inferior brittle base material, silica, using a bottom-up approach rooted in atomistic modeling. Our analysis reveals drastic changes in the material crack-propagation resistance (R-curve) solely due to the introduction of hierarchical structures that also result in a vastly increased toughness and defect-tolerance, enabling stable crack propagation over an extensive range of crack sizes. Over a range of up to four hierarchy levels, we find an exponential increase in the defect-tolerance approaching hundred micrometers without introducing additional mechanisms or materials. This presents a significant departure from the defect-tolerance of the base material, silica, which is brittle and highly sensitive even to extremely small nanometer-scale defects.
doi:10.1038/srep00035
PMCID: PMC3216522  PMID: 22355554
13.  Silk Self-Assembly Mechanisms and Control-From Thermodynamics to Kinetics 
Biomacromolecules  2012;13(3):826-832.
Silkworms and spiders generate fibres that exhibit high strength and extensibility. The underlying mechanisms involved in processing silk proteins into fiber form remain incompletely understood, resulting in the failure to fully recapitulate the remarkable properties of native fibers in vitro from regenerated silk solutions. In the present study, the extensibility and high strength of regenerated silks were achieved by mimicking the natural spinning process. Conformational transitions inside micelles, followed by aggregation of micelles and their stabilization as they relate to the metastable structure of silk are described. Subsequently, the mechanisms to control the formation of nanofibrous structures were elucidated. The results clarify that the self-assembly of silk in aqueous solution is a thermodynamically driven process where kinetics also play a key role. Four key factors, molecular mobility, charge, hydrophilic interactions and concentration underlie the process. Adjusting these factors can balance nanostructure and conformational composition, and be used to achieve silk-based materials with properties comparable to native fibers. These mechanisms suggest new directions to design silk-based multifunctional materials.
doi:10.1021/bm201731e
PMCID: PMC3302850  PMID: 22320432
Silk Self-Assembly; Biomaterials; Kinetics; Nanostructure
14.  Sequential origin in the high performance properties of orb spider dragline silk 
Scientific Reports  2012;2:782.
Major ampullate (MA) dragline silk supports spider orb webs, combining strength and extensibility in the toughest biomaterial. MA silk evolved ~376 MYA and identifying how evolutionary changes in proteins influenced silk mechanics is crucial for biomimetics, but is hindered by high spinning plasticity. We use supercontraction to remove that variation and characterize MA silk across the spider phylogeny. We show that mechanical performance is conserved within, but divergent among, major lineages, evolving in correlation with discrete changes in proteins. Early MA silk tensile strength improved rapidly with the origin of GGX amino acid motifs and increased repetitiveness. Tensile strength then maximized in basal entelegyne spiders, ~230 MYA. Toughness subsequently improved through increased extensibility within orb spiders, coupled with the origin of a novel protein (MaSp2). Key changes in MA silk proteins therefore correlate with the sequential evolution high performance orb spider silk and could aid design of biomimetic fibers.
doi:10.1038/srep00782
PMCID: PMC3482764  PMID: 23110251
15.  Antheraea pernyi Silk Fiber: A Potential Resource for Artificially Biospinning Spider Dragline Silk 
The outstanding properties of spider dragline silk are likely to be determined by a combination of the primary sequences and the secondary structure of the silk proteins. Antheraea pernyi silk has more similar sequences to spider dragline silk than the silk from its domestic counterpart, Bombyx mori. This makes it much potential as a resource for biospinning spider dragline silk. This paper further verified its possibility as the resource from the mechanical properties and the structures of the A. pernyi silks prepared by forcible reeling. It is surprising that the stress-strain curves of the A. pernyi fibers show similar sigmoidal shape to those of spider dragline silk. Under a controlled reeling speed of 95 mm/s, the breaking energy was 1.04 × 105 J/kg, the tensile strength was 639 MPa and the initial modulus was 9.9 GPa. It should be noted that this breaking energy of the A. pernyi silk approaches that of spider dragline silk. The tensile properties, the optical orientation and the β-sheet structure contents of the silk fibers are remarkably increased by raising the spinning speeds up to 95 mm/s.
doi:10.1155/2010/683962
PMCID: PMC2864894  PMID: 20454537
16.  Blueprint for a High-Performance Biomaterial: Full-Length Spider Dragline Silk Genes 
PLoS ONE  2007;2(6):e514.
Spider dragline (major ampullate) silk outperforms virtually all other natural and manmade materials in terms of tensile strength and toughness. For this reason, the mass-production of artificial spider silks through transgenic technologies has been a major goal of biomimetics research. Although all known arthropod silk proteins are extremely large (>200 kiloDaltons), recombinant spider silks have been designed from short and incomplete cDNAs, the only available sequences. Here we describe the first full-length spider silk gene sequences and their flanking regions. These genes encode the MaSp1 and MaSp2 proteins that compose the black widow's high-performance dragline silk. Each gene includes a single enormous exon (>9000 base pairs) that translates into a highly repetitive polypeptide. Patterns of variation among sequence repeats at the amino acid and nucleotide levels indicate that the interaction of selection, intergenic recombination, and intragenic recombination governs the evolution of these highly unusual, modular proteins. Phylogenetic footprinting revealed putative regulatory elements in non-coding flanking sequences. Conservation of both upstream and downstream flanking sequences was especially striking between the two paralogous black widow major ampullate silk genes. Because these genes are co-expressed within the same silk gland, there may have been selection for similarity in regulatory regions. Our new data provide complete templates for synthesis of recombinant silk proteins that significantly improve the degree to which artificial silks mimic natural spider dragline fibers.
doi:10.1371/journal.pone.0000514
PMCID: PMC1885213  PMID: 17565367
17.  Water-Insoluble Silk Films with Silk I Structure 
Acta biomaterialia  2009;6(4):1380-1387.
Water-insoluble regenerated silk materials are normally achieved by increasing β-sheet content (silk II). In the present study, water-insoluble silk films were prepared by controlling very slow drying of B. mori silk solutions, resulting in the formation of stable films with dominating silk I instead of silk II structure. Wide angle x-ray scattering (WAXS) indicated that the silk films stabilized by slow drying were mainly composed of silk I rather than silk II, while water- and methanol-annealed silk films had a higher silk II content. The silk films prepared through slow drying had a globule-like structure in the core with nano-filaments. The core region was composed of silk I and silk II, and these regions are surrounded by hydrophilic nano-filaments containing random, turns, and α-helix secondary structures. The insoluble silk films prepared by slow drying had unique thermal, mechanical and degradative properties. DSC results revealed that silk I crystals had stable thermal properties up to 250°C, without crystallization above the Tg, but degraded in lower temperature than silk II structure. Compared with water- and methanol-annealed films, the films prepared through slow drying achieved better mechanical ductility and more rapid enzymatic degradation, reflective of the differences in secondary structure achieved via differences in post processing of the cast silk films. Importantly, the silk I structure, a key intermediate secondary structure for the formation of mechanically robust natural silk fibers, was successfully generated in the present approach of very slow drying, mimicking the natural process. The results also point to a new mode to generate new types of silk biomaterials, where mechanical properties can be enhanced, and degradation rates increased, yet water insolubility is maintained along with low beta sheet content.
doi:10.1016/j.actbio.2009.10.041
PMCID: PMC2830340  PMID: 19874919
silk I; silk II; water-insoluble; films
18.  Bioprospecting Finds the Toughest Biological Material: Extraordinary Silk from a Giant Riverine Orb Spider 
PLoS ONE  2010;5(9):e11234.
Background
Combining high strength and elasticity, spider silks are exceptionally tough, i.e., able to absorb massive kinetic energy before breaking. Spider silk is therefore a model polymer for development of high performance biomimetic fibers. There are over 41.000 described species of spiders, most spinning multiple types of silk. Thus we have available some 200.000+ unique silks that may cover an amazing breadth of material properties. To date, however, silks from only a few tens of species have been characterized, most chosen haphazardly as model organisms (Nephila) or simply from researchers' backyards. Are we limited to ‘blindly fishing’ in efforts to discover extraordinary silks? Or, could scientists use ecology to predict which species are likely to spin silks exhibiting exceptional performance properties?
Methodology
We examined the biomechanical properties of silk produced by the remarkable Malagasy ‘Darwin's bark spider’ (Caerostris darwini), which we predicted would produce exceptional silk based upon its amazing web. The spider constructs its giant orb web (up to 2.8 m2) suspended above streams, rivers, and lakes. It attaches the web to substrates on each riverbank by anchor threads as long as 25 meters. Dragline silk from both Caerostris webs and forcibly pulled silk, exhibits an extraordinary combination of high tensile strength and elasticity previously unknown for spider silk. The toughness of forcibly silked fibers averages 350 MJ/m3, with some samples reaching 520 MJ/m3. Thus, C. darwini silk is more than twice tougher than any previously described silk, and over 10 times better than Kevlar®. Caerostris capture spiral silk is similarly exceptionally tough.
Conclusions
Caerostris darwini produces the toughest known biomaterial. We hypothesize that this extraordinary toughness coevolved with the unusual ecology and web architecture of these spiders, decreasing the likelihood of bridgelines breaking and collapsing the web into the river. This hypothesis predicts that rapid change in material properties of silk co-occurred with ecological shifts within the genus, and can thus be tested by combining material science, behavioral observations, and phylogenetics. Our findings highlight the potential benefits of natural history–informed bioprospecting to discover silks, as well as other materials, with novel and exceptional properties to serve as models in biomimicry.
doi:10.1371/journal.pone.0011234
PMCID: PMC2939878  PMID: 20856804
19.  Flexibility regeneration of silk fibroin in vitro 
Biomacromolecules  2012;13(7):2148-2153.
Although natural silk fibers have excellent strength and flexibility, the regenerated silk materials generally become brittle in the dry state. How to reconstruct the flexibility for silk fibroin has bewildered scientists for many years. In the present study, the flexible regenerated silk fibroin films were achieved by simulating the natural forming and spinning process. Silk fibroin films composed of silk I structure were firstly prepared by slow drying process. Then the silk fibroin films were stretched in the wet state, following the structural transition from silk I to silk II. The difference between the flexible film and different brittle regenerated films was investigated to reveal the critical factors in regulating the flexibility of regenerated silk materials. Compared to the methanol-treated silk films, although having similar silk II structure and water content, the flexible silk films contained more bound water rather than free water, implying the great influence of bound water on the flexibility. Then, further studies revealed that the distribution of bound water was also a critical factor in improving silk flexibility in the dry state, which could be regulated by the nano-assembly of silk fibroin. Importantly, the results further elucidate the relation between mechanical properties and silk fibroin structures, pointing to a new mode of generating new types of silk materials with enhanced mechanical properties in the dry state, which would facilitate the fabrication and application of regenerated silk fibroin materials in different fields.
doi:10.1021/bm300541g
PMCID: PMC3393754  PMID: 22632113
silk; mechanical regeneration; flexibility; bound water
20.  Post-secretion processing influences spider silk performance 
Phenotypic variation facilitates adaptations to novel environments. Silk is an example of a highly variable biomaterial. The two-spidroin (MaSp) model suggests that spider major ampullate (MA) silk is composed of two proteins—MaSp1 predominately contains alanine and glycine and forms strength enhancing β-sheet crystals, while MaSp2 contains proline and forms elastic spirals. Nonetheless, mechanical properties can vary in spider silks without congruent amino acid compositional changes. We predicted that post-secretion processing causes variation in the mechanical performance of wild MA silk independent of protein composition or spinning speed across 10 species of spider. We used supercontraction to remove post-secretion effects and compared the mechanics of silk in this ‘ground state’ with wild native silks. Native silk mechanics varied less among species compared with ‘ground state’ silks. Variability in the mechanics of ‘ground state’ silks was associated with proline composition. However, variability in native silks did not. We attribute interspecific similarities in the mechanical properties of native silks, regardless of amino acid compositions, to glandular processes altering molecular alignment of the proteins prior to extrusion. Such post-secretion processing may enable MA silk to maintain functionality across environments, facilitating its function as a component of an insect-catching web.
doi:10.1098/rsif.2012.0277
PMCID: PMC3427525  PMID: 22628213
biomaterial plasticity; MaSp expression model; mechanical properties; orb web; spider silk; supercontraction
21.  Recombinant Minimalist Spider Wrapping Silk Proteins Capable of Native-Like Fiber Formation 
PLoS ONE  2012;7(11):e50227.
Spider silks are desirable biomaterials characterized by high tensile strength, elasticity, and biocompatibility. Spiders produce different types of silks for different uses, although dragline silks have been the predominant focus of previous studies. Spider wrapping silk, made of the aciniform protein (AcSp1), has high toughness because of its combination of high elasticity and tensile strength. AcSp1 in Argiope trifasciata contains a 200-aa sequence motif that is repeated at least 14 times. Here, we produced in E. coli recombinant proteins consisting of only one to four of the 200-aa AcSp1 repeats, designated W1 to W4. We observed that purified W2, W3 and W4 proteins could be induced to form silk-like fibers by shear forces in a physiological buffer. The fibers formed by W4 were ∼3.4 µm in diameter and up to 10 cm long. They showed an average tensile strength of 115 MPa, elasticity of 37%, and toughness of 34 J cm−3. The smaller W2 protein formed fewer fibers and required a higher protein concentration to form fibers, whereas the smallest W1 protein did not form silk-like fibers, indicating that a minimum of two of the 200-aa repeats was required for fiber formation. Microscopic examinations revealed structural features indicating an assembly of the proteins into spherical structures, fibrils, and silk-like fibers. CD and Raman spectral analysis of protein secondary structures suggested a transition from predominantly α-helical in solution to increasingly β-sheet in fibers.
doi:10.1371/journal.pone.0050227
PMCID: PMC3509139  PMID: 23209681
22.  Solid-State NMR Comparison of Various Spiders’ Dragline Silk Fiber 
Biomacromolecules  2010;11(8):2039-2043.
Major ampullate (dragline) spider silk is a coveted biopolymer due to its combination of strength and extensibility. The dragline silk of different spiders have distinct mechanical properties that can be qualitatively correlated to the protein sequence. This study uses amino acid analysis and carbon-13 solid-state NMR to compare the molecular composition, structure and dynamics of major ampullate dragline silk of four orb-web spider species (Nephila clavipes, Araneus gemmoides, Argiope aurantia and Argiope argentata) and one cobweb species (Latrodectus hesperus). The mobility of the protein backbone and amino acid side chains in water exposed silk fibers is shown to correlate to the proline content. This implies that regions of major ampullate spidroin 2 protein, which is the only dragline silk protein with any significant proline content, become significantly hydrated in dragline spider silk.
doi:10.1021/bm100399x
PMCID: PMC2922512  PMID: 20593757
solid-state NMR; spider silk; major ampullate silk; hydration dynamics; dragline silk; protein polymer
23.  Bond energy effects on strength, cooperativity and robustness of molecular structures 
Interface Focus  2011;1(5):734-743.
A fundamental challenge in engineering biologically inspired materials and systems is the identification of molecular structures that define fundamental building blocks. Here, we report a systematic study of the effect of the energy of chemical bonds on the mechanical properties of molecular structures, specifically, their strength and robustness. By considering a simple model system of an assembly of bonds in a cluster, we demonstrate that weak bonding, as found for example in H-bonds, results in a highly cooperative behaviour where clusters of bonds operate synergistically to form relatively strong molecular clusters. The cooperative effect of bonding results in an enhanced robustness since the drop of strength owing to the loss of a bond in a larger cluster only results in a marginal reduction of the strength. Strong bonding, as found in covalent interactions such as disulphide bonds or in the backbone of proteins, results in a larger mechanical strength. However, the ability for bonds to interact cooperatively is lost, and, as a result, the overall robustness is lower since the mechanical strength hinges on individual bonds rather than a cluster of bonds. The systematic analysis presented here provides general insight into the interplay of bond energy, robustness and other geometric parameters such as bond spacing. We conclude our analysis with a correlation of structural data of natural protein structures, which confirms the conclusions derived from our study.
doi:10.1098/rsfs.2011.0038
PMCID: PMC3262282  PMID: 23050078
molecular mechanics; strength; robustness; failure; deformation; materiomics
24.  Interactions between Spider Silk and Cells – NIH/3T3 Fibroblasts Seeded on Miniature Weaving Frames 
PLoS ONE  2010;5(8):e12032.
Background
Several materials have been used for tissue engineering purposes, since the ideal matrix depends on the desired tissue. Silk biomaterials have come to focus due to their great mechanical properties. As untreated silkworm silk has been found to be quite immunogenic, an alternative could be spider silk. Not only does it own unique mechanical properties, its biocompatibility has been shown already in vivo. In our study, we used native spider dragline silk which is known as the strongest fibre in nature.
Methodology/Principal Findings
Steel frames were originally designed and manufactured and woven with spider silk, harvesting dragline silk directly out of the animal. After sterilization, scaffolds were seeded with fibroblasts to analyse cell proliferation and adhesion. Analysis of cell morphology and actin filament alignment clearly revealed adherence. Proliferation was measured by cell count as well as determination of relative fluorescence each after 1, 2, 3, and 5 days. Cell counts for native spider silk were also compared with those for trypsin-digested spider silk. Spider silk specimens displayed less proliferation than collagen- and fibronectin-coated cover slips, enzymatic treatment reduced adhesion and proliferation rates tendentially though not significantly. Nevertheless, proliferation could be proven with high significance (p<0.01).
Conclusion/Significance
Native spider silk does not require any modification to its application as a biomaterial that can rival any artificial material in terms of cell growth promoting properties. We could show adhesion mechanics on intracellular level. Additionally, proliferation kinetics were higher than in enzymatically digested controls, indicating that spider silk does not require modification. Recent findings concerning reduction of cell proliferation after exposure could not be met. As biotechnological production of the hierarchical composition of native spider silk fibres is still a challenge, our study has a pioneer role in researching cellular mechanics on native spider silk fibres.
doi:10.1371/journal.pone.0012032
PMCID: PMC2918503  PMID: 20711495
25.  Recombinant DNA production of spider silk proteins 
Microbial biotechnology  2013;6(6):651-663.
Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks.
doi:10.1111/1751-7915.12081
PMCID: PMC3815454  PMID: 24119078

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