Nanomechanical strength mechanisms of hierarchical biological materials and tissues

Biological protein materials (BPMs), intriguing hierarchical structures formed by assembly of chemical building blocks, are crucial for critical functions of life. The structural details of BPMs are fascinating: They represent a combination of universally found motifs such as α-helices or β-sheets with highly adapted protein structures such as cytoskeletal networks or spider silk nanocomposites. BPMs combine properties like strength and robustness, self-healing ability, adaptability, changeability, evolvability and others into multi-functional materials at a level unmatched in synthetic materials. The ability to achieve these properties depends critically on the particular traits of these materials, first and foremost their hierarchical architecture and seamless integration of material and structure, from nano to macro. Here, we provide a brief review of this field and outline new research directions, along with a review of recent research results in the development of structure–property relationships of biological protein materials exemplified in a study of vimentin intermediate filaments.     

天然丝的形成及人工纺丝的研究进展

蜘蛛丝和蚕丝是性能优异的天然丝类材料,具有极高的力学性能、良好的生物相容性和生物可降解性,可广泛应用于纺织、光学、电子、生物医学和环境工程等领域。迄今为止,已经有湿法纺丝、干法纺丝和静电纺丝等多种在实验室规模下进行人工纺丝的方法。然而,现阶段大部分的人工丝纤维性能仍比不上天然丝纤维。处理好人工丝纤维层级结构和力学性能之间的关系,是人工纺丝领域亟待解决的问题。文中围绕天然丝纤维的形成、丝纤维力学性能与层级结构的关系、人工纺丝领域的研究进展和丝纤维的应用等方面进行了介绍。     

The role played by modified bioinspired surfaces in interfacial properties of biomaterials

The success of a biomaterial relies on an appropriate interaction between the surface of that biomaterial and the surrounding environment; more specifically, the success of a biomaterial depends on how fluids, proteins, and cells interact with the foreign material. For this reason, the surface properties of biomaterial, such as composition, charge, wettability, and roughness, must be optimized for a desired application to be achieved. In this review we highlight different bioinspired approaches that are used to manipulate and fine-tune the interfacial properties of biomaterials. Inspired by noteworthy natural processes, researchers have developed materials with a functional anatomy that range from hierarchical hybrid structures to self-cleaning interfaces. In this review we focus on (1) the creation of particles and modified surfaces inspired by the structure and composition of biogenic mineralized tissues, (2) the development of biofunctional coatings, (3) materials inspired by biomembranes and proteins, and (4) the design of superwettable materials. Our intention is to point out different bioinspired methodologies that have been used to design materials for biomedical applications and to discuss how interfacial properties modified by manipulation of these materials determine their final biological response. Our objective is to present future research directions and to highlight the potential of bioinspired materials. We hope this review will provide an understanding of the interplay between interfacial properties and biological response so that successful biomaterials can be achieved.     

Hierarchical Structures Based on Two‐Dimensional Nanomaterials for Rechargeable Lithium Batteries

Two‐dimensional (2D) nanomaterials (i.e., graphene and its derivatives, transition metal oxides and transition metal dichalcogenides) are receiving a lot attention in energy storage application because of their unprecedented properties and great diversities. However, their re‐stacking or aggregation during the electrode fabrication process has greatly hindered their further developments and applications in rechargeable lithium batteries. Recently, rationally designed hierarchical structures based on 2D nanomaterials have emerged as promising candidates in rechargeable lithium battery applications. Numerous synthetic strategies have been developed to obtain hierarchical structures and high‐performance energy storage devices based on these hierarchical structure have been realized. This review summarizes the synthesis and characteristics of three styles of hierarchical architecture, namely three‐dimensional (3D) porous network nanostructures, hollow nanostructures and self‐supported nanoarrays, presents the representative applications of hierarchical structured nanomaterials as functional materials for lithium ion batteries, lithium‐sulfur batteries and lithium‐oxygen batteries, meanwhile sheds light particularly on the relationship between structure engineering and improved electrochemical performance; and provides the existing challenges and the perspectives for this fast emerging field.     

Synthesis of hierarchical materials

A major goal of material science is to produce hierarchical materials that are ordered on all length scales, from the molecular (1-100 A) via the nano (10-100 nm) to the meso (1-100 microm). In these materials, the larger-scale properties can be controlled by choosing molecular characteristics. Methods developed to produce three-dimensional, bulk-like hierarchical structures include biomimetic methods, which use polypeptides as building blocks, and amphiphile and colloidal templating, which use amphiphilic or colloidal mesophases as templates for inorganic mesoporous materials. Designing finite mesostructures with a given geometry still remains a challenge.     

Engineering tubulin: microtubule functionalization approaches for nanoscale device applications

With the emergences of engineered devices at microscale and nanoscale dimensions, there is a growing need for controlled actuation and transport at these length scales. The kinesin–microtubule system provides a highly evolved biological transport system well suited for these tasks. Accordingly, there is an ongoing effort to create hybrid nanodevices that integrate biological components with engineered materials for applications such as biological separations, nanoscale assembly, and sensing. Adopting microtubules for these applications generally requires covalent attachment of biotin, fluorophores, or other biomolecules to tubulin enable surface or cargo attachment, or visualization. This review summarizes different strategies for functionalizing microtubules for application-focused as well as basic biological research. These functionalization strategies must maintain the integrity of microtubule proteins so that they do not depolymerize and can be transported by kinesin motors, while adding utility such as the ability to reversibly bind cargo. The relevant biochemical and electrical properties of microtubules are discussed, as well as strategies for microtubule stabilization and long-term storage. Next, attachment strategies, such as antibodies and DNA hybridization that have proven useful to date, are discussed in the context of ongoing hybrid nanodevice research. The review concludes with a discussion of less explored opportunities, such as harnessing the utility of tubulin posttranslational modifications and the use of recombinant tubulin that may enable future progress in nanodevice development.     

Precision materials: Computational design methods of accurate protein materials

Nature has evolved a vast repertoire of structures and functions based on an ordered, orchestrated, protein building-blocks assembly. For decades these sophisticated materials have been studied, mimicked, and repurposed, yet recently, computational protein engineering methods provided an alternative route: creating protein materials de-novo, surpassing evolutionary constraints and optimized for specific tasks. We highlight two areas of research that fundamentally accelerate design of structurally well-defined programmable protein materials. First, implementations of hierarchical assembly and geometric sampling (docking) strategies to create designable backbones under pre-specified symmetry constraints. Second, progress in protein–protein interfaces and sequence design methods, using Rosetta, that drive programmable supramolecular assemblies. These approaches have proven effective in generating diverse protein assemblies in 0-, 1-, 2-, and 3-dimensional architectures (constituting single or multiple components), and as part of a synthetic or a biological system. We expect these methods shall transform the toolbox of protein designers developing next generation synthetic and biological materials.     

Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways

As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model) motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all). We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair.     

Cellulose‐based Supercapacitors: Material and Performance Considerations

One of the biggest challenges we will face over the next few decades is finding a way to power the future while maintaining strong socioeconomic growth and a clean environment. A transition from the use of fossil fuels to renewable energy sources is expected. Cellulose, the most abundant natural biopolymer on earth, is a unique, sustainable, functional material with exciting properties: it is low‐cost and has hierarchical fibrous structures, a high surface area, thermal stability, hydrophilicity, biocompatibility, and mechanical flexibility, which makes it ideal for use in sustainable, flexible energy storage devices. This review focuses on energy storage applications involving different forms of cellulose (i.e., cellulose microfibers, nanocellulose fibers, and cellulose nanocrystals) in supercapacitors, with particular emphasis on new trends and performance considerations relevant to these fields. Recent advances and approaches to obtaining high capacity devices are evaluated and the limitations of cellulose‐based systems are discussed. For the first time, a combination of device‐specific factors such as electrode structures, mass loadings, areal capacities, and volumetric properties are taken into account, so as to evaluate and compare the energy storage performance and to better assess the merits of cellulose‐based materials with respect to real applications.     

Flaw tolerant bulk and surface nanostructures of biological systems

Bone-like biological materials have achieved superior mechanical properties through hierarchical composite structures of mineral and protein. Gecko and many insects have evolved hierarchical surface structures to achieve extraordinary adhesion capabilities. We show that the nanometer scale plays a key role in allowing these biological systems to achieve their superior properties. We suggest that the principle of flaw tolerance may have had an overarching influence on the evolution of the bulk nanostructure of bone-like materials and the surface nanostructure of gecko-like animal species. We demonstrate that the nanoscale sizes allow the mineral nanoparticles in bone to achieve optimum fracture strength and the spatula nanoprotrusions in Gecko to achieve optimum adhesion strength. In both systems, strength optimization is achieved by restricting the characteristic dimension of the basic structure components to nanometer scale so that crack-like flaws do not propagate to break the desired structural link. Continuum modeling and atomistic simulations have been conducted to verify the concept of flaw tolerance at nanoscale.     

Biomimetic self-assembly of apatite hybrid materials: From a single molecular template to bi-/multi-molecular templates

The self-assembly of apatite and proteins is a critical process to induce the formation of the bones and teeth in vertebrates. Although hierarchical structures and biomineralization mechanisms of the mineralized tissues have been intensively studied, most researches focus on the self-assembly biomimetic route using one single-molecular template, while the natural bone is an outcome of a multi-molecular template co-assembly process. Inspired by such a mechanism in nature, a novel strategy based on multi-molecular template co-assembly for fabricating bone-like hybrid materials was firstly proposed by the authors. In this review article we have summarized the new trends from single-molecular template to bi-/multi-molecular template systems in biomimetic fabrication of apatite hybrid materials. So far, many novel apatite hybrid materials with controlled morphologies and hierarchical structures have been successfully achieved using bi-/multi-molecular template strategy, and are found to have multiple common features in comparison with natural mineralized tissues. The carboxyl, carbonyl and amino groups of the template molecules are identified to initiate the nucleation of calcium phosphate during the assembling process. For bi-/multi-molecular templates, the incorporation of multiple promotion sites for calcium and phosphate ions precisely enables to regulate the apatite nucleation from the early stage. The roles of acidic molecules and the synergetic effects of protein templates have been significantly recognized in recent studies. In addition, a specific attention is paid to self-assembling of apatite nanoparticles into ordered structures on tissue regenerative scaffolds due to their promising clinical applications ranging from implant grafts, coatings to drug and gene delivery.     

Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins

Autophagy is an intracellular degradation process, through which cytosolic materials are delivered to the lysosome. Despite recent identification of many autophagy-related genes, how autophagosomes are generated remains unclear. Here, we examined the hierarchical relationships among mammalian Atg proteins. Under starvation conditions, ULK1, Atg14, WIPI-1, LC3 and Atg16L1 target to the same compartment, whereas DFCP1 localizes adjacently to these Atg proteins. In terms of puncta formation, the protein complex including ULK1 and FIP200 is the most upstream unit and is required for puncta formation of the Atg14-containing PI3-kinase complex. Puncta formation of both DFCP1 and WIPI-1 requires FIP200 and Atg14. The Atg12-Atg5-Atg16L1 complex and LC3 are downstream units among these factors. The punctate structures containing upstream Atg proteins such as ULK1 and Atg14 tightly associate with the ER, where the ER protein Vacuole membrane protein 1 (VMP1) also transiently localizes. These structures are formed even when cells are treated with wortmannin to suppress autophagosome formation. These hierarchical analyses suggest that ULK1, Atg14 and VMP1 localize to the ER-associated autophagosome formation sites in a PI3-kinase activity-independent manner.     

Electronic,transport, magnetic,and optical properties of graphene nanoribbons and their optical sensing applications: A comprehensive review

Low dimensional materials have attracted great research interest from both theoretical and experimental point of views. These materials exhibit novel physical and chemical properties due to the confinement effect in low dimensions. The experimental observations of graphene open a new platform to study the physical properties of materials restricted to two dimensions. This featured article provides a review on the novel properties of quasi one-dimensional (1D) material known as graphene nanoribbon. Graphene nanoribbons can be obtained by unzipping carbon nanotubes (CNT) or cutting the graphene sheet. Alternatively, it is also called the finite termination of graphene edges. It gives rise to different edge geometries, namely zigzag and armchair, among others. There are various physical and chemical techniques to realize these materials. Depending on the edge type termination, these are called the zigzag and armchair graphene nanoribbons (ZGNR and AGNR). These edges play an important role in controlling the properties of graphene nanoribbons. The present review article provides an overview of the electronic, transport, optical, and magnetic properties of graphene nanoribbons. However, there are different ways to tune these properties for device applications. Here, some of them, such as external perturbations and chemical modifications, are highlighted. Few applications of graphene nanoribbon have also been briefly discussed.     

Interfacial Effects of Superhydrophobic Plant Surfaces： A Review

Nature is a huge gallery of art involving nearly perfect structures and properties over the millions of years of development. Many plants and animals show water-repellent properties with fine micro-structures, such as lotus leaf, water skipper and wings of butterfly. Inspired by these special surfaces, the artificial superhydrophobic surfaces have attracted wide attention in both basic research and industrial applications. The wetting properties of superhydrophobic surfaces in nature are affected by the chemical compositions and the surface topographies. So it is possible to realize the biomimetic superhydrophobic surfaces by tuning their surface roughness and surface free energy correspondingly. This review briefly introduces the physical-chemical basis of superhydrophobic plant surfaces in nature to explain how the superhydrophobicity of plant surfaces can be applied to different biomimetic functional materials with relevance to technological applications. Then, three classical effects of natural surfaces are classified： lotus effect, salvinia effect, and petal effect, and the promising strategies to fabricate biomimetic su- perhydrophobic materials are highlighted. Finally, the prospects and challenges of this area in the future are proposed.     

On optimal hierarchy of load-bearing biological materials

Load-bearing biological materials such as shell, mineralized tendon and bone exhibit two to seven levels of structural hierarchy based on constituent materials (biominerals and proteins) of relatively poor mechanical properties. A key question that remains unanswered is what determines the number of hierarchical levels in these materials. Here we develop a quasi-self-similar hierarchical model to show that, depending on the mineral content, there exists an optimal level of structural hierarchy for maximal toughness of biocomposites. The predicted optimal levels of hierarchy and cooperative deformation across multiple structural levels are in excellent agreement with experimental observations.     

Protein-protein interactions as a target for drugs in proteomics

Protein-protein interactions play a central role in numerous processes in the cell and are one of the main fields of functional proteomics. This review highlights the methods of bioinformatics and functional proteomics of protein-protein interaction investigation. The structures and properties of contact surfaces, forces involved in protein-protein interactions, kinetic and thermodynamic parameters of these reactions were considered. The properties of protein contact surfaces depend on their functions. The contact surfaces of permanent complexes resemble domain contacts or the protein core and it is reasonable to consider such complex formation as a continuation of protein folding. Characteristics of contact surfaces of temporary protein complexes share some similarities with active sites of enzymes. The contact surfaces of the temporary protein complexes have unique structure and properties and they are more conservative in comparison with active site of enzymes. So they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations were undertaken to find or design small molecules that block protein dimerization or protein(peptide)-receptor interaction, or, on the contrary, to induce protein dimerization.     

Prion-based nanomaterials and their emerging applications

ABSTRACT

Protein misfolding and aggregation into highly ordered fibrillar structures have been traditionally associated with pathological processes. Nevertheless, nature has taken advantage of the particular properties of amyloids for functional purposes, like in the protection of organisms against environmental changing conditions. Over the last decades, these fibrillar structures have inspired the design of new nanomaterials with intriguing applications in biomedicine and nanotechnology such as tissue engineering, drug delivery, adhesive materials, biodegradable nanocomposites, nanowires or biosensors. Prion and prion-like proteins, which are considered a subclass of amyloids, are becoming ideal candidates for the design of new and tunable nanomaterials. In this review, we discuss the particular properties of this kind of proteins, and the current advances on the design of new materials based on prion sequences.     

Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins

Autophagy is an intracellular degradation process, through which cytosolic materials are delivered to the lysosome. Despite recent identification of many autophagy-related genes, how autophagosomes are generated remains unclear. Here, we examined the hierarchical relationships among mammalian Atg proteins. Under starvation conditions, ULK1, Atg14, WIPI-1, LC3 and Atg16L1 target to the same compartment, whereas DFCP1 localizes adjacently to these Atg proteins. In terms of puncta formation, the protein complex including ULK1 and FIP200 is the most upstream unit and is required for puncta formation of the Atg14-containing PI3-kinase complex. Puncta formation of both DFCP1 and WIPI-1 requires FIP200 and Atg14. The Atg12-Atg5-Atg16L1 complex and LC3 are downstream units among these factors. The punctate structures containing upstream Atg proteins such as ULK1 and Atg14 tightly associate with the ER, where the ER protein vacuole membrane protein 1 (VMP1) also transiently localizes. These structures are formed even when cells are treated with wortmannin to suppress autophagosome formation. These hierarchical analyses suggest that ULK1, Atg14 and VMP1 localize to the ER-associated autophagosome formation sites in a PI3-kinase activity-independent manner.Key words: autophagosome, PI3-kinase, isolation membrane, endoplasmic reticulum, ULK     

Recent Developments on and Prospects for Electrode Materials with Hierarchical Structures for Lithium‐Ion Batteries

Since their successful commercialization in 1990s, lithium‐ion batteries (LIBs) have been widely applied in portable digital products. The energy density and power density of LIBs are inadequate, however, to satisfy the continuous growth in demand. Considering the cost distribution in battery system, it is essential to explore cathode/anode materials with excellent rate capability and long cycle life. Nanometer‐sized electrode materials could quickly take up and store numerous Li⁺ ions, afforded by short diffusion channels and large surface area. Unfortunately, low thermodynamic stability of nanoparticles results in electrochemical agglomeration and raises the risk of side reactions on electrolyte. Thus, micro/nano and hetero/hierarchical structures, characterized by ordered assembly of different sizes, phases, and/or pores, have been developed, which enable us to effectively improve the utilization, reaction kinetics, and structural stability of electrode materials. This review summarizes the recent efforts on electrode materials with hierarchical structures, and discusses the effects of hierarchical structures on electrochemical performance in detail. Multidimensional self‐assembled structures can achieve integration of the advantages of materials with different sizes. Core/yolk–shell structures provide synergistic effects between the shell and the core/yolk. Porous structures with macro‐, meso‐, and micropores can accommodate volume expansion and facilitate electrolyte infiltration.     

Preparation of biosilica structures from frustules of diatoms and their applications: current state and perspectives

Frustules, the silica shells of diatoms, have unique porous architectures with good mechanical strength. In recent years, biologists have learned more about the mechanism of biosilica shells formation; meanwhile, physicists have revealed their optical and microfluidic properties, and chemists have identified ways to modify them into various materials while maintaining their hierarchical structures. These efforts have provided more opportunities to use biosilica structures in microsystems and other commercial products. This review focuses on the preparation of biosilica structures and their applications, especially in the development of microdevices. We discuss existing methods of extracting biosilica from diatomite and diatoms, introduce methods of separating biosilica structures by shape and sizes, and summarize recent studies on diatom-based devices used for biosensing, drug delivery, and energy applications. In addition, we introduce some new findings on diatoms, such as the elastic deformable characteristics of biosilica structures, and offer perspectives on planting diatom biosilica in microsystems.