Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks

Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro. Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved. Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules. In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and diversity – in the following referred to as the universality-diversity paradigm (UDP) – is an overarching feature in protein materials. This paradigm is a paradox: How can a structure be universal and diverse at the same time? In protein materials, the coexistence of universality and diversity is enabled by utilizing hierarchies, which serve as an additional dimension beyond the 3D or 4D physical space. This may be crucial to understand how their structure and properties are linked, and how these materials are capable of combining seemingly disparate properties such as strength and robustness. Here we illustrate how the UDP enables to unify universal building blocks and highly diversified patterns through formation of hierarchical structures that lead to multi-functional, robust yet highly adapted structures. We illustrate these concepts in an analysis of three types of intermediate filament proteins, including vimentin, lamin and keratin

Flaw-tolerance in silk fibrils explains strength, extensibility and toughness of spider silk

Silk is an ancient but remarkably strong, extensible and tough material made from simple protein building blocks. Earlier work has shown that the particular molecular geometry of silk with a composite of semi-amorphous and nanocrystalline beta-sheet protein domains provides the structural basis for its characteristic softening-stiffening behavior and remarkable strength at the nanoscale. Yet, an open question remains as to how these nanoscale properties are upscaled so effectively to create strong, extensible and tough silk fibers. Here we discover that the geometric confinement of fibrils to ≈50-100 nm width and arranged in bundles to form larger-scale silk fibers, is the key to explaining the upscaling of the mechanical properties of silk from the atomistic scale upwards. We find that under this geometric confinement, hundreds of thousands of protein domains unfold simultaneously and thereby act synergistically to resist deformation and failure, providing access to enhanced large-scale strength, extensibility and toughness. Moreover, since the material is in a flaw-tolerant state under this geometric confinement, structural inhomogeneities such as cavities or tears that typically act as stress concentrators do not compromise the material performance. Indeed, experimental work showed that the diameter of silk fibrils that make up larger-scale silk fibers are on the order of 20-100 nm, in agreement with our findings. The exploitation of this mechanism in engineering design enables the synthesis of hierarchical fiber materials for superior performance despite limited and inferior building blocks

Materials by design—A perspective from atoms to structures

Biological materials are effectively synthesized, controlled, and used for a variety of purposes in Nature—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays 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 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, even linking music to materials science.National Science Foundation (U.S.) (CAREER 0642545)United States. Office of Naval Research (PECASE N00014-10-1-0562)United States. Air Force Office of Scientific Research (FA9550-11-1-0199)National Institutes of Health (U.S.) (U01 EB014976

Hierarchical nanomechanics of collagen microfibrils

Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to connective tissues. Collagen is also the dominating material in the extracellular matrix (ECM) and is thus crucial for cell differentiation, growth and pathology. However, fundamental questions remain with respect to the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response. By using x-ray diffraction data of a collagen fibril reported by Orgel et al. (Proceedings of the National Academy of Sciences USA, 2006) in combination with protein structure identification methods, here we present an experimentally validated model of the nanomechanics of a collagen microfibril that incorporates the full biochemical details of the amino acid sequence of the constituting molecules. We report the analysis of its mechanical properties under different levels of stress and solvent conditions, using a full-atomistic force field including explicit water solvent. Mechanical testing of hydrated collagen microfibrils yields a Young’s modulus of ≈300 MPa at small and ≈1.2 GPa at larger deformation in excess of 10% strain, in excellent agreement with experimental data. Dehydrated, dry collagen microfibrils show a significantly increased Young’s modulus of ≈1.8 to 2.25 GPa (or ≈6.75 times the modulus in the wet state) owing to a much tighter molecular packing, in good agreement with experimental measurements (where an increase of the modulus by ≈9 times was found). Our model demonstrates that the unique mechanical properties of collagen microfibrils can be explained based on their hierarchical structure, where deformation is mediated through mechanisms that operate at different hierarchical levels. Key mechanisms involve straightening of initially disordered and helically twisted molecules at small strains, followed by axial stretching of molecules, and eventual molecular uncoiling at extreme deformation. These mechanisms explain the striking difference of the modulus of collagen fibrils compared with single molecules, which is found in the range of 4.8±2 GPa or ≈10-20 times greater. These findings corroborate the notion that collagen tissue properties are highly scale dependent and nonlinear elastic, an issue that must be considered in the development of models that describe the interaction of cells with collagen in the extracellular matrix. A key impact the atomistic model of collagen microfibril mechanics reported here is that it enables the bottom-up elucidation of structure-property relationships in the broader class of collagen materials such as tendon or bone, including studies in the context of genetic disease where the incorporation of biochemical, genetic details in material models of connective tissue is essential

Molecular Modeling and Mechanics of Acrylic Adhesives on a Graphene Substrate with Roughness

Understanding the mechanics of amorphous polymeric adhesives on a solid substrate at the fundamental scale level is critical for designing and optimizing the mechanics of composite materials. Using molecular dynamics simulations, we investigate the interfacial strength between graphene and polyacrylic and discuss how the surface roughness of graphene affects the interfacial strength in different loading directions. Our results show that a single angstrom increase in graphene roughness can lead to almost eight times higher shear strength, and that such result is insensitive to compression. We have also revealed that the graphene roughness has modest effect on tensile strength of the interface. Our simulations elucidate the molecular mechanism of these different effects in different loading conditions and provide insights for composite designs.Henkel Corporatio

Computational and theoretical modeling of intermediate filament networks: Structure, mechanics and disease

Intermediate filaments, in addition to microtubules and actin microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that in most cells, intermediate filament proteins play key roles to reinforce cells subjected to large-deformation, and that they participate in signal transduction, and it was proposed that their nanomechanical properties are critical to perform those functions. However, it is still poorly understood how the nanoscopic structure, as well as the combination of chemical composition, molecular structure and interfacial properties of these protein molecules contribute to the biomechanical properties of filaments and filament networks. Here we review recent progress in computational and theoretical studies of the intermediate filaments network at various levels in the protein’s structure. A multiple scale method is discussed, used to couple molecular modeling with atomistic detail to larger-scale material properties of the networked material. It is shown that a finer-trains-coarser methodology as discussed here provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments, coupling experiment and simulation. It further allows us to improve the understanding of associated disease mechanisms and lays the foundation for engineering the mechanical properties of biomaterials.United States. Air Force Office of Scientific ResearchNational Science Foundation (U.S.)United States. Office of Naval Researc

Failure of Aβ(1-40) amyloid fibrils under tensile loading

Amyloid fibrils and plaques are detected in the brain tissue of patients affected by Alzheimer’s disease, but have also been found as part of normal physiological processes such as bacterial adhesion. Due to their highly organized structures, amyloid proteins have also been used for the development of nanomaterials, for a variety of applications including biomaterials for tissue engineering, nanolectronics, or optical devices. Past research on amyloid fibrils resulted in advances in identifying their mechanical properties, revealing a remarkable stiffness. However, the failure mechanism under tensile loading has not been elucidated yet, despite its importance for the understanding of key mechanical properties of amyloid fibrils and plaques as well as the growth and aggregation of amyloids into long fibers and plaques. Here we report a molecular level analysis of failure of amyloids under uniaxial tensile loading. Our molecular modeling results demonstrate that amyloid fibrils are extremely stiff with a Young’s modulus in the range of 18–30 GPa, in good agreement with previous experimental and computational findings. The most important contribution of our study is our finding that amyloid fibrils fail at relatively small strains of 2.5%–4%, and at stress levels in the range of 1.02 to 0.64 GPa, in good agreement with experimental findings. Notably, we find that the strength properties of amyloid fibrils are extremely length dependent, and that longer amyloid fibrils show drastically smaller failure strains and failure stresses. As a result, longer fibrils in excess of hundreds of nanometers to micrometers have a greatly enhanced propensity towards spontaneous fragmentation and failure. We use a combination of simulation results and simple theoretical models to define critical fibril lengths where distinct failure mechanisms dominate.United States. Office of Naval Research (Grant NN00014-08-1-0844

Mechanical properties of crosslinks controls failure mechanism of hierarchical intermediate filament networks

Intermediate filaments are one of the key components of the cytoskeleton in eukaryotic cells, and their mechanical properties are found to be equally important for physiological function and disease. While the mechanical properties of single full length filaments have been studied, how the mechanical properties of crosslinks affect the mechanical property of the intermediate filament network is not well understood. This paper applies a mesoscopic model of the intermediate network with varied crosslink strengths to investigate its failure mechanism under the extreme mechanical loading. It finds that relatively weaker crosslinks lead to a more flaw tolerant intermediate filament network that is also 23% stronger than the one with strong crosslinks. These findings suggest that the mechanical properties of interfacial components are critical for bioinspired designs which provide intriguing mechanical properties. Key words: failure mechanism; flow tolerance; intermediate filament; protein network; soft material; rupture; crosslink strength; bioinspired desig

Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils

Spider silk is one of the strongest, most extensible and toughest biological materials known, exceeding the properties of many engineered materials including steel. Silks feature a hierarchical architecture where highly organized, densely H-bonded beta-sheet nanocrystals are arranged within a semi-amorphous protein matrix consisting of 31-helices and beta-turn protein structures. By using a bottom-up molecular-based mesoscale model that bridges the scales from Angstroms to hundreds of nanometers, here we show that the specific combination of a crystalline phase and a semi-amorphous matrix is crucial for the unique properties of silks. Specifically, our results reveal that the superior mechanical properties of spider silk can be explained solely by structural effects, where the geometric confinement of beta-sheet nanocrystals combined with highly extensible semi-amorphous domains with a large hidden length is the key to reach great strength and great toughness, despite the dominance of mechanically inferior chemical interactions such as H-bonding. Our model directly shows that semi-amorphous regions unravel first when silk is being stretched, leading to the large extensibility of silk. Conversely, the large-deformation mechanical properties and ultimate tensile strength of silk is controlled by the strength of beta-sheet nanocrystals, which is directly related to their size, where small beta-sheet nanocrystals are crucial to reach outstanding levels of strength and toughness. Our model agrees well with observations in recent experiments, where it was shown that a significant change in the strength and toughness can be achieved solely by tuning the size of beta-sheet nanocrystals. Our findings unveil the material design strategy that enables silks to achieve superior material performance despite simple and inferior constituents, resulting in a new paradigm in materials design where enhanced functionality is not achieved using complex building blocks, but rather through the utilization of simple repetitive constitutive elements arranged in hierarchical structures

Molecular biomechanics of collagen molecules

Collagenous tissues, made of collagen molecules, such as tendon and bone, are intriguing materials that have the ability to respond to mechanical forces by altering their structures from the molecular level up, and convert them into biochemical signals that control many biological and pathological processes such as wound healing and tissue remodeling. It is clear that collagen synthesis and degradation are influenced by mechanical loading, and collagenous tissues have a remarkable built-in ability to alter the equilibrium between material formation and breakdown. However, how the mechanical force alters structures of collagen molecules and how the structural changes affect collagen degradation at molecular level is not well understood. The purpose of this article is to review the biomechanics of collagen, using a bottom-up approach that begins with the mechanics of collagen molecules. The current understanding of collagen degradation mechanisms is presented, followed by a discussion of recent studies on how mechanical force mediates collagen breakdown. Understanding the biomechanics of collagen molecules will provide the basis for understanding the mechanobiology of collagenous tissues. Addressing challenges in this field provides an opportunity for developing treatments, designing synthetic collagen materials for a variety of biomedical applications, and creating a new class of ‘smart’ structural materials that autonomously grow when needed, and break down when no longer required, with applications in nanotechnology, devices and civil engineering.National Science Foundation (U.S.)United States. Office of Naval Research. Presidential Early Career Award for Scientists and EngineersNational Institutes of Health (U.S.) (U01EB014976