X-ray diffraction evidence for cross-bridge formation in relaxed muscle fibers at various ionic strengths

Equatorial x-ray diffraction patterns from single skinned rabbit psoas fibers were studied at various ionic strengths to obtain structural information regarding cross-bridge formation in relaxed muscle fibers. At ionic strengths between 20 and 50 mM, the intensity of the 11 reflection, I11, of the relaxed state was close to that of the rigor state, whereas the intensity of the 10 reflection, I10, was approximately twice that of rigor reflection. Calculations by two-dimensional Fourier synthesis indicated that substantial extra mass was associated with the thin filaments under these conditions. With increasing ionic strength between 20 and 100 mM, I10 increased and I11 decreased in an approximately linear way, indicating net transfer of mass away from the thin filaments towards the thick filaments. These results provided evidence that cross-bridges were formed in a relaxed fiber at low ionic strengths, and that the number of cross-bridges decreased as ionic strength was raised. Above mu = 100 mM, I10 and I11 both decreased, indicating the onset of increasing disorder within the filament lattice.     

Investigation of the nanofibrillar morphology in silk fibers by small angle X-ray scattering and atomic force microscopy.

Small angle X-ray scattering (SAXS) and atomic force microscopy (AFM) measurements have been shown to be consistent with the presence of nanofibrils in the cocoon silk of Bombyx mori and the dragline silk of Nephila clavipes. The transverse dimensions and correlation lengths range from > 59 to 220 nm and in the axial direction from > 80 to 230 nm. Also, the two-dimensional Fourier transforms of the height profiles of AFM topographic images of interior surfaces of B. mori follow a power law approximately the same as that for the Porod region of the SAXS data. In this manner, the AFM can be used to help remove ambiguity about the scatterers responsible for SAXS patterns.     

X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation

Most serpins are associated with protease inhibition, and their ability to form loop-sheet polymers is linked to conformational disease and the human serpinopathies. Here we describe the structural and functional dissection of how a unique serpin, the non-histone architectural protein, MENT (Myeloid and Erythroid Nuclear Termination stage-specific protein), participates in DNA and chromatin condensation. Our data suggest that MENT contains at least two distinct DNA-binding sites, consistent with its simultaneous binding to the two closely juxtaposed linker DNA segments on a nucleosome. Remarkably, our studies suggest that the reactive centre loop, a region of the MENT molecule essential for chromatin bridging in vivo and in vitro, is able to mediate formation of a loop-sheet oligomer. These data provide mechanistic insight into chromatin compaction by a non-histone architectural protein and suggest how the structural plasticity of serpins has adapted to mediate physiological, rather than pathogenic, loop-sheet linkages.     

Review structure of silk by raman spectromicroscopy: from the spinning glands to the fibers

Raman spectroscopy has long been proved to be a useful tool to study the conformation of protein-based materials such as silk. Thanks to recent developments, linearly polarized Raman spectromicroscopy has appeared very efficient to characterize the molecular structure of native single silk fibers and spinning dopes because it can provide information relative to the protein secondary structure, molecular orientation, and amino acid composition. This review will describe recent advances in the study of the structure of silk by Raman spectromicroscopy. A particular emphasis is put on the spider dragline and silkworm cocoon threads, other fibers spun by orb-weaving spiders, the spinning dope contained in their silk glands and the effect of mechanical deformation. Taken together, the results of the literature show that Raman spectromicroscopy is particularly efficient to investigate all aspects of silk structure and production. The data provided can lead to a better understanding of the structure of the silk dope, transformations occurring during the spinning process, and structure and mechanical properties of native fibers.     

X-ray structural evidence for a local helix-loop transition in alpha-lactalbumin.

The three-dimensional structure of human alpha-lactalbumin for two crystal forms has been determined by x-ray analysis. One crystal (the form LT) was obtained at pH 4.2 and room temperature, while the other crystal (the form HT) was grown at pH 6.5 and 37 degrees C. The backbone structure for Lys1-Ile95 residues is almost conserved between the two structures as indicated by the root mean square difference of 0.30 A for the superposition of equivalent C alpha atoms. The calcium ion is surrounded by seven oxygen atoms of three carboxyl groups, two carbonyl groups, and two water molecules, which form a distorted pentagonal bipyramid in both structures. A large difference in polypeptide folding is found in the region of Leu96-Leu123 residues. Especially in the region of Trp104-Cys111 residues, a distorted alpha-helix is observed in the form HT while a loop structure is formed in the other crystal. The fact that the crystals of both forms appeared in the same batch at pH 6.5 and room temperature indicates that the human alpha-lactalbumin structure is highly fluctuated in solution and the folding and unfolding of the alpha-helix of Trp104-Cys111 residues are in equilibrium. Since the crystal of the form HT exclusively appeared around the physiological temperature, the structure of this form can be considered as the native structure. The partially unfolded structure in the form LT indicates that the local denaturation occurs even at room temperature.     

Synthetic spider silk fibers spun from Pyriform Spidroin 2, a glue silk protein discovered in orb-weaving spider attachment discs

Spider attachment disc silk fibers are spun into a viscous liquid that rapidly solidifies, gluing dragline silk fibers to substrates for locomotion or web construction. Here we report the identification and artificial spinning of a novel attachment disc glue silk fibroin, Pyriform Spidroin 2 (PySp2), from the golden orb weaver Nephila clavipes . MS studies support PySp2 is a constituent of the pyriform gland that is spun into attachment discs. Analysis of the PySp2 protein architecture reveals sequence divergence relative to the other silk family members, including the cob weaver glue silk fibroin PySp1. PySp2 contains internal block repeats that consist of two subrepeat units: one dominated by Ser, Gln, and Ala and the other Pro-rich. Artificial spinning of recombinant PySp2 truncations shows that the Ser-Gln-Ala-rich subrepeat is sufficient for the assembly of polymeric subunits and subsequent fiber formation. These studies support that both orb- and cob-weaving spiders have evolved highly polar block-repeat sequences with the ability to self-assemble into fibers, suggesting a strategy to allow fiber fabrication in the liquid environment of the attachment discs.     

Calcium-mediated changes in gap junction structure: evidence from the low angle X-ray pattern

Rat liver gap junctions were isolated in Ca2+-free media and analyzed in controlled environments by x-ray diffraction of partially oriented pellets. Different treatments of the same preparations were compared. The ordered hexagonal lattices gave rise to detail that was sensitive to low Ca2+ concentrations (0.05 mM), but not to Mg2+ (up to 0.16 mM) or pH (between 6.0 and 8.0). The major Ca2+-mediated responses were reductions in the intensity of the (1, 0) peak and in the off- equatorial contributions to the (2, 1) peak, and changes of scale equivalent to a decrease (approximately 2%) in lattice dimension, but an increase (approximately 4%) in the dimension perpendicular to the lattice. A simple structural interpretation of these findings is that Ca2+ induces the subunits of the channel-forming assembly, the connexon, to align more nearly parallel to the channel, thereby causing the connexon to become slightly longer and more radially compact. The rearrangement is of the same nature as one found under less physiological circumstances by electron microscopy (Unwin, P. N. T., and G. Zampighi, 1980, Nature (Lond.)., 283:545-549), and may be part of a coordinated mechanism by which the channel closes.     

X-ray structure of a maquette scaffold

Maquettes are de novo designed mimicries of nature used to test the construction and engineering criteria of oxidoreductases. One type of scaffold used in maquette construction is a four-alpha-helical bundle. The sequence of the four-alpha-helix bundle maquettes follows a heptad repeat pattern typical of left-handed coiled-coils. Initial designs were molten globular due partly to the minimalist approach taken by the designers. Subsequent iterative redesign generated several structured scaffolds with similar heme binding properties. Variant [I(6)F(13)](2), a structured scaffold, was partially resolved with NMR spectroscopy and found to have a set of mobile inter-helical packing interfaces. Here, the X-ray structure of a similar peptide ([I(6)F(13)M(31)](2) i.e. ([CGGG EIWKL HEEFLKK FEELLKL HEERLKKM](2))(2) which we call L31M), has been solved using MAD phasing and refined to 2.8A resolution. The structure shows that the maquette scaffold is an anti-parallel four-helix bundle with "up-up-down-down" topology. No pre-formed heme-binding pocket exists in the protein scaffold. We report unexpected inter-helical crossing angles, residue positions and translations between the helices. The crossing angles between the parallel helices are -5 degrees rather than the expected +20 degrees for typical left-handed coiled-coils. Deviation of the scaffold from the design is likely due to the distribution and size of hydrophobic residues. The structure of L31M points out that four identical helices may interact differently in a bundle and heptad repeats with an alternating [HPPHHPP]/[HPPHHPH] (H: hydrophobic, P: polar) pattern are not a sufficient design criterion to generate left-hand coiled-coils.     

Polarization microscopic evidence for an oriented cytoplasmic structure in the "dark" variants of adrenalin-storing cells.

A diffuse cytoplasmic birefringence confined to "dark" adrenalinstoring cells has been described. The main optical characteristics of the birefringence factor include: regular orientation of birefringence relative to the base-apex axis of cells; additive anisotropic staining with methods based on the principle of topo-optical staining reactions; dependence of birefringence on labile morphologic properties. On the basis of the capacity of the macromolecular matrix of chromaffin granules to form lamellar liposomal structures in vitro it has been proposed that a reorientation of molecular organization in the matrix of chromaffin cells is responsible for the observed optical phenomenon. The direction of birefringence was explained by a preferential direction of contractile forces acting during "dark" cell formation.     

Thermally induced alpha-helix to beta-sheet transition in regenerated silk fibers and films

The structure of thin films cast from regenerated solutions of Bombyx mori cocoon silk in hexafluoroisopropyl alcohol (HFIP) was studied by synchrotron X-ray diffraction during heating. A solid-state conformational transition from an alpha-helical structure to the well-known beta-sheet silk II structure occurred at a temperature of approximately 140 degrees C. The transition appeared to be homogeneous, as both phases do not coexist within the resolution of the current study. Modulated differential scanning calorimetry (DSC) of the films showed an endothermic melting peak followed by an exothermic crystallization peak, both occurring near 140 degrees C. Oriented fibers were also produced that displayed this helical molecular conformation. Subsequent heating above the structural transition temperature produced oriented beta-sheet fibers very similar in structure to B. mori cocoon fibers. Heat treatment of silk films at temperatures well below their degradation temperature offers a controllable route to materials with well-defined structures and mechanical behavior.     

Further evidence for importance of the subunit combination of silk fibroin in its efficient secretion from the posterior silk gland cells

A locus responsible for the Nd-s mutation of the silkworm, Bombyx mori, has been mapped very close to or within the fibroin light (L) chain gene on the 14th chromosome (Takei, F., K. Kimura, S. Mizuno, T. Yamamoto, and K. Shimura, 1984, Jpn. J. Genet., 59:307-313). A strain of B. mori carrying the homozygous Nd-sD mutation (Nd-sD/Nd-sD; Nd-sD is allelic to Nd-s) secretes less than 0.3% of fibroin into the lumen of the posterior silk gland compared with a strain carrying the homozygous wild-type alleles (+/+). The small amount of fibroin that is secreted in the Nd-sD/Nd-sD strain consists of the heavy (H) chain only and lacks the L chain, although the L chain mRNA and the proteins that are cross-reactable with the anti-L chain serum are present in the posterior silk gland cells. In the hybrid silkworm, Nd-sD/+, the H chain derived from either the Nd-sD or + allele forms disulfide linkage with the L chain derived from the + allele and these fibroins are secreted into the lumen with an equal efficiency, but the L chain derived from the Nd-sD allele remains in the cell unbound to the H chain. Some evidence suggesting structural abnormality of the L chain derived from the Nd-sD allele is presented. These results, together with the previous results on the effect of the H chain gene-linked Nd(2) mutation (Takei, F., F. Oyama, K. Kimura, A. Hyodo, S. Mizuno, and K. Shimura, 1984, J. Cell Biol., 99:2005-2010), strongly suggest that the H-L subunit combination of silk fibroin is important for its efficient secretion.     

Secretory production of spider silk proteins in metabolically engineered Corynebacterium glutamicum for spinning into tough fibers

Spider dragline silk is a remarkable fiber made of unique proteins—spidroins—secreted and stored as a concentrated aqueous dope in the major ampullate gland of spiders. This feat has inspired engineering of microbes to secrete spidroins for spinning into tough synthetic fibers, which remains a challenge due to the aggregation-prone feature of the spidroins and low secretory capacity of the expression hosts. Here we report metabolic engineering of Corynebacterium glutamicum to efficiently secrete recombinant spidroins. Using a model spidroin MaSpI16 composed of 16 consensus repeats of the major ampullate spidroin 1 of spider Trichonephila clavipes, we first identified the general Sec protein export pathway for its secretion via N-terminal fusion of a translocation signal peptide. Next we improved the spidroin secretion levels by selection of more suitable signal peptides, multiplexed engineering of the bacterial host, and by high cell density cultivation of the resultant recombinant strains. The high abundance (>65.8%) and titer (554.7 mg L^–1) of MaSpI16 in the culture medium facilitated facile, chromatography-free recovery of the spidroin with a purity of 93.0%. The high solubility of the purified spidroin enabled preparation of highly concentrated aqueous dope (up to 66%) amenable for spinning into synthetic fibers with an appreciable toughness of 70.0 MJ m⁻³. The above metabolic and processing strategies were also found applicable for secretory production of the higher molecular weight spidroin MaSpI64 (64 consensus repeats) to yield similarly tough fibers. These results suggest the good potential of secretory production of protein polymers for sustainable supply of fibrous materials.     

A method for studying the structure of uniaxially aligned biopolymers using solid state 15N-nmr: Application to Bombyx mori silk fibroin fibers

Recent advances in the application of solid state nmr spectroscopy to uniformly aligned biopolymers have opened a window through which to view the detailed structure of biological macromolecules that are unable to be seen with standard techniques for structure determination such as x-ray diffraction. Atomic resolution structural details are obtained from solid state nmr data in the form of bond orientations, which yield the relative positions of specific atoms within the molecule. For static aligned systems such as fibers, in which rapid reorientation about the axis of alignment does not occur, it has generally been necessary to perform trial and error line-shape simulations to extract structural details from nmr spectra arising from a single type of nuclear spin interaction. In the present work, a new method is developed in which solid state ¹⁵N-nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds. Analytical expressions are derived that utilize spectral features read from 15N chemical shift anisotropy line shapes to calculate a discrete number of possible orientations for a specific site. The ¹⁵N-¹H dipolar interaction is employed to further narrow the number of unique orientations possible for a given site. With this method, a neighborhood of possible orientations is quickly determined, and full line-shape simulations within this region of allowed space can be performed to refine the limits of orientation. This technique demonstrates the use of a single type of isotopic label to determine the orientation of a specific molecular group such as a peptide plane within a protein. Results from the application of this method to the Bombyx mori silk fibroin protein provide structural detail that is consistent with currently accepted structural models based on fiber diffraction studies. © 1993 John Wiley & Sons, Inc.     

New process to form a silk fibroin porous 3-D structure

A new process to form fibroin spongy porous 3-D structure is reported herein. The process involves freezing and thawing fibroin aqueous solution in the presence of a small amount of an organic solvent. The process requires no freeze-drying, chemical cross-linking, or the aid of other polymeric materials. The solvent concentration, fibroin concentration, freezing temperature, and freezing duration affect the sponge formation, its porous structure, and its mechanical properties. Measurements by XRD and FTIR indicate that silk I and silk II crystalline structures exist in the fibroin sponge and that the secondary structure of fibroin is transformed to a beta-sheet from a random coil during this process. The tensile strength decreased slightly, but the fibroin sponge showed no deformation after autoclaving. Therefore, the fibroin sponge was sterilized using an autoclave. For 3 weeks, MC3T3 cells proliferated in the sterilized fibroin sponge. The fibroin sponge formed by this new process is applicable as a tissue-engineering scaffold because it is formed from biocompatible pure silk fibroin and offers both porous structure and mechanical properties that are suitable for cell growth and handling.