Levels Of Structural Hierarchy Research Articles

Protein secondary structure in spider silk nanofibrils

Nanofibrils play a pivotal role in spider silk and are responsible for many of the impressive properties of this unique natural material. However, little is known about the internal structure of these protein fibrils. We carry out polarized Raman and polarized Fourier-transform infrared spectroscopies on native spider silk nanofibrils and determine the concentrations of six distinct protein secondary structures, including β-sheets, and two types of helical structures, for which we also determine orientation distributions. Our advancements in peak assignments are in full agreement with the published silk vibrational spectroscopy literature. We further corroborate our findings with X-ray diffraction and magic-angle spinning nuclear magnetic resonance experiments. Based on the latter and on polypeptide Raman spectra, we assess the role of key amino acids in different secondary structures. For the recluse spider we develop a highly detailed structural model, featuring seven levels of structural hierarchy. The approaches we develop are directly applicable to other proteinaceous materials.

A multiscale finite element investigation on the role of intra- and extra-fibrillar mineralisation on the elastic properties of bone tissue

Lamellar bone is one of the fundamental structural units of bone tissue and it consists of mineralised collagen fibrils (MCFs) embedded within an extra-fibrillar matrix comprised of hydroxyapatite minerals distributed throughout a matrix of non-collagenous proteins (NCPs). While both intra- and extra-fibrillar phases provide a critical contribution to tissue-level behaviour, the mechanical implications of their structural arrangement, and in particular the relative distribution of HA minerals between both phases, remains poorly understood. This study presents a multiscale finite element framework to investigate the role of intra- and extra-fibrillar mineralisation on the elastic properties of bone tissue by considering two levels of structural hierarchy. At the nanoscale, representative volume elements (RVEs) of both MCFs and the extra-fibrillar matrix were developed, and a homogenisation strategy was used to determine the effective elastic properties of each phase. At the sub-micron level, an RVE of lamellar bone that accounted for newly reported patterns of mineral platelets encircling collagen fibrils was used to predict the effective response of lamellar bone tissue, with material properties established from the previous length scale. The results demonstrated that the overall mineral content in the tissue is the biggest contributor to the effective elastic properties of lamellar bone. While this is perhaps unsurprising, importantly, it was demonstrated that the extra-fibrillar matrix (and mineral therein) is the phase that makes the primary contribution to the elastic response of the tissue. The two main reasons that the extra-fibrillar matrix dominated the load-bearing response are (i) the greater proportion of mineral content compared to the intra-fibrillar regions and (ii) the highly ordered arrangement of mineral platelets that are aligned to the longitudinal axis of MCFs. Both of these features resulted in extra-fibrillar mineral strain ratios that were consistently higher than intra-fibrillar mineral strain ratios under axial loading. As a result, the predicted elastic properties of MCFs were much lower than the extra-fibrillar matrix, indicating that intra-fibrillar mineralisation only provided a modest contribution to the stiffness of bone tissue. Collectively, the predicted results of the multiscale approach compared well to the range properties measured through various experimental testing methods, highlighting its potential to provide further insight into the role of sub-tissue features of tissue biomechanics.

Cartilage polymers: From viscoelastic solutions to weak gels*

AbstractThe dynamic properties of the polymeric components of cartilage are important for understanding the many biological functions of this biological tissue. Knowledge of the rheology of these materials is also crucial for the development of therapeutic treatments for diseases, such as arthritis, in which cartilage loses its functional physiological properties. In the present work complementary noninvasive techniques, rheology and dynamic light scattering (DLS) are used to probe the structural and dynamic properties of solutions of the principal proteoglycan components of cartilage extracellular matrix at different levels of structural hierarchy (chondroitin sulfate, aggrecan, aggrecan‐hyaluronic acid complex). It is shown that the bottlebrush shaped aggrecan molecules form large, loosely organized polyelectrolyte domains comprised of molecules organized into diffuse branched polymer network structures permeated by a diffuse cloud of counter‐ions. The rheological behaviors of these polymer solutions vary from viscoelastic solutions, consistent with the formation of dynamic polymer clusters in solution, to “weak gel” materials exhibiting approximate power law shear stress relaxation or creep over a wide range of timescales.

How Do Molecular Motions Affect Structures and Properties at Molecule and Aggregate Levels?

Molecular motions are essential natures of matter and play important roles in their structures and properties. However, owing to the diversity and complexity of structures and behaviors, the study of motion-structure-property relationships remains a challenge, especially at all levels of structural hierarchy from molecules to macro-objects. Herein, luminogens showing aggregation-induced emission (AIE), namely, 9-(pyrimidin-2-yl)-carbazole (PyCz) and 9-(5-R-pyrimidin-2-yl)-carbazole [R = Cl (ClPyCz), Br (BrPyCz), and CN (CyPyCz)], were designed and synthesized, to decipher the dependence of materials' structures and properties on molecular motions at the molecule and aggregate levels. Experimental and theoretical analysis demonstrated that the active intramolecular motions in the excited state of all molecules at the single-molecule level endowed them with more twisted structural conformations and weak emission. However, owing to the restriction of intramolecular motions in the nano/macroaggregate state, all the molecules assumed less twisted conformations with bright emission. Unexpectedly, intermolecular motions could be activated in the macrocrystals of ClPyCz, BrPyCz, and CyPyCz through the introduction of external perturbations, and synergic strong and weak intermolecular interactions allowed their crystals to undergo reversible deformation, which effectively solved the problem of the brittleness of organic crystals, while endowing them with excellent elastic performance. Thus, the present study provided insights on the motion-structure-property relationship at each level of structural hierarchy and offered a paradigm to rationally design multifunctional AIE-based materials.

Structural and Chemical Hierarchy in Hydroxyapatite Coatings.

Hydroxyapatite coatings need similarly shaped splats as building blocks and then a homogeneous microstructure to unravel the structural and chemical hierarchy for more refined improvements to implant surfaces. Coatings were thermally sprayed with differently sized powders (20–40, 40–63 and 63–80 µm) to produce flattened homogeneous splats. The surface was characterized for splat shape by profilometry and Atomic force microscopy (AFM), crystal size by AFM, crystal orientation by X-ray diffraction (XRD) and structural variations by XRD. Chemical composition was assessed by phase analysis, but variations in chemistry were detected by XRD and Raman spectroscopy. The resulting surface electrical potential was measured by Kelvin probe AFM. Five levels of structural hierarchy were suggested: the coating, the splat, oriented crystals, alternate layers of oxyapatite and hydroxyapatite (HAp) and the suggested anion orientation. Chemical hierarchy was present over a lower range of order for smaller splats. Coatings made from smaller splats exhibited a greater electrical potential, inferred to arise from oxyapatite, and supplemented by ordered OH− ions in a rehydroxylated surface layer. A model has been proposed to show the influence of structural hierarchy on the electrical surface potential. Structural hierarchy is proposed as a means to further refine the properties of implant surfaces.

Nanostructure of calcium-silicate-hydrates in fine recycled aggregate concrete

Our research objective is to foster a multiscale understanding of fine recycled aggregate concrete using a bottom-up approach. We investigate the influence of fine recycled concrete aggregates on the structure of calcium-silicate-hydrates. To this end, we introduce a new thought model for fine recycled aggregate concrete with four levels of structural hierarchy: beam, mortar, binder, and C–S–H gel levels. We characterize the behavior of fine recycled aggregate concrete and natural sand concrete using analytical methods such as X-ray diffraction, and scanning electron microscopy, along with depth-based mechanical testing methods such as micro-indentation and nano-indentation. Micromechanical modeling integrated with statistical deconvolution methods is applied to quantify the phase distribution of natural sand mortar and fine recycled concrete aggregate mortar. We observe that fine recycled aggregate concrete exhibits a higher volume fraction of calcium silicate hydrates. Furthermore, the presence of fine recycled concrete aggregates leads to nanostructural changes at the C–S–H gel level. Fine recycled aggregate concrete exhibits a higher volume fraction of loosely-packed low-density calcium silicate hydrates compared to natural sand concrete. Calcium silicate hydrates in fine recycled aggregate concrete exhibit a higher C–S–H gel porosity. Finally, the C–S–H gel porosity in fine recycled aggregate concrete accounts for 56.2% of the total porosity. These results suggest that to improve the mechanical and transport properties of fine recycled aggregate concrete, it is essential to reduce the C–S–H gel porosity of calcium silicate hydrates and increase the fraction of optimally-packed high-density calcium silicate hydrates.

Constructing a structural model of troponin using site-directed spin labeling: EPR and PRE-NMR.

The relative ease of introducing a paramagnetic species onto a protein, and advances in electron paramagnetic resonance (EPR) over the past two decades, have established spin labeling as a vital structural biology technique for revealing the functional workings of the troponin muscle regulatory complex-an ~80kDa heterotrimeric protein switch for turning on striated muscle contraction. Through the site-directed spin labeling (SDSL) of cysteine residues at key sites in troponin, a molecular-level understanding of the troponin muscle regulatory system across all levels of structural hierarchy has been achieved. Through the application of EPR, mobility and accessibility trends in the EPR signals of the spin labels attached to consecutive residues can reveal the secondary structure of troponin elements and also help map the interaction between subunits. Distance restraints calculated from the interspin interactions between spin label pairs have helped with building a structural model of the troponin complex. Further, when SDSL is paired with NMR, paramagnetic relaxation enhancement (PRE)-NMR has been used to obtain high-resolution structural detail for both intra- and interdomain interactions in troponin and revealed details of protein conformational changes and dynamics accompanying troponin function. In this review, we provide an overview of the SDSL labeling methodology and its application towards building a dynamic structural model of the multi-subunit troponin complex which details the calcium-induced conformational changes intimately linked to muscle regulation. We also describe how the SDSL method, in conjunction with EPR or NMR, can be used to obtain insights into structural perturbations to troponin caused by disease-causing mutations.

Impact energy absorption performances of ordinary and hierarchical chiral structures

Auxetic chiral structures consisting of circular ring nodes and tangentially connected ligaments are engineered systems that exhibit excellent flexibility, vibration attenuation, impact resistance performances. In this paper, the out-of-plane dynamic crash behaviors of anti-tetrachiral, hexachiral and hierarchical chiral structures are studied. The energy absorption efficiency, plateau stress, peak stress of chiral structures with different ligament length, node radius, ligament thickness and level of structural hierarchy under different external crashing conditions are compared, and identical mass per area of different unit cell configurations are assumed. It is found that anti-tetrachiral structure is able to generate higher plateau stress and better energy absorption efficiency than hexachiral structures. Making use of the mechanical benefits of structural hierarchy, novel hierarchical chiral structures are proposed for improving the crash energy absorption abilities of chiral structures, and relations between crash energy absorption performances and unit cell geometries are explored, such as: energy absorption efficiency, plateau stress of chiral structures. Based on systematical analysis, optimized chiral and hierarchical chiral cellular structure can be designed for impact energy absorption in protective sandwich structures.

Bottom-up Formation of Carbon-Based Structures with Multilevel Hierarchy from MOF-Guest Polyhedra.

Three-dimensional carbon-based structures have proven useful for tailoring material properties in structural mechanical and energy storage applications. One approach to obtain them has been by carbonization of selected metal–organic frameworks (MOFs) with catalytic metals, but this is not applicable to most common MOF structures. Here, we present a strategy to transform common MOFs, by guest inclusions and high-temperature MOF–guest interactions, into complex carbon-based, diatom-like, hierarchical structures (named for the morphological similarities with the naturally existing diatomaceous species). As an example, we introduce metal salt guests into HKUST-1-type MOFs to generate a family of carbon-based nano-diatoms with two to four levels of structural hierarchy. We report control of the morphology by simple changes in the chemistry of the MOF and guest, with implications for the formation mechanisms. We demonstrate that one of these structures has unique advantages as a fast-charging lithium-ion battery anode. The tunability of composition should enable further studies of reaction mechanisms and result in the growth of a myriad of unprecedented carbon-based structures from the enormous variety of currently available MOF–guest candidates.

Dissecting Virus Infectious Cycles by Cryo-Electron Microscopy.

In response to events such as receptor binding and endocytic triggers, viruses undergo large-scale, dynamic conformational changes necessary for cell entry and genome delivery. In later stages of the infectious cycle, replication machinery must read and synthesize nucleic acid strands to generate new copies of genetic material, and structural proteins must assemble and package the appropriate contents in order to produce new infectious particles. Structural elucidation of these events is key to understanding them and their inhibition by antiviral agents such as neutralizing antibodies and drugs. Electron microscopy is a versatile technique that offers the ability to resolve three-dimensional structures of individual viral proteins and whole virions in multiple functional states, even in cells at different stages of infection (Fig 1). Here we focus on the use of transmission electron microscopy of frozen-hydrated specimens, i.e., cryo-electron microscopy (cryo-EM). A major advantage of cryo-EM over other structural approaches is that samples of a broad range of sizes can be imaged under near-physiological conditions with native hydration intact. This approach does not require the specimen to be fixed, stained, or coaxed into a crystalline lattice. This versatility has enabled cryo-EM to expand the envelope of structural virology and opened new avenues for understanding the molecular and cellular processes of virus infection and pathogenesis. Fig 1 Cryo-electron microscopy (cryo-EM) enables one to gain insight into viruses over many levels of structural hierarchy, ranging from determination of near-atomic resolution structures of subunits and symmetrical virus assemblies to ultrastructural analysis ... In this micro-review, we examine general approaches and recent applications of cryo-EM to virology. The reader is referred to a number of excellent reviews for more in-depth discussion of current methodology (e.g., [1,2]). Electron microscopy and structural virology have a long, shared history dating to the first images of bacteriophages gathered using some of the earliest electron microscopes [3]. As the technique of cryogenically preserving unfixed samples was being developed, again, viruses were among the first test subjects that helped to demonstrate the utility of cryo-EM for characterizing structure of large biological assemblies [4–6].

Protein function from its emergence to diversity in contemporary proteins

The goal of this work is to learn from nature the rules that govern evolution and the design of protein function. The fundamental laws of physics lie in the foundation of the protein structure and all stages of the protein evolution, determining optimal sizes and shapes at different levels of structural hierarchy. We looked back into the very onset of the protein evolution with a goal to find elementary functions (EFs) that came from the prebiotic world and served as building blocks of the first enzymes. We defined the basic structural and functional units of biochemical reactions—elementary functional loops. The diversity of contemporary enzymes can be described via combinations of a limited number of elementary chemical reactions, many of which are performed by the descendants of primitive prebiotic peptides/proteins. By analyzing protein sequences we were able to identify EFs shared by seemingly unrelated protein superfamilies and folds and to unravel evolutionary relations between them. Binding and metabolic processing of the metal- and nucleotide-containing cofactors and ligands are among the most abundant ancient EFs that became indispensable in many natural enzymes. Highly designable folds provide structural scaffolds for many different biochemical reactions. We show that contemporary proteins are built from a limited number of EFs, making their analysis instrumental for establishing the rules for protein design. Evolutionary studies help us to accumulate the library of essential EFs and to establish intricate relations between different folds and functional superfamilies. Generalized sequence-structure descriptors of the EF will become useful in future design and engineering of desired enzymatic functions.

Easily Repairable Networks: Reconnecting Nodes after Damage

We introduce a simple class of distribution networks that withstand damage by being repairable instead of redundant. Instead of asking how hard it is to disconnect nodes through damage, we ask how easy it is to reconnect nodes after damage. We prove that optimal networks on regular lattices have an expected cost of reconnection proportional to the lattice length, and that such networks have exactly three levels of structural hierarchy. We extend our results to networks subject to repeated attacks, in which the repairs themselves must be repairable. We find that, in exchange for a modest increase in repair cost, such networks are able to withstand any number of attacks.

Mechanical properties of hierarchical lattices

This paper focuses on the stiffness and strength of lattices with multiple hierarchical levels. We examine two-dimensional and three-dimensional lattices with up to three levels of structural hierarchy. At each level, the topology and the orientation of the lattice are prescribed, while the relative density is varied over a defined range. The properties of selected hierarchical lattices are obtained via a multiscale approach applied iteratively at each hierarchical level. The results help to quantify the effect that multiple orders of structural hierarchy produces on stretching and bending dominated lattices. Material charts for the macroscopic stiffness and strength illustrate how the property range of the lattices can expand as subsequent levels of hierarchy are added. The charts help to gain insight into the structural benefit that multiple hierarchies can impart to the macroscopic performance of a lattice.

Handedness Inversions in a Simple Model of Fibrillar Superstructure Formation

Aggregation of misfolded proteins into amyloid fibrils has been linked to several disorders such as Alzheimer's disease, or diabetes mellitus type II. Factors such as low pH, high temperature, and agitation have been recognized to accelerate this process in vitro. Amyloid fibrils from unrelated proteins share similar features on different levels of structural hierarchy: e.g. cross-beta structure, and tendency of individual fibrils to form intertwined chiral superstructures with defined morphological handedness and optical activity.In this work we investigate this phenomenon numerically with the use of coarse-grained numerical model of chiral fibrils. The aggregate morphologies, chirality and stability are then analyzed as a function of temperature and initial pitch of the fibrils. The simulations show the existence of a critical pitch below which the handedness of the aggregates is opposite to that of the constituting fibrils. We also observe and analyze the process of spontaneous chirality inversion of individual fibrils in the aggregate. This inversion is accompanied by a helical wave propagation along the fibril axis, with a kink separating left-haded and right-handed regions moving along the chain. The frequency of this process is strongly dependent on the initial pitch of the fibrils with a local maximum near the critical pitch.

Formation of hollow spherical and doughnut microcapsules by evaporation induced self-assembly of nanoparticles: effects of particle size and polydispersity

Understanding the role of various physicochemical parameters is essential in order to control the microstructure during evaporation induced self-assembly in drying colloidal droplets. In the present work, the effect of particle size and its distribution on formation of spherical and doughnut shaped hollow microcapsules during rapid evaporation induced self-assembly of colloidal droplets has been elucidated. It has been demonstrated that hollow spherical microcapsules with substantial shell thickness are formed for small size and low polydispersity of the nanoparticles in a virgin dispersion. A few of such microcapsules, even with relatively significant shell thickness, burst in order to equilibrate force balance during drying. In contrast, when the size and polydispersity are relatively high, a morphological transformation occurs and the drying droplets release the strain through formation of doughnut shaped grains. Two levels of structural hierarchy and ageing effects of the assembled microcapsules are investigated using small-angle neutron/X-ray scattering and scanning electron microscopy.

Nanostructural Alteration in Bone Quantified in Terms of Orientation Distribution of Mineral Crystals: A Possible Tool for Fracture Risk Assessment

There may be different causes of failures in bone; however, their origin generally lies at the lowest level of structural hierarchy, i.e., at the mineral-collagen composite. Any change in the nanostructure affects the affinity or bonding effectiveness between and within the phases at this level, and hence determines the overall strength and quality of bone. In this study, we propose a novel concept to assess change in the nanostructure and thereby change in the bonding status at this level by revealing change in the orientation distribution characteristics of mineral crystals. Using X-ray diffraction method, a parameter called Degree of Orientation (DO) has been quantified. The DO accounts for the azimuthal distribution of mineral crystals and represents their effective amount along any direction. Changes in the DOs in cortical bone samples from bovine femur with different preferential orientations of mineral crystals were estimated under external loads. Depending on the applied loads, change in the azimuthal distribution of the DOs and the degree of reversibility of the crystals was observed to vary. The characteristics of nanostructural change and thereby possible affect on the strength of bone was then predicted from the reversible or irreversible characteristics of distributed mineral crystals. Significant changes in the organization of mineral crystals were observed; however, variations in the applied stresses and elastic moduli were not evinced at the macroscale level. A novel concept to assess the alteration in nanostructure on the basis of mineral crystals orientation distribution has been proposed. The importance of nanoscale level information obtained noninvasively has been emphasized, which acts as a precise tool to estimate the strength and predict the possible fracture risks in bone.

Hierarchical and non-hierarchical mineralisation of collagen

Biomineralisation of collagen involves functional motifs incorporated in extracellular matrix protein molecules to accomplish the objectives of stabilising amorphous calcium phosphate into nanoprecursors and directing the nucleation and growth of apatite within collagen fibrils. Here we report the use of small inorganic polyphosphate molecules to template hierarchical intrafibrillar apatite assembly in reconstituted collagen in the presence of polyacrylic acid to sequester calcium and phosphate into transient amorphous nanophases. The use of polyphosphate without a sequestration analogue resulted only in randomly-oriented extrafibrillar precipitations along the fibrillar surface. Conversely, the use of polyacrylic acid without a templating analogue resulted only in non-hierarchical intrafibrillar mineralisation with continuous apatite strands instead of discrete crystallites. The ability of using simple non-protein molecules to recapitulate different levels of structural hierarchy in mineralised collagen signifies the ultimate simplicity in Nature’s biomineralisation design principles and challenges the need for using more complex recombinant matrix proteins in bioengineering applications.

Networked interpenetrating connections of icosahedra: Effects on shear transformations in metallic glass

The local structures of metallic glasses have been analyzed previously in term of various types of short-range order (SRO). However, the SRO alone, neglecting the interconnection of neighboring icosahedra to medium range and beyond, is insufficient to account for the structure–property relationship in metallic glasses. In this study, we use molecular dynamics (MD) simulations of Cu–Zr binary metallic glasses to examine the effects of the next level of structural hierarchy: the interpenetrating connection of icosahedra (ICOI) and the linkage of the medium-range ICOI patches to form networks of icosahedra over extended range. The mechanical properties of these metallic glasses, especially the shear transformations that mediate plasticity, are found to be dependent on the degree of ICOI and development of the ICOI network. The evolution of the ICOI network during shear deformation, as well as the composition dependence, has been monitored and discussed.

Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen–hydroxyapatite biomaterials

Hard biomaterials such as bone, dentin, and nacre have primarily an organic phase (e.g. tropocollagen (TC)) and a mineral phase (e.g. hydroxyapatite (HAP) or aragonite) arranged in a staggered arrangement at the nanoscopic length scale. Interfacial interactions between the organic phase and the mineral phase as well as the structural effects arising due to the staggered arrangement significantly affect the strength of such biomaterials. The effect of such factors is intricately intertwined with the chemical environment of such materials. In the present investigation, an idealized TC–HAP composite system under tensile loading is analyzed using explicit three-dimensional (3-D) molecular dynamics (MD) simulations to develop an understanding of these factors. The material system is analyzed in three different environments: (1) in the absence of water molecules (non-hydrated), (2) in the presence of water molecules (hydrated), and (3) in the presence of water molecules with calcium ions (ionized water). The analyses focus on understanding the correlations among factors such as the structural arrangement, the peak stress during deformation, Young's modulus, the peak interfacial strength, and the length scale of the localization of peak stress during deformation. Analyses show that maximizing the contact area between the TC and HAP phases results in higher interfacial strength as well as higher fracture strength. Due to the staggered arrangement, the orientation of HAP crystals has insignificant effect on the biomaterial strength. Analyses based on strength scaling as a function of structural hierarchy level reveal that while peak strength follows a multiscaling relation, the fracture strength does not. The peak strain for failure was found to be independent of the changes in levels of structural hierarchy. Overall, the analyses, being limited in size due to the computational time constraint, point out important correlations between the mechanical strength and chemically influenced structural hierarchy of biomaterials.

Hierarchical Models of Chemical Infiltrated Carbon/Carbon Composites

In the last years there has been an increasing interest in the multi-scale mechanics of the materials, i.e. in predicting the macroscopic constitutive response on the basis of the underlying microstructure. At each level of structural hierarchy, one may model the material as a continuum, and the representative volume element problem can be formulated in terms of standard equilibrium and boundary conditions. The overall physical behaviour of these micro-heterogeneous materials depends strongly on the shape, size, orientation, properties and spatial distribution of their microconstituents. For prediction of the macroscopic behaviour of such materials the multi-scale homogenization techniques were developed. As an example of such investigation we develop the hierarchical material model of the chemical vapour infiltrated carbon fiber composites (CFCs) with a unidirectional or random distribution of fibers. The approach based on hierarchical structural modeling can be used to theoretically predict the mechanical parameters of CFCs with different microstructure and to develop virtual materials with prescribed mechanical properties.