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1.  Effect of sodium chloride on the structure and stability of spider silk’s N-terminal protein domain 
Biomaterials science  2013;1(3):276-284.
A spider’s ability to store silk protein solutions at high concentration is believed to be related to the protein’s terminal domains. It has been suggested that a shift in salt concentration and pH can have a significant influence on the assembly process. Based on experimental data, a model has been proposed in which the N-terminal domain exists as a monomer during storage and assembles into a homodimer upon spinning. Here we perform a systematic computational study using atomistic, coarse-grained and well-tempered metadynamics simulation to understand how the NaCl concentration in the solution affects the N-terminal domain of the silk protein. Our results show that a high salt concentration, as found during storage, weakens key salt bridges between the monomers, inducing a loss in bond energy by 28.6% in a single salt bridge. As a result dimer formation is less likely as 35.5% less energy is required to unfold the dimer by mechanical force. Conversely, homodimer formation appears to be more likely at low salt concentrations as the salt bridge stays at the lower energy state. The link between salt concentration, structure and stability of the N-terminal domain provides a possible mechanism that prevents premature fiber formation during storage.
doi:10.1039/C2BM00140C
PMCID: PMC3700428  PMID: 23833703
Salt bridge; spidroin; assembly; metadynamics; free-energy landscape; coarse-grained model; nanomechanics; molecular dynamics
2.  Materials by Design—A Perspective From Atoms to Structures 
Biological materials are effectively synthesized, controlled, and used for a variety of purposes—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science.
doi:10.1557/mrs.2013.26
PMCID: PMC3806500  PMID: 24163499
Nanotechnology; biology; music; simulation; theory; experiment; design; manufacturing; nanomechanics; protein; bio-inspired; materiomics
3.  The role of capture spiral silk properties in the diversification of orb webs 
Among a myriad of spider web geometries, the orb web presents a fascinating, exquisite example in architecture and evolution. Orb webs can be divided into two categories according to the capture silk used in construction: cribellate orb webs (composed of pseudoflagelliform silk) coated with dry cribellate threads and ecribellate orb webs (composed of flagelliform silk fibres) coated by adhesive glue droplets. Cribellate capture silk is generally stronger but less-extensible than viscid capture silk, and a body of phylogenic evidence suggests that cribellate capture silk is more closely related to the ancestral form of capture spiral silk. Here, we use a coarse-grained web model to investigate how the mechanical properties of spiral capture silk affect the behaviour of the whole web, illustrating that more elastic capture spiral silk yields a decrease in web system energy absorption, suggesting that the function of the capture spiral shifted from prey capture to other structural roles. Additionally, we observe that in webs with more extensible capture silk, the effect of thread strength on web performance is reduced, indicating that thread elasticity is a dominant driving factor in web diversification.
doi:10.1098/rsif.2012.0473
PMCID: PMC3481582  PMID: 22896566
spider web mechanics; evolution; viscid capture silk; cribellate capture silk; Deinopoidea; Araneoidea
4.  Materials by Design: Merging Proteins and Music 
Nano today  2012;7(6):488-495.
Tailored materials with tunable properties are crucial for applications as biomaterials, for drug delivery, as functional coatings, or as lightweight composites. An emerging paradigm in designing such materials is the construction of hierarchical assemblies of simple building blocks into complex architectures with superior properties. We review this approach in a case study of silk, a genetically programmable and processable biomaterial, which, in its natural role serves as a versatile protein fiber with hierarchical organization to provide structural support, prey procurement or protection of eggs. Through an abstraction of knowledge from the physical system, silk, to a mathematical model using category theory, we describe how the mechanism of spinning fibers from proteins can be translated into music through a process that assigns a set of rules that governs the construction of the system. This technique allows one to express the structure, mechanisms and properties of the ‘material’ in a very different domain, ‘music’. The integration of science and art through categorization of structure-property relationships presents a novel paradigm to create new bioinspired materials, through the translation of structures and mechanisms from distinct hierarchical systems and in the context of the limited number of building blocks that universally governs these systems.
doi:10.1016/j.nantod.2012.09.001
PMCID: PMC3752788  PMID: 23997808
Nanotechnology; biology; music; theory; experiment; arts; design; manufacturing; nanomechanics; protein
5.  A review of combined experimental and computational procedures for assessing biopolymer structure–process–property relationships 
Biomaterials  2012;33(33):8240-8255.
Tailored biomaterials with tunable functional properties are desirable for many applications ranging from drug delivery to regenerative medicine. To improve the predictability of biopolymer materials functionality, multiple design parameters need to be considered, along with appropriate models. In this article we review the state of the art of synthesis and processing related to the design of biopolymers, with an emphasis on the integration of bottom-up computational modeling in the design process. We consider three prominent examples of well-studied biopolymer materials – elastin, silk, and collagen – and assess their hierarchical structure, intriguing functional properties and categorize existing approaches to study these materials. We find that an integrated design approach in which both experiments and computational modeling are used has rarely been applied for these materials due to difficulties in relating insights gained on different length- and time-scales. In this context, multiscale engineering offers a powerful means to accelerate the biomaterials design process for the development of tailored materials that suit the needs posed by the various applications. The combined use of experimental and computational tools has a very broad applicability not only in the field of biopolymers, but can be exploited to tailor the properties of other polymers and composite materials in general.
doi:10.1016/j.biomaterials.2012.06.054
PMCID: PMC3787124  PMID: 22938765
Biopolymers; Material design; Elastin; Collagen; Silk; Integration
6.  Multifunctionality and Control of the Crumpling and Unfolding of Large-Area Graphene 
Nature materials  2013;12(4):321-325.
Crumpled graphene films are broadly used, for instance in electronics1, energy storage2, 3, composites4, 5, and biomedicine6. Although it is known that the degree of crumpling affects graphene's properties and the performance of graphene-based devices and materials3, 5, 7, the controlled folding and unfolding of crumpled graphene films has not been demonstrated. Here we report an approach to reversibly control the crumpling and unfolding of large-area graphene sheets. We show with experiments, atomistic simulations and theory that, by harnessing the mechanical instabilities of graphene adhered on a biaxially pre-stretched polymer substrate and by controlling the relaxation of the pre-strains in a particular order, graphene films can be crumpled into tailored self-organized hierarchical structures that mimic superhydrophobic leaves. The approach enables us to fabricate large-area conductive coatings and electrodes showing superhydrophobicity, high transparency, and tunable wettability and transmittance. We also demonstrate that crumpled graphene-polymer laminates can be used as artificial-muscle actuators.
doi:10.1038/nmat3542
PMCID: PMC3605241  PMID: 23334002
7.  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
8.  How protein materials balance strength, robustness, and adaptability 
HFSP Journal  2010;4(1):26-40.
Proteins form the basis of a wide range of biological materials such as hair, skin, bone, spider silk, or cells, which play an important role in providing key functions to biological systems. The focus of this article is to discuss how protein materials are capable of balancing multiple, seemingly incompatible properties such as strength, robustness, and adaptability. To illustrate this, we review bottom-up materiomics studies focused on the mechanical behavior of protein materials at multiple scales, from nano to macro. We focus on alpha-helix based intermediate filament proteins as a model system to explain why the utilization of hierarchical structural features is vital to their ability to combine strength, robustness, and adaptability. Experimental studies demonstrating the activation of angiogenesis, the growth of new blood vessels, are presented as an example of how adaptability of structure in biological tissue is achieved through changes in gene expression that result in an altered material structure. We analyze the concepts in light of the universality and diversity of the structural makeup of protein materials and discuss the findings in the context of potential fundamental evolutionary principles that control their nanoscale structure. We conclude with a discussion of multiscale science in biology and de novo materials design.
doi:10.2976/1.3267779
PMCID: PMC2880027  PMID: 20676305
9.  Molecular mechanism of force induced stabilization of collagen against enzymatic breakdown 
Biomaterials  2012;33(15):3852-3859.
Collagen cleavage, facilitated by collagenases of the matrix metalloproteinase (MMP) family, is crucial for many physiological and pathological processes such as wound healing, tissue remodeling, cancer invasion and organ morphogenesis. Earlier work has shown that mechanical force alters the cleavage rate of collagen. However, experimental results yielded conflicting data on whether applying force accelerates or slows down the degradation rate. Here we explain these discrepancies and propose a molecular mechanism by which mechanical force might change the rate of collagen cleavage. We find that a type I collagen heterotrimer is unfolded in its equilibrium state and loses its triple helical structure at the cleavage site without applied force, possibly enhancing enzymatic breakdown as each chain is exposed and can directly undergo hydrolysis. Under application of force, the naturally unfolded region refolds into a triple helical structure, potentially protecting the molecule against enzymatic breakdown. In contrast, a type I collagen homotrimer retains a triple helical structure even without applied force, making it more resistant to enzyme cleavage. In the case of the homotrimer, the application of force may directly lead to molecular unwinding, resulting in a destabilization of the molecule under increased mechanical loading. Our study explains how force may regulate the formation and breakdown of collagenous tissue.
doi:10.1016/j.biomaterials.2012.02.001
PMCID: PMC3309414  PMID: 22401852
Collagen; collagenolysis; collagen degradation; molecular mechanics; protein structure; local unfolding
10.  Structural Characterization of Minor Ampullate Spidroin Domains and Their Distinct Roles in Fibroin Solubility and Fiber Formation 
PLoS ONE  2013;8(2):e56142.
Spider silk is protein fibers with extraordinary mechanical properties. Up to now, it is still poorly understood how silk proteins are kept in a soluble form before spinning into fibers and how the protein molecules are aligned orderly to form fibers. Minor ampullate spidroin is one of the seven types of silk proteins, which consists of four types of domains: N-terminal domain, C-terminal domain (CTD), repetitive domain (RP) and linker domain (LK). Here we report the tertiary structure of CTD and secondary structures of RP and LK in aqueous solution, and their roles in protein stability, solubility and fiber formation. The stability and solubility of individual domains are dramatically different and can be explained by their distinct structures. For the tri-domain miniature fibroin, RP-LK-CTDMi, the three domains have no or weak interactions with one another at low protein concentrations (<1 mg/ml). The CTD in RP-LK-CTDMi is very stable and soluble, but it cannot stabilize the entire protein against chemical and thermal denaturation while it can keep the entire tri-domain in a highly water-soluble state. In the presence of shear force, protein aggregation is greatly accelerated and the aggregation rate is determined by the stability of folded domains and solubility of the disordered domains. Only the tri-domain RP-LK-CTDMi could form silk-like fibers, indicating that all three domains play distinct roles in fiber formation: LK as a nucleation site for assembly of protein molecules, RP for assistance of the assembly and CTD for regulating alignment of the assembled molecules.
doi:10.1371/journal.pone.0056142
PMCID: PMC3571961  PMID: 23418525
11.  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
12.  Structure and stability of the lamin A tail domain and HGPS mutant 
Journal of structural biology  2011;175(3):425-433.
Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging syndrome caused by the expression and accumulation of a mutant form of lamin A, Δ50 lamin A. As a component of the cell's nucleoskeleton, lamin A plays an important role in the mechanical stabilization of the nuclear envelope and in other nuclear functions. It is largely unknown how the characteristic 50 amino acid deletion affects the conformation of the mostly intrinsically disordered tail domain of lamin A. Here we perform replica exchange molecular dynamics simulations of the tail domain and determine an ensemble of semi-stable structures. Based on these structures we show that the ZMPSTE 24 cleavage site on the precursor form of the lamin A tail domain orients itself in such a way as to facilitate cleavage during the maturation process. We confirm our simulated structures by comparing the thermodynamic properties of the ensemble structures to in vitro stability measurements. Using this combination of techniques, we compare the size, heterogeneity of size, thermodynamic stability of the Ig-fold, as well as the mechanisms of force-induced denaturation. Our data shows that the Δ50 lamin A tail domain is more compact and displays less heterogeneity than the mature lamin A tail domain. Altogether these results suggest that the altered structure and stability of the tail domain can explain changed protein-protein and protein-DNA interactions and may represent an etiology of the disease. Also, this study provides the first molecular structure(s) of the lamin A tail domain, which is confirmed by thermodynamic tests.
doi:10.1016/j.jsb.2011.05.015
PMCID: PMC3150306  PMID: 21635954
Laminopathy; structure; mechanics; protein stability; nuclear mechanics
13.  Veins Improve Fracture Toughness of Insect Wings 
PLoS ONE  2012;7(8):e43411.
During the lifetime of a flying insect, its wings are subjected to mechanical forces and deformations for millions of cycles. Defects in the micrometre thin membranes or veins may reduce the insect’s flight performance. How do insects prevent crack related material failure in their wings and what role does the characteristic vein pattern play? Fracture toughness is a parameter, which characterises a material’s resistance to crack propagation. Our results show that, compared to other body parts, the hind wing membrane of the migratory locust S. gregaria itself is not exceptionally tough (1.04±0.25 MPa√m). However, the cross veins increase the wing’s toughness by 50% by acting as barriers to crack propagation. Using fracture mechanics, we show that the morphological spacing of most wing veins matches the critical crack length of the material (1132 µm). This finding directly demonstrates how the biomechanical properties and the morphology of locust wings are functionally correlated in locusts, providing a mechanically ‘optimal’ solution with high toughness and low weight. The vein pattern found in insect wings thus might inspire the design of more durable and lightweight artificial ‘venous’ wings for micro-air-vehicles. Using the vein spacing as indicator, our approach might also provide a basis to estimate the wing properties of endangered or extinct insect species.
doi:10.1371/journal.pone.0043411
PMCID: PMC3425546  PMID: 22927966
14.  Nanoscale Strain-Hardening of Keratin Fibres 
PLoS ONE  2012;7(7):e41814.
Mammalian appendages such as hair, quill and wool have a unique structure composed of a cuticle, a cortex and a medulla. The cortex, responsible for the mechanical properties of the fibers, is an assemblage of spindle-shaped keratinized cells bound together by a lipid/protein sandwich called the cell membrane complex. Each cell is itself an assembly of macrofibrils around 300 nm in diameter that are paracrystalline arrays of keratin intermediate filaments embedded in a sulfur-rich protein matrix. Each macrofibril is also attached to its neighbors by a cell membrane complex. In this study, we combined atomic force microscopy based nano-indentation with peak-force imaging to study the nanomechanical properties of macrofibrils perpendicular to their axis. For indentation depths in the 200 to 500 nm range we observed a decrease of the dynamic elastic modulus at 1 Hz with increasing depth. This yielded an estimate of 1.6GPa for the lateral modulus at 1 Hz of porcupine quill’s macrofibrils. Using the same data we also estimated the dynamic elastic modulus at 1 Hz of the cell membrane complex surrounding each macrofibril, i.e., 13GPa. A similar estimate was obtained independently through elastic maps of the macrofibrils surface obtained in peak-force mode at 1 kHz. Furthermore, the macrofibrillar texture of the cortical cells was clearly identified on the elasticity maps, with the boundaries between macrofibrils being 40–50% stiffer than the macrofibrils themselves. Elasticity maps after indentation also revealed a local increase in dynamic elastic modulus over time indicative of a relaxation induced strain hardening that could be explained in term of a α-helix to β-sheet transition within the macrofibrils.
doi:10.1371/journal.pone.0041814
PMCID: PMC3404990  PMID: 22848616
15.  Slip-Flow and Heat Transfer of a Non-Newtonian Nanofluid in a Microtube 
PLoS ONE  2012;7(5):e37274.
The slip-flow and heat transfer of a non-Newtonian nanofluid in a microtube is theoretically studied. The power-law rheology is adopted to describe the non-Newtonian characteristics of the flow, in which the fluid consistency coefficient and the flow behavior index depend on the nanoparticle volume fraction. The velocity profile, volumetric flow rate and local Nusselt number are calculated for different values of nanoparticle volume fraction and slip length. The results show that the influence of nanoparticle volume fraction on the flow of the nanofluid depends on the pressure gradient, which is quite different from that of the Newtonian nanofluid. Increase of the nanoparticle volume fraction has the effect to impede the flow at a small pressure gradient, but it changes to facilitate the flow when the pressure gradient is large enough. This remarkable phenomenon is observed when the tube radius shrinks to micrometer scale. On the other hand, we find that increase of the slip length always results in larger flow rate of the nanofluid. Furthermore, the heat transfer rate of the nanofluid in the microtube can be enhanced due to the non-Newtonian rheology and slip boundary effects. The thermally fully developed heat transfer rate under constant wall temperature and constant heat flux boundary conditions is also compared.
doi:10.1371/journal.pone.0037274
PMCID: PMC3352882  PMID: 22615961
16.  Evidence of the Most Stretchable Egg Sac Silk Stalk, of the European Spider of the Year Meta menardi 
PLoS ONE  2012;7(2):e30500.
Spider silks display generally strong mechanical properties, even if differences between species and within the same species can be observed. While many different types of silks have been tested, the mechanical properties of stalks of silk taken from the egg sac of the cave spider Meta menardi have not yet been analyzed. Meta menardi has recently been chosen as the “European spider of the year 2012”, from the European Society of Arachnology. Here we report a study where silk stalks were collected directly from several caves in the north-west of Italy. Field emission scanning electron microscope (FESEM) images showed that stalks are made up of a large number of threads, each of them with diameter of 6.03±0.58 µm. The stalks were strained at the constant rate of 2 mm/min, using a tensile testing machine. The observed maximum stress, strain and toughness modulus, defined as the area under the stress-strain curve, are 0.64 GPa, 751% and 130.7 MJ/m3, respectively. To the best of our knowledge, such an observed huge elongation has never been reported for egg sac silk stalks and suggests a huge unrolling microscopic mechanism of the macroscopic stalk that, as a continuation of the protective egg sac, is expected to be composed by fibres very densely and randomly packed. The Weibull statistics was used to analyze the results from mechanical testing, and an average value of Weibull modulus (m) is deduced to be in the range of 1.5–1.8 with a Weibull scale parameter (σ0) in the range of 0.33–0.41 GPa, showing a high coefficient of correlation (R2 = 0.97).
doi:10.1371/journal.pone.0030500
PMCID: PMC3275603  PMID: 22347380
17.  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
18.  Category Theoretic Analysis of Hierarchical Protein Materials and Social Networks 
PLoS ONE  2011;6(9):e23911.
Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting functional properties of biological protein materials by developing so-called ologs. An olog is like a “concept web” or “semantic network” except that it follows a rigorous mathematical formulation based on category theory. This key difference ensures that an olog is unambiguous, highly adaptable to evolution and change, and suitable for sharing concepts with other olog. We consider simple cases of beta-helical and amyloid-like protein filaments subjected to axial extension and develop an olog representation of their structural and resulting mechanical properties. We also construct a representation of a social network in which people send text-messages to their nearest neighbors and act as a team to perform a task. We show that the olog for the protein and the olog for the social network feature identical category-theoretic representations, and we proceed to precisely explicate the analogy or isomorphism between them. The examples presented here demonstrate that the intrinsic nature of a complex system, which in particular includes a precise relationship between structure and function at different hierarchical levels, can be effectively represented by an olog. This, in turn, allows for comparative studies between disparate materials or fields of application, and results in novel approaches to derive functionality in the design of de novo hierarchical systems. We discuss opportunities and challenges associated with the description of complex biological materials by using ologs as a powerful tool for analysis and design in the context of materiomics, and we present the potential impact of this approach for engineering, life sciences, and medicine.
doi:10.1371/journal.pone.0023911
PMCID: PMC3169555  PMID: 21931622
19.  Force-Induced Unfolding Simulations of the Human Notch1 Negative Regulatory Region: Possible Roles of the Heterodimerization Domain in Mechanosensing 
PLoS ONE  2011;6(7):e22837.
Notch receptors are core components of the Notch signaling pathway and play a central role in cell fate decisions during development as well as tissue homeostasis. Upon ligand binding, Notch is sequentially cleaved at the S2 site by an ADAM protease and at the S3 site by the γ-secretase complex. Recent X-ray structures of the negative regulatory region (NRR) of the Notch receptor reveal an auto-inhibited fold where three protective Lin12/Notch repeats (LNR) of the NRR shield the S2 cleavage site housed in the heterodimerization (HD) domain. One of the models explaining how ligand binding drives the NRR conformation from a protease-resistant state to a protease-sensitive one invokes a mechanical force exerted on the NRR upon ligand endocytosis. Here, we combined physics-based atomistic simulations and topology-based coarse-grained modeling to investigate the intrinsic and force-induced folding and unfolding mechanisms of the human Notch1 NRR. The simulations support that external force applied to the termini of the NRR disengages the LNR modules from the heterodimerization (HD) domain in a well-defined, largely sequential manner. Importantly, the mechanical force can further drive local unfolding of the HD domain in a functionally relevant fashion that would provide full proteolytic access to the S2 site prior to heterodimer disassociation. We further analyzed local structural features, intrinsic folding free energy surfaces, and correlated motions of the HD domain. The results are consistent with a model in which the HD domain possesses inherent mechanosensing characteristics that could be utilized during Notch activation. This potential role of the HD domain in ligand-dependent Notch activation may have implications for understanding normal and aberrant Notch signaling.
doi:10.1371/journal.pone.0022837
PMCID: PMC3145759  PMID: 21829530
20.  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
21.  Deformation micromechanisms of collagen fibrils under uniaxial tension 
Collagen, an essential building block of connective tissues, possesses useful mechanical properties due to its hierarchical structure. However, little is known about the mechanical properties of collagen fibril, an intermediate structure between the collagen molecule and connective tissue. Here, we report the results of systematic molecular dynamics simulations to probe the mechanical response of initially unflawed finite size collagen fibrils subjected to uniaxial tension. The observed deformation mechanisms, associated with rupture and sliding of tropocollagen molecules, are strongly influenced by fibril length, width and cross-linking density. Fibrils containing more than approximately 10 molecules along their length and across their width behave as representative volume elements and exhibit brittle fracture. Shorter fibrils experience a more graceful ductile-like failure. An analytical model is constructed and the results of the molecular modelling are used to find curve-fitted expressions for yield stress, yield strain and fracture strain as functions of fibril structural parameters. Our results for the first time elucidate the size dependence of mechanical failure properties of collagen fibrils. The associated molecular deformation mechanisms allow the full power of traditional material and structural engineering theory to be applied to our understanding of the normal and pathological mechanical behaviours of collagenous tissues under load.
doi:10.1098/rsif.2009.0390
PMCID: PMC2874230  PMID: 19897533
collagen mechanics; collagen fibril; mesoscopic model; failure micromechanism; size effect
22.  Superhydrophobic Surface Based on a Coral-Like Hierarchical Structure of ZnO 
PLoS ONE  2010;5(12):e14475.
Background
Fabrication of superhydrophobic surfaces has attracted much interest in the past decade. The fabrication methods that have been studied are chemical vapour deposition, the sol-gel method, etching technique, electrochemical deposition, the layer-by-layer deposition, and so on. Simple and inexpensive methods for manufacturing environmentally stable superhydrophobic surfaces have also been proposed lately. However, work referring to the influence of special structures on the wettability, such as hierarchical ZnO nanostructures, is rare.
Methodology
This study presents a simple and reproducible method to fabricate a superhydrophobic surface with micro-scale roughness based on zinc oxide (ZnO) hierarchical structure, which is grown by the hydrothermal method with an alkaline aqueous solution. Coral-like structures of ZnO were fabricated on a glass substrate with a micro-scale roughness, while the antennas of the coral formed the nano-scale roughness. The fresh ZnO films exhibited excellent superhydrophilicity (the apparent contact angle for water droplet was about 0°), while the ability to be wet could be changed to superhydrophobicity after spin-coating Teflon (the apparent contact angle greater than 168°). The procedure reported here can be applied to substrates consisting of other materials and having various shapes.
Results
The new process is convenient and environmentally friendly compared to conventional methods. Furthermore, the hierarchical structure generates the extraordinary solid/gas/liquid three-phase contact interface, which is the essential characteristic for a superhydrophobic surface.
doi:10.1371/journal.pone.0014475
PMCID: PMC3012683  PMID: 21209931
23.  Correction: Plasticity of Intermediate Filament Subunits 
PLoS ONE  2010;5(9):10.1371/annotation/8f182672-e11e-48d5-8a74-c401b8bd5ecc.
doi:10.1371/annotation/8f182672-e11e-48d5-8a74-c401b8bd5ecc
PMCID: PMC2947707
24.  Soft Matrices Suppress Cooperative Behaviors among Receptor-Ligand Bonds in Cell Adhesion 
PLoS ONE  2010;5(8):e12342.
The fact that biological tissues are stable over prolonged periods of time while individual receptor-ligand bonds only have limited lifetime underscores the critical importance of cooperative behaviors of multiple molecular bonds, in particular the competition between the rate of rupture of closed bonds (death rate) and the rate of rebinding of open bonds (birth rate) in a bond cluster. We have recently shown that soft matrices can greatly increase the death rate in a bond cluster by inducing severe stress concentration near the adhesion edges. In the present paper, we report a more striking effect that, irrespective of stress concentration, soft matrices also suppress the birth rate in a bond cluster by increasing the local separation distance between open bonds. This is shown by theoretical analysis as well as Monte Carlo simulations based on a stochastic-elasticity model in which stochastic descriptions of molecular bonds and elastic descriptions of interfacial force/separation are unified in a single modeling framework. Our findings not only are important for understanding the role of elastic matrices in cell adhesion, but also have general implications on adhesion between soft materials.
doi:10.1371/journal.pone.0012342
PMCID: PMC2925891  PMID: 20808789
25.  Plasticity of Intermediate Filament Subunits 
PLoS ONE  2010;5(8):e12115.
Intermediate filaments (IFs) assembled in vitro from recombinantly expressed proteins have a diameter of 8–12 nm and can reach several micrometers in length. IFs assemble from a soluble pool of subunits, tetramers in the case of vimentin. Upon salt addition, the subunits form first unit length filaments (ULFs) within seconds and then assembly proceeds further by end-to-end fusion of ULFs and short filaments. So far, IF subunits have mainly been observed by electron microscopy of glycerol sprayed and rotary metal shadowed specimens. Due to the shear forces during spraying the IF subunits appear generally as straight thin rods. In this study, we used atomic force microscopy (AFM), cryo-electron microscopy (cryo-EM) combined with molecular modeling to investigate the conformation of the subunits of vimentin, desmin and keratin K5/K14 IFs in various conditions. Due to their anisotropic shape the subunits are difficult to image at high resolution by cryo-EM. In order to enhance contrast we used a cryo-negative staining approach. The subunits were clearly identified as thin, slightly curved rods. However the staining agent also forced the subunits to aggregate into two-dimensional networks of dot-like structures. To test this conformational change further, we imaged dried unfixed subunits on mica by AFM revealing a mixture of extended and dot-like conformations. The use of divalent ions such as calcium and magnesium, as well as glutaraldehyde exposure favored compact conformations over elongated ones. These experimental results as well as coarse-grained molecular dynamics simulations of a vimentin tetramer highlight the plasticity of IF subunits.
doi:10.1371/journal.pone.0012115
PMCID: PMC2930322  PMID: 20814582

Results 1-25 (51)