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PubMedDate not supplied

X-ray evidence for a "super"-secondary structure in silk fibers.

X-ray studies on degummed B. mori silk fibers and on hydrogels prepared under a variety of conditions reveal moderately small angle reflections. These reflections are often highly oriented and are correlated to silk II lattice reflections. A superstructure can explain these features. Silk fibroin hydrogels were monitored as they dried to form the silk II structure. The silk II wide angle and moderately small angle patterns obtained from dried hydrogels and silk fibers are identical. The "superstructure" reflections at moderately small angle (3-7 nm) were first to appear, followed by the "intersheet" spacing, and then the remainder of the silk II wide angle scattering pattern. Thus, any superstructure hypothesized for the hydrogels (and for Silk II in fibers) must be both stable in a highly hydrated environment and must convert to silk II with little large scale diffusion. A folded structure, similar to amyloids and cross-beta-sheets but with much longer beta-strand stems, is proposed for silk II in fibers.

Animals↗

PubMedDate not supplied

Characterization of a protein-based adhesive elastomer secreted by the Australian frog Notaden bennetti.

When provoked, Notaden bennetti frogs secrete an exudate which rapidly forms a tacky elastic solid ("frog glue"). This protein-based material acts as a promiscuous pressure-sensitive adhesive that functions even in wet conditions. We conducted macroscopic tests in air to assess the tensile strength of moist glue (up to 78 +/- 8 kPa) and the shear strength of dry glue (1.7 +/- 0.3 MPa). We also performed nanomechanical measurements in water to determine the adhesion (1.9-7.2 nN or greater), resilience (43-56%), and elastic modulus (170-1035 kPa) of solid glue collected in different ways. Dry glue contains little carbohydrate and consists mainly of protein. The protein complement is rich in Gly (15.8 mol %), Pro (8.8 mol %), and Glu/Gln (14.1 mol %); it also contains some 4-hydroxyproline (4.6 mol %) but no 5-hydroxylysine or 3,4-dihydroxyphenylalanine (L-Dopa). Denaturing gel electrophoresis of the glue reveals a characteristic pattern of proteins spanning 13-400 kDa. The largest protein (Nb-1R, apparent molecular mass 350-500 kDa) is also the most abundant, and this protein appears to be the key structural component. The solid glue can be dissolved in dilute acids; raising the ionic strength causes the glue components to self-assemble spontaneously into a solid which resembles the starting material. We describe scattering studies on dissolved and solid glue and provide microscopy images of glue surfaces and sections, revealing a porous interior that is consistent with the high water content (85-90 wt %) of moist glue. In addition to compositional similarities with other biological adhesives and well-known elastomeric proteins, the circular dichroism spectrum of dissolved glue is almost identical to that for soluble elastin and electron and scanning probe microscopy images invite comparison with silk fibroins. Covalent cross-linking does not seem to be necessary for the glue to set.

Adhesiveness↗

PubMed2006

Carbon nanotube reinforced Bombyx mori silk nanofibers by the electrospinning process.

Nanocomposite fibers of Bombyx mori silk and single wall carbon nanotubes (SWNT) were produced by the electrospinning process. Regenerated silk fibroin dissolved in a dispersion of carbon nanotubes in formic acid was electrospun into nanofibers. The morphology, structure, and mechanical properties of the electrospun nanofibers were examined by field emission environmental scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, and microtensile testing. TEM of the reinforced fibers shows that the single wall carbon nanotubes are embedded in the fibers. The mechanical properties of the SWNT reinforced fiber show an increase in Young's modulus up to 460% in comparison with the un-reinforced aligned fiber, but at the expense of the strength and strain to failure.

Animals↗

PubMed2006

Conformational study of silk-like peptides containing the calcium-binding sequence from calbindin D9k using 13C CP/MAS NMR spectroscopy.

The calcium-binding sites of calbindin D(9k) have a helix-loop-helix motif. In this study, the helix motifs were replaced by several Ala-Gly repeating regions designed on the basis of the primary sequences of several silk fibroins. The synthesized peptides were treated with several organic solvents to modify the secondary structure of the Ala-Gly repeating regions. The local structures of the Ala-Gly repeating regions, as well as the calcium-binding motif, D(9k)-loop (D(9k)L), were determined by (13)C CP/MAS NMR spectroscopy. In the four peptides containing D(9k)L synthesized, the poly(Ala) domains retain the ability to undergo a conformational transition from alpha-helical to beta-sheet in (A)(12)-D(9k)L despite the presence of the D(9k)L domain at the center of the peptide molecule, but the presence of this domain in the other model peptides synthesized has a marked effect on the conformation of the added silk-like domains. The results showed that the structures of the Ala-Gly repeating regions can be controlled by the choice of both the organic solvent and the amino acid sequence of the Ala-Gly repeating regions without disrupting the secondary structure of D(9k)L suggesting that it may retain its ability to bind calcium ions.

Binding Sites↗

PubMed2006

Conformational study of silklike peptides modified by the addition of the calcium-binding sequence from the shell nacreous matrix protein MSI60 using 13C CP/MAS NMR spectroscopy.

The calcium-binding site of the pearl oyster (Pinctada fucata) nacreous layer matrix protein MSI60 was introduced between different Ala-Gly repeating regions derived from the primary sequences of several silk fibroins. Several different organic solvents whose effect on the repetitive domains of silk peptides is well-understood were used to modify the secondary structure of the flanking Ala-Gly repeating regions. The local conformations of the flanking Ala-Gly repeating regions as well as the calcium-binding motif, MSI60, were determined by 13C CP/MAS NMR spectroscopy. The secondary structures of the polyalanine, poly(Ala), domains were modified by the solvent treatments in a predictable fashion, suggesting that only the solvent treatment and not the conformation of the MSI60 domain affected the conformation of poly(Ala) regions. Ala-Gly domains behaved differently, taking random coil conformation regardless of the choice of solvent, indicating that their secondary structure is affected by the central MSI60 domain. The conformation of the MSI60 domain is not altered by the solvent treatments, suggesting that it may retain its ability to bind calcium ions. This was confirmed using a calcium-binding assay. The assay further showed that the calcium-binding capability of MSI60 in the synthetic peptides was most effective when the flanking domain was in the beta-sheet structure.

Amino Acid Sequence↗

PubMedDate not supplied

Genetic engineering of structural protein polymers.

Genetic and protein engineering are components of a new polymer chemistry that provide the tools for producing macromolecular polyamide copolymers of diversity and precision far beyond the current capabilities of synthetic polymer chemistry. The genetic machinery allows molecular control of chemical and physical chain properties. Nature utilizes this control to formulate protein polymers into materials with extraordinary mechanical properties, such as the strength and toughness of silk and the elasticity and resilience of mammalian elastin. The properties of these materials have been attributed to the presence of short repeating oligopeptide sequences contained in the proteins, fibroin, and elastin. We have produced homoblock protein polymers consisting exclusively of silk-like crystalline blocks and elastin-like flexible blocks. We have demonstrated that each homoblock polymer as produced by microbial fermentation exhibits measurable properties of crystallinity and elasticity. Additionally, we have produced alternating block copolymers of various amounts of silk-like and elastin-like blocks, ranging from a ratio of 1:4 to 2:1, respectively. The crystallinity of each copolymer varies with the amount of crystalline block interruptions. The production of fiber materials with custom-engineered mechanical properties is a potential outcome of this technology.

Amino Acid Sequence↗

PubMed2003

Determination of the torsion angles of alanine and glycine residues of model compounds of spider silk (AGG)(10) using solid-state NMR methods.

Spiders synthesize several kinds of silk fibers. In the primary structure of spider silk, one of the major ampullate (dragline, frame) silks, spidroin 1, and flagelliform silk (core fibers of adhesive spiral), there are common repeated X-Gly-Gly (X = Ala, Leu, Pro, Tyr, Glu, and Arg) sequences, which are considered to be related to the elastic character of these fibers. In this paper, two dimensional spin diffusion solid-state NMR under off magic angle spinning (OMAS), (13)C chemical shift contour plots, and Rotational Echo DOuble Resonance (REDOR) were applied to determine the torsion angles of one Ala and two kinds of Gly residues in the Ala-Gly-Gly sequence of (13)C=O isotope-labeled (Ala-Gly-Gly)(10). The torsion angles were determined to be (phi, psi) = (-90 degrees, 150 degrees ) within an experimental error of +/-10 degrees for each residue. This conformation is characterized as 3(1) helix which is in agreement with the structure proposed from the X-ray powder diffraction pattern of poly(Ala-Gly-Gly). The 3(1) helix of (Ala-Gly-Gly)(10) does not change by formic acid treatment although (Ala-Gly)(15) easily changes from the silk I conformation (the structure of Bombyx mori silk fibroin before spinning in the solid state) to silk II conformation (the structure of the silk fiber after spinning) by such treatment. Thus, the 3(1) helix conformation of (Ala-Gly-Gly)(10) is considered very stable. Furthermore, the torsion angles of the 16th Leu residue of (Leu-Gly-Gly)(10) were also determined as (phi, psi) = (-90 degrees, 150 degrees ) and this peptide is also considered to take 3(1) helix conformation.

Alanine↗

PubMed2003

The silk protein, sericin, protects against cell death caused by acute serum deprivation in insect cell culture.

Sericin is the silk protein that covers fibroin fibers and functions as a 'glue' in the cocoons of silkworms, and its most abundant component, Ser1, contains repeats of Ser- and Thr-rich 38 amino acid residues. The viability of Sf9 insect cells was 20, 57 and 49% on the fifth day and 41, 91 and 70% on the ninth day after serum deprivation in the presence of no additives, 3000 microg sericin hydrolysate and 350 microg SerD (the peptide containing the two repetitive units) ml(-1), respectively. Thus, the sericin samples were useful in preventing cell death and promoting cellular growth after acute serum deprivation.

Animals↗

PubMed2003

Molecular nanosprings in spider capture-silk threads.

Spider capture silk is a natural material that outperforms almost any synthetic material in its combination of strength and elasticity. The structure of this remarkable material is still largely unknown, because spider-silk proteins have not been crystallized. Capture silk is the sticky spiral in the webs of orb-weaving spiders. Here we are investigating specifically the capture spiral threads from Araneus, an ecribellate orb-weaving spider. The major protein of these threads is flagelliform protein, a variety of silk fibroin. We present models for molecular and supramolecular structures of flagelliform protein, derived from amino acid sequences, force spectroscopy (molecular pulling) and stretching of bulk capture web. Pulling on molecules in capture-silk fibres from Araneus has revealed rupture peaks due to sacrificial bonds, characteristic of other self-healing biomaterials. The overall force changes are exponential for both capture-silk molecules and intact strands of capture silk.

Animals↗

PubMed2002

Soluble silk-like organic matrix in the nacreous layer of the bivalve Pinctada maxima.

Nacre organic matrix has been conventionally classified as both 'water-soluble' and 'water-insoluble', based on its solubility in aqueous solutions after decalcification with acid or EDTA. Some characteristics (aspartic acid-rich, silk-fibroin-like content) were specifically attributed to either one or the other. The comparative study on the technique of extraction (extraction with water alone vs. demineralization with EDTA) presented here, seems to reveal that this generally accepted classification may need to be reconsidered. Actually, the nondecalcified soluble organic matrix, extracted in ultra-pure water, displays many of the characteristics of what until now has been called 'insoluble matrix'. We present the results obtained on this extract and on a conventional EDTA-soluble matrix, with various characterization methods: fractionation by size-exclusion and anion-exchange HPLC, amino acid analysis, glycosaminoglycan and calcium quantification, SDS/PAGE and FTIR spectroscopy. We propose that the model for the interlamellar matrix sheets of nacre given by Nakahara [In: Biomineralization and Biological Metal Accumulation, Westbroek, P. & deJong, E.W., eds, (1983) pp. 225-230. Reidel, Dordrecht, Holland] and Weiner and Traub [Phil. Trans. R. Soc. Lond. B (1984) 304, 425-434] may no longer be valid. The most recent model, proposed by Levi-Kalisman et al. [J. Struct. Biol. (2001) 135, 8-17], seemed to be more in accordance with our findings.

Amino Acids↗

PubMed1999

Primary structure and possible functions of a trypsin inhibitor of Bombyx mori.

A protein with a low molecular mass of 6027 was purified from cocoon shell of silkworm, Bombyx mori. Two-dimensional polyacrylamide gel electrophoresis (2D/PAGE) resolved this protein into a single spot with pI 4.3 and Mr 6000. Amino acid sequence analysis revealed that this protein consists of 55 amino acids, six of these being cysteine residues and is highly homologous to bovine pancreatic trypsin inhibitor-type inhibitors. The 6-kDa protein is heat stable and acid stable and inhibits bovine trypsin by forming a low-dissociation complex with trypsin in a 1 : 1 molar ratio (Ki = 2.8 x 10-10), but does not alpha-chymotrypsin. This cocoon shell-associated trypsin inhibitor (CSTI) was thus concluded to belong to the bovine pancreatic trypsin inhibitor class. CSTI was developmentally regulated in the silk gland at the final stage of larval growth, and its specific distribution in the middle silk gland, an organ in which silk proteins are stored during the final larval instar, occurred before the onset of spinning. This inhibitor protects the tryptic degradation of fibroin light (L) chain in vitro. These results suggest that this trypsin inhibitor may play an important part on regulating proteolytic activity in the silk gland or protecting silk proteins from degradation during histolysis.

Amino Acid Sequence↗

PubMed2001

Insect silk contains both a Kunitz-type and a unique Kazal-type proteinase inhibitor.

Insect silk is made up of structural fibrous (fibroins) and sticky (sericins) proteins, and contains a few small peptides of hitherto unknown functions. We demonstrate that two of these peptides inhibit bacterial and fungal proteinases (subtilisin, proteinase K and pronase). These 'silk proteinase inhibitors' 1 and 2 (SPI 1 and 2) are produced in the middle section of the silk-secreting glands prior to cocoon spinning and their production is controlled at transcription level. The full length cDNA of pre-SPI 1 contains 443 nucleotides and encodes a peptide of 76 amino-acid residues, of which 20 make up a signal sequence. The mature SPI 1 (6056.7 Da, 56 residues) is a typical thermostable Kunitz-type proteinase inhibitor with Arg in P1 position. The cDNA of pre-SPI 2 consists of 260 nucleotides and yields a putative secretory peptide of 58 amino-acid residues. The functional SPI 2 (3993 Da, 36 residues) is a single-domain Kazal-type proteinase inhibitor with unique structural features: free segment of the N-terminus is reduced to a single amino-acid residue, lack of CysI and CysV precludes formation of the A-ring and provides increased flexibility to the C-ring, and absence of several residues around the normal position of CysV shortens and changes the alpha helix segment of the protein. The structure reveals that the length and arrangement of the B-ring, including exposure of the P1 residue, and the position of the C-terminus relative to the B-loop, are essential for the activity of the Kazal-type inhibitors.

Amino Acid Sequence↗

PubMed2000

Promotive effects of a silk film on epidermal recovery from full-thickness skin wounds.

We examined the effects of the transparent fibroin film (silk film) on full-thickness skin wounds. Full-thickness dermatotomies (15 mm x 9 mm) were prepared on the dorsal wall of CRJ:CD-1 nu/nu (ICR nu/nu) mice. The area of the wounds dressed with silk film was reduced to 10% of that made by the dermatotomy 14 days after the dermatotomy and were covered with regenerated epidermis 21 days after the dermatotomy. In contrast, less recovery and epidermal regeneration were found 14 days after dermatotomy in the wounds dressed with a conventional hydrocolloid dressing (Duro Active). Furthermore, only partial incomplete epidemal growth was obtained 21 days after dermatotomy. Most importantly, the healing time of wounds dressed with silk film was 7 days shorter than those dressed with DuoActive dressing. The silk film showed an almost similar or slightly better promotive effect as the lyophilized porcine dermis (Alloask D), which is used as a dressing for burns, ulcers, and decubitis. Histologic findings revealed that there was greater collagen regeneration and less inflammation and neutrophil-lymphocyte infiltration of the wounds dressed with silk film than with DuoActive dressing. It is clear that regeneration of the epidermis and dermis of the wound beds covered with silk film was faster than with DuoActive dressing. Finally, silk film is easily obtainable, sterilizable, and transparent, and it allows easy observation of tissue recovery. Therefore, silk film offers advantages over other dressings and may be clinically useful for wound treatment.

Animals↗

PubMed1980

Transcription units of chicken ovalbumin gene observed after injection of cloned complete genes into Xenopus oocyte nuclei.

The organization of transcription of a well-characterized protein encoding gene was studied by microinjection and electron microscopy. Circular recombinant DNA molecules containing the complete chicken ovalbumin sequences (7.7 kilobases, contained in 11.5 kilobases of chicken DNA) were microinjected into germinal vesicles of living oocytes of the clawed toad Xenopus laevis, and their transcription was studied in nuclear spread preparations. Evaluation of spread chromatin showed a limited number of observed molecules transcribed in "specific" patterns--i.e., circular chromatin molecules containing transcription units approximately 2.3 micrometer long, consisting of regular series of densely packed lateral ribonucleoprotein fibrils gradually increasing in length. The appearance of these fibril gradients was similar to that of actively transcribed endogenous protein encoding genes contained in lampbrush-chromosome loops of the same nuclei and to the putative Bombyx silk fibroin transcription units. In addition, less-regular arrays of transcript fibrils were seen in some circles, including fully fibril-covered molecules, indicative of the occurrence of irregular transcriptional events. The results of this heterologous transcription experiment indicate that the transcriptional machinery of the amphibian oocyte nucleus is capable of transcribing protein encoding genes from an avian species in typical regular arrays of transcription units.

Animals↗

PubMed1981

Discrete-length repeated sequences in eukaryotic genomes.

Two of the four repeated DNA sequences near the 5' end of the silk fibroin gene hybridize with discrete-length families of repeated DNA. These two families comprise 0.5% of the animal's genome. A repeated sequence with a conserved length has also been found in the short class of moderately repeated sequences in the sea urchin. The discrete length, interspersion, and sequence fidelity of these moderately repeated sequences suggests that each has been multiplied as a discrete unit. Thus, transposition mechanisms may be responsible for the multiplication and dispersion of a large class of repeated sequences in phylogenetically diverse eukaryotic genomes. The repeat we have studied in most detail differs from previously described eukaryotic transposable elements: it is much shorter (1300 base pairs) and does not have terminal repetitions detectable by DNA hybridization. A simple technique for identifying such discrete-length repeated sequences is described.

Animals↗

PubMed1982

Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes.

We have attempted to ascertain the correlation between the genetic information content in the exons and the surrounding intron sequences with regard to their spatial arrangement within a gene. A comparison is made of the sizes, taken from recent publications, of exons and introns of approximately equal to 80 different protein-coding chromosomal genes, mostly from higher eukaryotes. The exons of these genes do not show very marked variation in size and can be classified into three major discrete and two minor additional size groups, whereas individual introns vary considerably in size within and between genes. Notwithstanding, the overall length of all introns present within a given gene is a function of the total size, mostly corresponding to the total genetic information content, of the exons. Three cases that violate this exon-size dependency of introns are genes coding for (i) histone H1, feather keratin, and interferons, (ii) tubulin and actin, and (iii) silk fibroin. The exons of these genes are larger than 0.7 kilobase pair in total size and the genes show a strong sequence homogeneity among the repetitious family members or internal repeats of coding sequences within the gene. We propose that conservation of sequences, which is required by the family members, internal repeats, or the entire gene, would actually motivate the removal of introns.

Animals↗

PubMed1990

Structure of a protein superfiber: spider dragline silk.

Spider major ampullate (dragline) silk is an extracellular fibrous protein with unique characteristics of strength and elasticity. The silk fiber has been proposed to consist of pseudocrystalline regions of antiparallel beta-sheet interspersed with elastic amorphous segments. The repetitive sequence of a fibroin protein from major ampullate silk of the spider Nephila clavipes was determined from a partial cDNA clone. The repeating unit is a maximum of 34 amino acids long and is not rigidly conserved. The repeat unit is composed of three different segments: (i) a 6 amino acid segment that is conserved in sequence but has deletions of 3 or 6 amino acids in many of the repeats; (ii) a 13 amino acid segment dominated by a polyalanine sequence of 5-7 residues; (iii) a 15 amino acid, highly conserved segment. The latter is predominantly a Gly-Gly-Xaa repeat with Xaa being alanine, tyrosine, leucine, or glutamine. The codon usage for this DNA is highly selective, avoiding the use of cytosine or guanine in the third position. A model for the physical properties of fiber formation, strength, and elasticity, based on this repetitive protein sequence, is presented.

Amino Acid Sequence↗

PubMed1998

A potential mediator of collagenous block copolymer gradients in mussel byssal threads.

Mussel byssal threads contain unusual block copolymer-like proteins that combine collagen with flanking domains that resemble silk-fibroin (preCol-D) or elastin (preCol-P). These are distributed in complementary gradients along the length of the threads and as precursors in the mussel foot. We discuss a 76-kDa precursor, preCol-NG, from a cDNA library of the foot where it has no gradient but rather is distributed evenly along the distal to proximal axis. A pepsin-resistant fragment of preCol-NG has been confirmed in byssal threads. Like preCol-D and -P, this protein has a central collagenous domain, flanking domains, an acidic patch, and histidine-rich termini. The flanking domains of preCol-NG resemble the glycine-rich proteins of plant cell walls with tandem XGlyn repeats where X denotes alanine, leucine, or asparagine but not proline. Similarity with the (glycine-alanine) repeats and poly(alanine) runs of arthropod silks also exists. Based on available evidence, a model of preCol axial assembly is proposed in which preCol-NG functions as a mediator between preCol-D/-P molecules. This is consistent with the observed progression of mechanical properties in byssal threads.

Amino Acid Sequence↗