Persistence length and stochastic fragmentation of supramolecular nanotubes under mechanical force

Dual enzyme-powered chemotactic cross β amyloid based functional nanomotors

Nanomotor chassis constructed from biological precursors and powered by biocatalytic transformations can offer important applications in the future, specifically in emergent biomedical techniques. Herein, cross β amyloid peptide-based nanomotors (amylobots) were prepared from short amyloid peptides. Owing to their remarkable binding capabilities, these soft constructs are able to host dedicated enzymes to catalyze orthogonal substrates for motility and navigation. Urease helps in powering the self-diffusiophoretic motion, while cytochrome C helps in providing navigation control. Supported by the simulation model, the design principle demonstrates the utilization of two distinct transport behaviours for two different types of enzymes, firstly enhanced diffusivity of urease with increasing fuel (urea) concentration and secondly, chemotactic motility of cytochrome C towards its substrate (pyrogallol). Dual catalytic engines allow the amylobots to be utilized for enhanced catalysis in organic solvent and can thus complement the technological applications of enzymes.

A Critical Study on DNA Probes Attached to Microplate for CRISPR/Cas12 Trans-Cleavage Activity

CRISPR/Cas12-based biosensors are emerging tools for diagnostics. However, their application of heterogeneous formats needs the efficient detection of Cas12 activity. We investigated DNA probes attached to the microplate surface and cleaved by Cas12a. Single-stranded (ss) DNA probes (19 variants) and combined probes with double-stranded (ds) and ssDNA parts (eight variants) were compared. The cleavage efficiency of dsDNA-probes demonstrated a bell-shaped dependence on their length, with a cleavage maximum of 50%. On the other hand, the cleavage efficiency of ssDNA probes increased monotonously, reaching 70%. The most effective ssDNA probes were integrated with fluorescein, antibodies, and peroxidase conjugates as reporters for fluorescent, lateral flow, and chemiluminescent detection. Long ssDNA probes (120-145 nt) proved the best for detecting Cas12a trans-activity for all of the tested variants. We proposed a test system for the detection of the nucleocapsid (N) gene of SARS-CoV-2 based on Cas12 and the ssDNA-probe attached to the microplate surface; its fluorescent limit of detection was 0.86 nM. Being united with pre-amplification using recombinase polymerase, the system reached a detection limit of 0.01 fM, thus confirming the effectiveness of the chosen ssDNA probe for Cas12-based biosensors.

Cyclotide Nanotubes as a Novel Potential Drug-Delivery System: Characterization and Biocompatibility

Cyclotides are a class of cyclic peptides that can be self-assembled. This study aimed to discover the properties of cyclotide nanotubes. We performed differential scanning calorimetric (DSC) to characterize their properties. Then, we incorporated the coumarin as a probe and identified the morphology of nanostructures. The stability of cyclotide nanotubes after 3 months of keeping at -20 °C was determined by field emission scanning electron microscopy (FESEM). The cytocompatibility of cyclotide nanotubes was evaluated on peripheral blood mononuclear cells. In vivo, studies were also conducted on female C57BL/6 mice by intraperitoneally administration of nanotubes at 5, 50, and 100 mg/kg doses. Blood sampling was done before and 24 h after nanotube administration and complete blood count tests were conducted. DSC thermogram showed that the cyclotide nanotubes were stable after heating until 200 °C. Fluorescence microscopy images proved that the self-assembled structures of cyclotide can encapsulate the coumarin. FESEM proved that these nanotubes were stable even after 3 months. The results of the cytotoxicity assay and in-vivo study confirmed that these novel prepared nanotubes were biocompatible. These results suggested that the cyclotide nanotubes could be considered as a new carrier in biological fields while they are biocompatible.

Phase stability of colloidal spheres mixed with semiflexible supramolecular polymers

HYPOTHESIS

Mixtures of colloids and supramolecular polymers may exhibit stimuli-responsive phase behaviour. However, in theoretical descriptions of such systems, the polymers are commonly described either as flexible chains or as rigid rods, while in experimental systems supramolecular polymers usually fall in between these two limits. We expect the flexibility of the polymers to have a profound effect on the stimuli-responsive phase behaviour.

THEORY

We propose a general approach to predict the phase behaviour of colloidal hard spheres mixed with covalent or supramolecular polymers of arbitrary persistence length using free volume theory and an interpolation between flexible and rigid chains.

FINDINGS

The binodals are predicted to shift to lower monomer concentrations as the persistence length is increased, making the polymers more efficient depletants. The persistence length is therefore an additional degree of freedom for manipulating the phase behaviour of colloid-polymer mixtures. We show that by manipulating the persistence length of temperature responsive supramolecular polymers, a wide range of phase diagrams with various topologies can be obtained. For example, we find phase diagrams with a critical point but no triple point or displaying two triple points for temperature-sensitive supramolecular polymers mixed with hard spheres.

Parallel Versus Antiparallel β-Sheet Structure in Cyclic Peptide Hybrids Containing γ- or δ-Cyclic Amino Acids

Cyclic peptides with disc-shaped structures have emerged as potent building blocks for the preparation of new biomaterials in fields ranging from biological to material science. In this work, we analyze in depth the self-assembling properties of a new type of cyclic peptides based on the alternation of α-residues and cyclic δ-amino acids (α,δ-CPs). To examine the preferred stacking properties adopted by cyclic peptides bearing this type of amino acids, we carried out a synergistic in vitro/in silico approximation by using simple dimeric models and then extended to nanotubes. Although these new cyclic peptides (α,δ-CPs) can interact either in a parallel or antiparallel fashion, our results confirm that although the parallel β-sheet is more stable, it can be switched to the antiparallel stacking by choosing residues that can establish favorable cross-strand interactions. Moreover, the subsequent comparison by using the same methodology but applied to α,γ-CPs models, up to the moment assumed as antiparallel-like d,l-α-CPs, led to unforeseen conclusions that put into question preliminary conjectures about these systems. Surprisingly, they tend to adopt a parallel β-sheet directed by the skeleton interactions. These results imply a change of paradigm with respect to cyclic peptide designs that should be considered for dimers and nanotubes.

Metallo-responsive self-assembly of lipophilic guanines in hydrocarbon solvents: a systematic SAXS structural characterization

Lipophilic guanines (LipoGs) in aprotic solvents undergo different self-assembly processes based on different H-bonded motifs. Cylindrical nanotubes made by π-π stacked guanine tetramers (G-quadruplexes) and flat, tape-like aggregates (G-ribbons) have been observed depending on the presence of alkali metal ions. To obtain information on the structural properties and stability of these LipoG aggregates, Small-Angle X-ray Scattering (SAXS) experiments have been performed in dodecane, both in the presence and in the absence of potassium ions. As a result, the occurrence of the two different metallo-responsive architectures (nanoribbons or columnar nanotubes) was confirmed and we reported here for the first time a systematic study on the dependence of the aggregate properties on composition, temperature and molecular unit structure. Even if dodecane was selected to favour LipoG solubility, a strong tendency to self-organize into ordered lyotropic phases was indeed detected.

New self-assembling peptide nanotubes of large diameter using δ-amino acids

Here we show that 4-aminocyclohexanecarboxylic acid is a rigid stretcher building block for the preparation of cyclic peptides that self-assemble to form peptide nanotubes with large diameter and hydrophobic pores. The hydrophobic properties of the resulting nanotubes provided by the two methylene groups per δ-residue allow the encapsulation of C60 moieties forming a new type of bionanopeapod structure.

Self-assembly of bis-salphen compounds: from semiflexible chains to webs of nanorings

The recently-observed self-assembly of certain salphen-based compounds into neuron-like networks of microrings interconnected with nano-thin strings may suggest a new highly-potent tool for nanoscale patterning. However, the mechanism behind such phenomena needs to be clarified before they can be applied in materials design. Here we show that, in contrast with what was initially presumed, the emergence of a "rings-and-rods" pattern is unlikely to be explained by merging, collapse and piercing of vesicles as in previously reported cases of nanorings self-assembly via non-bonding interactions. We propose an alternative explanation: the compounds under study form a 1D coordination polymer, the fibres of which are elastic enough to fold into toroidal globules upon solvent evaporation, while being able to link separate chains into extended networks. This becomes possible because the structure of the compound's scaffold is found to adopt a very different conformation from that inferred in the original work. Based on ab initio and molecular dynamics calculations we propose a step-by-step description of self-assembly process of a supramolecular structure which explains all the observed phenomena in a simple and clear way. The individual roles of the compound' s scaffold structure, coordination centres, functional groups and solvent effects are also explained, opening a route to control the morphology of self-assembled networks and to synthesize new compounds exhibiting similar behaviour.

Molecular dynamics-based strength estimates of beta solenoid proteins

The use of beta solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their mechanical strengths, we can efficiently design the proteins for specific functions. We present a study of the mechanical properties of seven beta solenoid proteins using GROMACS molecular dynamics software to produce force/torque-displacement data, implement umbrella sampling of bending/twisting trajectories, produce Potentials of Mean Force (PMFs), extract effective spring constants, and calculate rigidities for two bending and two twisting directions for each protein. We examine the differences between computing the strength values from force/torque-displacement data alone and PMF data, and show how higher precision estimates can be obtained from the former. In addition to the analysis of the methods, we report estimates for the bend/twist persistence lengths for each protein, which range from 0.5-3.4 μm. We note that beta solenoid proteins with internal disulfide bridges do not enjoy enhanced bending or twisting strength, and that the strongest correlate with bend/twist rigidity is the number of hydrogen bonds per turn. In addition, we compute estimates of the Young's modulus (Y) for each protein, which range from Y = 3.5 to 7.2 GPa.

Effect of Acetyl Group on Mechanical Properties of Chitin/Chitosan Nanocrystal: A Molecular Dynamics Study

Chitin fiber is the load-bearing component in natural chitin-based materials. In these materials, chitin is always partially deacetylated to different levels, leading to diverse material properties. In order to understand how the acetyl group enhances the fracture resistance capability of chitin fiber, we constructed atomistic models of chitin with varied acetylation degree and analyzed the hydrogen bonding pattern, fracture, and stress-strain behavior of these models. We notice that the acetyl group can contribute to the formation of hydrogen bonds that can stabilize the crystalline structure. In addition, it is found that the specimen with a higher acetylation degree presents a greater resistance against fracture. This study describes the role of the functional group, acetyl groups, in crystalline chitin. Such information could provide preliminary understanding of nanomaterials when similar functional groups are encountered.

Mechanical properties of single supramolecular polymers from correlative AFM and fluorescence microscopy

We characterize the structure and mechanical properties of 1,3,5-benzenetricarboxamide (BTA) supramolecular polymers using correlative AFM and fluorescence imaging.

Understanding emergent functions in self-assembled fibrous networks

Understanding self-assembly processes of nanoscale building blocks and characterizing their properties are both imperative for designing new hierarchical, network materials for a wide range of structural, optoelectrical, and transport applications. Although the characterization and choices of these material building blocks have been well studied, our understanding of how to precisely program a specific morphology through self-assembly still must be significantly advanced. In the recent study by Xie et al (2015 Nanotechnology 26 205602), the self-assembly of end-functionalized nanofibres is investigated using a coarse-grained molecular model and offers fundamental insight into how to control the structural morphology of nanofibrous networks. Varying nanoscale networks are observed when the molecular interaction strength is changed and the findings suggest that self-assembly through the tuning of molecular interactions is a key strategy for designing nanostructured networks with specific topologies.

In Silico Measurements of Twist and Bend Moduli for β-Solenoid Protein Self-Assembly Units

We compute potentials of mean force for bend and twist deformations via force pulling and umbrella sampling experiments for four β-solenoid proteins (BSPs) that show promise in nanotechnology applications. In all cases, we find quasi-Hooke's law behavior until the point of rupture. Bending moduli show modest anisotropy for two-sided and three-sided BSPs, and little anisotropy for a four-sided BSP. There is a slight clockwise/counterclockwise asymmetry in the twist potential of mean force, showing greater stiffness when the applied twist follows the intrinsic twist. When we extrapolate to beam theory appropriate for amyloid fibrils of the BSPs, we find bend/twist moduli which are somewhat smaller than those in the literature for other amyloid fibrils. Twist persistence lengths are on the order of a micron, and bend persistence lengths are several microns. Provided the intrinsic twist can be reversed, these results support the usage of BSPs in biomaterials applications.

Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry

We use atomistic nonequilibrium molecular dynamics simulations to demonstrate how specific ionic flux in peptide nanotubes can be regulated by tailoring the lumen chemistry through single amino acid substitutions. By varying the size and polarity of the functional group inserted into the nanotube interior, we are able to adjust the Na(+) flux by over an order of magnitude. Cl(-) is consistently denied passage. Bulky, nonpolar groups encourage interactions between the Na(+) and the peptide backbone carbonyl groups, disrupting the Na(+) solvation shell and slowing the transport of Na(+). Small groups have the opposite effect and accelerate flow. These results suggest that relative ion flux and selectivity can be precisely regulated in subnanometer pores by molecularly defining the lumen according to biological principles.

Structural, nanomechanical, and computational characterization of D,L-cyclic peptide assemblies

The rigid geometry and tunable chemistry of D,L-cyclic peptides makes them an intriguing building-block for the rational design of nano- and microscale hierarchically structured materials. Herein, we utilize a combination of electron microscopy, nanomechanical characterization including depth sensing-based bending experiments, and molecular modeling methods to obtain the structural and mechanical characteristics of cyclo-[(Gln-D-Leu)4] (QL4) assemblies. QL4 monomers assemble to form large, rod-like structures with diameters up to 2 μm and lengths of tens to hundreds of micrometers. Image analysis suggests that large assemblies are hierarchically organized from individual tubes that undergo bundling to form larger structures. With an elastic modulus of 11.3 ± 3.3 GPa, hardness of 387 ± 136 MPa and strength (bending) of 98 ± 19 MPa the peptide crystals are among the most robust known proteinaceous micro- and nanofibers. The measured bending modulus of micron-scale fibrils (10.5 ± 0.9 GPa) is in the same range as the Young's modulus measured by nanoindentation indicating that the robust nanoscale network from which the assembly derives its properties is preserved at larger length-scales. Materials selection charts are used to demonstrate the particularly robust properties of QL4 including its specific flexural modulus in which it outperforms a number of biological proteinaceous and nonproteinaceous materials including collagen and enamel. The facile synthesis, high modulus, and low density of QL4 fibers indicate that they may find utility as a filler material in a variety of high efficiency, biocompatible composite materials.

Tensile deformation and failure of amyloid and amyloid-like protein fibrils

Here we report a series of full atomistic molecular dynamics simulations of six amyloid or amyloid-like protein fibrils in order to systematically understand the effect of different secondary structure motifs on the mechanical tensile and failure response of cross-β protein fibrils. We find a similar failure behavior across the six structures; an initial failure event occurs at small strains involving cooperative rupture of a group of hydrogen bonds, followed by a slow one-by-one hydrogen bond rupture process as the remaining β-sheets peel off with very low applied stress. We also find that the ultimate tensile strength of the protein fibrils investigated scales directly with the number of hydrogen bonds per unit area which break in the initial rupture event. Our results provide insights into structure-property relationships in protein fibrils important for disease and engineering applications and lay the groundwork for the development of materials selection criteria for the design of de novo amyloid-based functional biomaterials.

Biological materials by design

In this topical review we discuss recent advances in the use of physical insight into the way biological materials function, to design novel engineered materials 'from scratch', or from the level of fundamental building blocks upwards and by using computational multiscale methods that link chemistry to material function. We present studies that connect advances in multiscale hierarchical material structuring with material synthesis and testing, review case studies of wood and other biological materials, and illustrate how engineered fiber composites and bulk materials are designed, modeled, and then synthesized and tested experimentally. The integration of experiment and simulation in multiscale design opens new avenues to explore the physics of materials from a fundamental perspective, and using complementary strengths from models and empirical techniques. Recent developments in this field illustrate a new paradigm by which complex material functionality is achieved through hierarchical structuring in spite of simple material constituents.

Directing the self-assembly of supra-biomolecular nanotubes using entropic forces

Peptide self-assembly, ubiquitous in biology, is one of the most promising 'bottom-up' approaches for the generation of synthetic supramolecular architectures. However, directing the self-assembly of functional peptides into predictable ordered structures most often requires precise tuning of weak intermolecular forces. Existing strategies are generally based on specific interactions between molecular mediators that require complex chemical synthesis pathways and elaborated design rules. Here we establish a theoretical framework that delineates a generic route towards directing the self-assembly of small peptides by simply using entropic forces generated by the polymer chains attached to the peptides. We demonstrate the viability of this concept for polymer-conjugated peptide nanotubes using coarse-grained molecular dynamics (CGMD) simulations combined with theoretical calculations. We show that conjugated polymer chains create an entropic penalty due to chain confinement upon assembly, and illustrate that the self-assembly process can be directed by merely varying the degree of polymer conjugation. Specifically, the entropic penalty, and consequently, the binding energy between peptides can be greatly varied by changing the length and the number of conjugated polymers. Extending this concept for peptides with different degrees of conjugation reveals a path towards controlling the stacking sequence of binary mixtures. Remarkably, we find that a large disparity in the conjugation degree of the two peptides results in a preference towards alternating mixed sequences that minimize the entropic penalty of confinement in the thermodynamic limit. Our study explains recent experiments on polymer-peptide conjugates and sets the stage for utilizing entropic forces to guide the stacking sequence of functional macrocycles in tubular assemblies.

Dimensions of Biological Cellulose Nanocrystals Maximize Fracture Strength

Cellulose nanocrystals (CNCs) exhibit outstanding mechanical properties exceeding that of Kevlar, serving as reinforcing domains in nature's toughest biological nanocomposites such as wood. To establish a molecular-level understanding of how CNCs develop high resistance to failure, here we present new analyses based on atomistic simulations on the fracture energy of Iβ CNCs. We show that the fracture energy depends on the crystal width, due to edge defects that significantly reduce the fracture energy of small crystals but have a negligible effect beyond a critical width. Additionally, collective effects of sheet stacking and stabilization by van der Waals interactions saturate at a critical crystal thickness that we predict with an analytical relationship based on a physical model. Remarkably, ideal dimensions optimizing fracture energy are found to be 4.8-5.6 nm in thickness (approximately 6-7 layers) and 6.2-7.3 nm in width (approximately 6-7 cellulose chains), which correspond to the common dimensions of CNCs found in nature. Our studies shed light on evolutionary principles that provide guidance toward high mechanical performance in natural and synthetic nanobiocomposites.