Molecular nanosprings in spider capture-silk threads

Silken toolkits: biomechanics of silk fibers spun by the orb web spider Argiope argentata (Fabricius 1775)

Orb-weaving spiders spin five fibrous silks from differentiated glands that contain unique sets of proteins. Despite diverse ecological functions, the mechanical properties of most of these silks are not well characterized. Here,we quantify the mechanical performance of this toolkit of silks for the silver garden spider Argiope argentata. Four silks exhibit viscoelastic behaviour typical of polymers, but differ statistically from each other by up to 250% in performance, giving each silk a distinctive suite of material properties. Major ampullate silk is 50% stronger than other fibers, but also less extensible. Aciniform silk is almost twice as tough as other silks because of high strength and extensibility. Capture spiral silk, coated with aqueous glue, is an order of magnitude stretchier than other silks. Dynamic mechanical properties are qualitatively similar, but quantitatively vary by up to 300% among silks. Storage moduli are initially nearly constant and increase after fiber yield, whereas loss tangents reach maxima of 0.1–0.2 at the yield. The remarkable mechanical diversity of Argiope argentata silks probably results in part from the different molecular structures of fibers and can be related to the specific ecological role of each silk. Our study indicates substantial potential to customize the mechanics of bioengineered silks.

Robust free-standing nanomembranes of organic/inorganic interpenetrating networks

Hybrid sol-gel materials have been a subject of intensive research during the past decades because these nanocomposites combine the versatility of organic polymers with the superior physical properties of glass. Here, we report the synthesis, by spin coating, of hybrid interpenetrating networks in the form of free-standing nanomembrane (around 35-nm thick) with unprecedented macroscopic size and characteristics. The quasi-2D interpenetration of the organic and inorganic networks brings to these materials a unique combination of properties that are not usually compatible within the same film: macroscopic robustness and homogeneity, nanoscale thickness, mechanical strength, high flexibility and optical transparency. Interestingly, such free-standing nanofilms of macroscopic size can seal large openings, are strong enough to hold amounts of liquid 70,000 times heavier than their own weight, and are flexible enough to reversibly pass through holes 30,000 times smaller than their own size.

Shematrin: A family of glycine-rich structural proteins in the shell of the pearl oyster Pinctada fucata

Random sequencing of molecules from a cDNA library constructed from mantle mRNA of the pearl oyster Pinctada fucata was used to obtain information on organic matrix proteins in the shell. In the determined sequences, we identified 7 distinct cDNAs encoding similar glycine-rich domains. Complete sequence analysis of these cDNAs showed that the predicted sequences of the proteins, which we named shematrins, possessed similar domains comprising repeat sequences of two or more glycines, followed by a hydrophobic amino acid. In addition, in shematrin-1, -2 and -3, a repeat domain designated as XGnX (where X is a hydrophobic amino acid) was conserved. It is of further note that all the shematrin proteins have RKKKY, RRKKY or RRRKY as their C-terminal sequence. According to northern blot analysis, all shematrins are exclusively expressed in the mantle, and particularly in the edge region of the mantle; furthermore, peptide fragments similar to shematrin-1 and -2 were detected in the prismatic layer of shells by MALDI-TOF/TOF MS analysis. These findings suggest that many of shematrins are synthesized in the mantle edge and secreted into the prismatic layer of the shell, where the protein family is thought to provide a framework for calcification.

Mechanism of titin unfolding by force: insight from quasi-equilibrium molecular dynamics calculations

We have studied the unfolding by force of one of the immunoglobulin domains of the muscle protein titin using molecular dynamics simulations at 300 K. Previous studies, done at constant pulling rates, showed that under the effect of the force two strands connected to each other by six backbone H-bonds are pulled apart. No details about the mechanism of H-bond breaking were provided. Our simulation protocol "pull and wait" was designed to correspond to very slow pulling, more similar to the rates used in experiments than are the protocols used in previous computational studies. Under these conditions interstrand backbone H-bonds are not "ripped apart" by the application of the force. Instead, small elongations produced by the force weaken specific backbone H-bonds with respect to water-backbone H-bonds. These weakened bonds allow a single water molecule to make H-bonds to the CO and the NH of the same backbone H-bond while they are still bound to each other. The backbone H-bond then breaks (distance > 3.6 A), but its donor and acceptor atoms remain bound to the same water molecule. Further separation of the chains takes place when a second water molecule makes an H-bond with either the protein backbone donor or acceptor atom. Thus, the force does not directly break the main chain H-bonds: it destabilizes them in such a way that they are replaced by H-bonds to water. With this mechanism, the force necessary to break all the H-bonds required to separate the two strands will be strongly dependent on the pulling speed. Further simulations carried out at low forces but long waiting times (> or = 500 ps, < or = 10 ns) show that, given enough time, even a very small pulling force (< 400 pN) is sufficient to destabilize the interstrand H-bonds and allow them to be replaced by H-bonds to two water molecules. As expected, increasing the temperature to 350 K allows the interstrand H-bonds to break at lower forces than those required at 300 K.

Shape memory in spider draglines

The ductility and strength of spider draglines means that they outperform the best synthetic fibres, but surprisingly little is known about the torsional properties of this remarkable filament. Unlike a mountain climber swinging from a rope, a spider suspended from its silk thread hardly ever twists. Here we show that a spider dragline has a torsional shape 'memory' in that it can reversibly and totally recover its initial form without any external stimulus; its observed relaxation dynamics indicate that these biological molecules have successively different torsional constants.

An in situ study of the nanomechanical properties of barnacle (Balanus amphitrite) cyprid cement using atomic force microscopy (AFM)

Cyprids are the final planktonic stage in the larval dispersal of barnacles and are responsible for surface exploration and attachment to appropriate substrata. The nanomechanical properties of barnacle (Balanus amphitrite) cyprid permanent cement were studied in situ using atomic force microscopy (AFM). Force curves were recorded from the cement disc continually over the course of its curing and these were subsequently analysed using custom software. Results showed a narrowing of the pull-off force distribution with time, as well as a reduction in molecular stretch length over time. In addition, there was a strong correlation between maximum pull-off force and molecular stretch length for the cement, suggesting 'curing' of the adhesive; some force curves also contained a 'fingerprint' of modular protein unfolding. This study provides the first direct experimental evidence in support of a putative 'tanning' mechanism in barnacle cyprid cement.

Structure - Property and Structure - Function Relations of Leafhopper (Kahaono montana) Silk

Kahaono montana Evans (Insecta: Hemiptera: Cicadellidae), an endemic Australian leafhopper, is unique among the insect order Hemiptera in producing a silk. In this study, the secondary structure of the protein comprising leafhopper silk, and the surface stretching mechanical properties of this biopolymer, were investigated using Fourier-transform infrared microscopy and atomic force microscopy, respectively. The curve-fitted amide I and amide III bands revealed a composition of 13.1% α-helix, 23.8% β-sheet, 25.5% random coil, and 37.6% aggregated side chains. The molecular stretching behaviour of raw and cleaned silk fibres differed markedly. Analysis of the AFM force curves showed an adhesive property of the raw silk, while the pure fibre showed only the presence of protein. These findings suggest that the silk fibres act as a structural support for other leafhopper secretions and together form a hydrophobic barrier that may protect the insects from rain and natural enemies. This is the first time such a use of silk has been found in a biological system.

Sacrificial bonds and hidden length: unraveling molecular mesostructures in tough materials

Sacrificial bonds and hidden length in structural molecules and composites have been found to greatly increase the fracture toughness of biomaterials by providing a reversible, molecular-scale energy-dissipation mechanism. This mechanism relies on the energy, of order 100 eV, needed to reduce entropy and increase enthalpy as molecular segments are stretched after being released by the breaking of weak bonds, called sacrificial bonds. This energy is relatively large compared to the energy needed to break the polymer backbone, of order a few eV. In many biological cases, the breaking of sacrificial bonds has been found to be reversible, thereby additionally providing a "self-healing" property to the material. Due to the nanoscopic nature of this mechanism, single molecule force spectroscopy using an atomic force microscope has been a useful tool to investigate this mechanism. Especially when investigating natural molecular constructs, force versus distance curves quickly become very complicated. In this work we propose various types of sacrificial bonds, their combination, and how they appear in single molecule force spectroscopy measurements. We find that by close analysis of the force spectroscopy curves, additional information can be obtained about the molecules and their bonds to the native constructs.

Thermodynamic calculations in biological systems

The ability to compute intra- and inter-molecular interactions provides the opportunity to gain a deeper understanding of previously intractable problems in biochemistry and biophysics. This review presents three examples in which molecular dynamics calculations were used to gain insight into the atomic detail underlying important experimental observations. The three examples are the following: (1) Entropic contribution to rate acceleration that results from conformational constraints imposed on the reactants; (2) Mechanism of force unfolding of a small protein molecule by the application of a force that separates its N- and C-terminals; and (3) Loss of translational entropy experienced by small molecules when they bind to proteins.

Single adhesive nanofibers from a live diatom have the signature fingerprint of modular proteins

The adhesive and mechanical properties of a cell-substratum adhesive secreted by live diatom cells were examined in situ using atomic force microscopy. The resulting force curves have a regular saw-tooth pattern, the characteristic fingerprint of modular proteins, and when bridged between tip and surface can repeatedly be stretched and relaxed resulting in precisely overlaying saw-tooth curves (up to approximately 600 successive cycles). The average rupture force of the peaks is 0.794 +/- 0.007 (mean +/- SE) nN at a loading rate of 0.8 microm/s and the average persistence length is 0.026 +/- <0.001 (mean +/- SE) nm (fit using the worm-like chain model). We propose that we are pulling on single adhesive nanofibers, each a cohesive unit composed of a set number of modular proteins aligned in register. Furthermore, we can observe and differentiate when up to three adhesive nanofibers are pulled based upon multimodal distributions of force and persistence length. The high force required for bond rupture, high extensibility (approximately 1.2 microm), and the accurate and rapid refolding upon relaxation, together provide strong and flexible properties ideally suited for the cell-substratum adhesion of this fouling diatom and allow us to understand the mechanism responsible for the strength of adhesion.

Sacrificial bonds and hidden length dissipate energy as mineralized fibrils separate during bone fracture

Properties of the organic matrix of bone as well as its function in the microstructure could be the key to the remarkable mechanical properties of bone. Previously, it was found that on the molecular level, calcium-mediated sacrificial bonds increased stiffness and enhanced energy dissipation in bone constituent molecules. Here we present evidence for how this sacrificial bond and hidden length mechanism contributes to the mechanical properties of the bone composite, by investigating the nanoscale arrangement of the bone constituents and their interactions. We find evidence that bone consists of mineralized collagen fibrils and a non-fibrillar organic matrix, which acts as a 'glue' that holds the mineralized fibrils together. We believe that this glue may resist the separation of mineralized collagen fibrils. As in the case of the sacrificial bonds in single molecules, the effectiveness of this mechanism increases with the presence of Ca2+ ions.

Solenoids and plectonemes in stretched and twisted elastomeric filaments

We study the behavior of a naturally straight highly extensible elastic filament subjected to large extensional and twisting strains. We find that two different phases can coexist for a range of parameter values: the plectoneme and the solenoid. A simple theory based on a neo-Hookean model for the material of the filament and accounting for the slender geometry suffices to explain these observations, and leads to a phase diagram that is consistent with observations. Extension and relaxation experiments on these phases show the presence of large hysteresis loops and sawtooth-like force-displacement curves which are different for the plectoneme and the solenoid.

Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.

Inhibition of Cyclooxygenase 2 Synthesis SuppressesHerpes simplexVirus Type 1 Reactivation

Recurrent herpes virus infection, in which the virus reactivates from the nervous system and causes painful lesions in peripheral tissues, is a significant clinical problem. Our recent studies showing that the amount of cyclooxygenase 2 (COX-2) in the trigeminal ganglia of heat-stressed untreated mice is higher than the amount in heat-stressed mice treated with the COX-2 inhibitor, celecoxib, have indicated that the prostaglandin synthesis pathway--and in particular COX-2--may be an intermediate in the pathway to herpes viral reactivation. To further study this process, we infected the corneas of mice using topical application to a lightly scratched epithelium and waited 30 days for Herpes simplex virus type 1 (HSV-1) latency to be established in the trigeminal ganglia. Prior to the induction of viral reactivation, the mice were treated orally with celecoxib. Treated and untreated mice were induced to undergo reactivation by immersion in 43 degrees C water for 10 min. The shedding of virus at the ocular surface was determined by culturing ocular swabs with indicator cells. The presence of infectious virus in the trigeminal ganglion was evaluated by incubating ganglion homogenates with indicator cells and observing for cytopathic effect. Celecoxib treatment significantly suppressed viral reactivation when given prophylactically by the gastrointestinal route. The numbers of corneas and ganglia containing infectious virus were significantly lower in the celecoxib-treated animals, compared to the placebo-treated mice. These experiments demonstrate that a selective COX-2 inhibitor can suppress hyperthermic stress-induced herpes viral reactivation in the nervous system. It may be possible to use COX-2 inhibitors to prevent viral reactivation in high-risk patients by drug prophylaxis.

Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single-molecule pulling experiments

We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each cross-link increases until it ruptures. The stochastic cross-link rupture process is assumed to be governed by first order kinetics with a rate that depends exponentially on the transmitted force. We have performed random searches to identify optimal cross-link configurations whose unfolding requires a large applied force (measure of strength) and/or large dissipated energy (measure of toughness). We found that such optimal chains always involve cross-links arranged to form parallel strands. The location of those optimal strands generally depends on the loading rate. Optimal chains with a small number of cross-links were found to be almost as strong and tough as optimal chains with a large number of cross-links. Furthermore, optimality of chains with a small number of cross-links can be easily destroyed by adding cross-links at random. The present findings are relevant for the interpretation of single molecule force probe spectroscopy studies of the mechanical unfolding of "load-bearing" proteins, whose native topology often involves parallel strand arrangements similar to the optimal configurations identified in the study.

Hierarchical chain model of spider capture silk elasticity

Spider capture silk is a biomaterial with both high strength and high elasticity, but the structural design principle underlying these remarkable properties is still unknown. It was revealed recently by atomic force microscopy that an exponential force-extension relationship holds both for capture silk mesostructures and for intact capture silk fibers [N. Becker et al., Nat. Mater. 2, 278 (2003)]]. In this Letter a simple hierarchical chain model was proposed to understand and reproduce this striking observation. In the hierarchical chain model, a polymer is composed of many structural motifs which organize into structural modules and supramodules in a hierarchical manner. Each module in this hierarchy has its own characteristic force. The repetitive patterns in the amino-acid sequence of the major flagelliform protein of spider capture silk is in support of this model.

Gumfooted lines in black widow cobwebs and the mechanical properties of spider capture silk

Orb-weaving spiders produce webs using two types of silk that have radically different mechanical properties. The dragline silk used to construct the supporting frame and radii of the web is stiff and as strong as steel, while the capture spiral is much weaker but more than ten times as extensible. This remarkable divergence in mechanical properties has been attributed to the aqueous glue that coats the capture spiral, which is thought to decrease capture spiral stiffness and increase its extensibility. However, discerning the effect of the aqueous glue on fiber performance is complicated because dragline silk and the capture spiral are assembled from different proteins, which may also affect mechanical performance. Here, we use the sticky gumfooted lines of black widow cobwebs to test the effect of the addition of aqueous glue on the mechanical properties of dragline silk. We also surveyed orb-webs spun by a broad range of species for bundles of looped silk. Such bundles, termed windlasses, have been thought to increase capture spiral extensibility by "paying out" additional lengths of silk. Our results suggest that neither plasticization of silk by aqueous glue nor excess silk in windlasses can by themselves account for the remarkable extensibility of orb-weaver capture silk compared to other spider silks. This argues that the unique amino acid motifs of the flagelliform fibroins that constitute the core of the capture spiral play an essential role in capture silk's extreme extensibility.

Protein Unfolding and Refolding Under Force: Methodologies for Nanomechanics

An increasing number of inter- and intramolecular interactions can nowadays be probed using single-molecule manipulation techniques. Protein unfolding and refolding is the most representative--though complex--of these interactions. Herein, we review the main modes of performing a force unfolding experiment: the velocity clamp and the new force clamp mode. We also compare some of the physical aspects behind the two most frequently used single-molecule manipulation instrumentations: optical tweezers and atomic force microscopes.

Force spectroscopy of collagen fibers to investigate their mechanical properties and structural organization

Tendons are composed of collagen and other molecules in a highly organized hierarchical assembly, leading to extraordinary mechanical properties. To probe the cross-links on the lower level of organization, we used a cantilever to pull substructures out of the assembly. Advanced force probe technology, using small cantilevers (length <20 microm), improved the force resolution into the sub-10 pN range. In the force versus extension curves, we found an exponential increase in force and two different periodic rupture events, one with strong bonds (jumps in force of several hundred pN) with a periodicity of 78 nm and one with weak bonds (jumps in force of <7 pN) with a periodicity of 22 nm. We demonstrate a good correlation between the measured mechanical behavior of collagen fibers and their appearance in the micrographs taken with the atomic force microscope.

Synergistic interactions of lipids and myelin basic protein

This report describes force measurements and atomic force microscope imaging of lipid-protein interactions that determine the structure of a model membrane system that closely mimics the myelin sheath. Our results suggest that noncovalent, mainly electrostatic and hydrophobic, interactions are responsible for the multilamellar structure and stability of myelin. We find that myelin basic protein acts as a lipid coupler between two apposed bilayers and as a lipid "hole-filler," effectively preventing defect holes from developing. From our protein-mediated-adhesion and force-distance measurements, we develop a simple quantitative model that gives a reasonably accurate picture of the molecular mechanism and adhesion of bilayer-bridging proteins by means of noncovalent interactions. The results and model indicate that optimum myelin adhesion and stability depend on the difference between, rather than the product of, the opposite charges on the lipid bilayers and myelin basic protein, as well as on the repulsive forces associated with membrane fluidity, and that small changes in any of these parameters away from the synergistically optimum values can lead to large changes in the adhesion or even its total elimination. Our results also show that the often-asked question of which membrane species, the lipids or the proteins, are the "important ones" may be misplaced. Both components work synergistically to provide the adhesion and overall structure. A better appreciation of the mechanism of this synergy may allow for a better understanding of stacked and especially myelin membrane structures and may lead to better treatments for demyelinating diseases such as multiple sclerosis.

WISE NMR characterization of nanoscale heterogeneity and mobility in supercontracted Nephila clavipes spider dragline silk

The addition of water to spider dragline silk results in fiber contraction to 50% its initial length and significant changes to the mechanical properties of the silk. This event has been termed supercontraction. A decrease in strength and increase in elasticity have been reported when the silk is in contact with water. Two-dimensional wide-line separation (WISE) nuclear magnetic resonance (NMR) is implemented to correlate (13)C chemical shifts with mobility by observing the corresponding (1)H line widths and line shapes in water-saturated spider dragline silk. The WISE NMR spectrum of the native silk exhibits (1)H line widths that are approximately 40 kHz for all carbon environments characteristic of a rigid organic system. In contrast, the water-saturated case displays a component of the (1)H line that is narrowed to approximately 5 kHz for the glycine C(alpha) and a newly resolved alanine helical environment while the alanine C(beta) corresponding to the beta-sheet conformation remains broad. These results indicate that water permeates the amorphous, glycine-rich matrix and not the crystalline, polyalanine beta-sheets. A delay time is added to the WISE NMR pulse sequence to monitor spin diffusion between the amorphous, mobile region and the crystalline domains. The time required for spin diffusion to reach spatial equilibrium is related to the length scale of the polyalanine crystallites. This technique is employed to measure crystalline domain sizes on the nanometer length scale in water-solvated spider dragline silk. These results provide further insight into the structure of spider silk and mechanism of supercontraction.