Biomolecular Self-assembly Research Articles

A broad-spectrum antibacterial hydrogel based on the synergistic action of Fmoc-phenylalanine and Fmoc-lysine in a co-assembled state.

Multicomponent biomolecular self-assembly is fundamental for accomplishing complex functionalities of biosystems. Self-assembling peptides, amino acids, and their conjugates serve as a versatile platform for developing biomaterials. However, the co-assembly of multiple building blocks showing synergistic interplay between individual components and producing biomaterials with emergent functional attributes is much less explored. In this study, we have formulated minimalistic co-assembled hydrogels composed of Fmoc-phenylalanine and Fmoc-lysine. The co-assembled systems display broad-spectrum antimicrobial potency, a feature absent in individual building blocks. A comprehensive biophysical analysis demonstrates the physicochemical features of the hydrogels eliciting the antibacterial response. MD simulation further reveals a unique fibrillar architecture with Fmoc-phenylalanine forming the fibril core surrounded by positively charged Fmoc-lysine surface residues, thereby enhancing the interaction with negatively charged bacterial membranes, causing membrane disruption and cell death. Thus, this study provides molecular-level insight into the emergent properties of a multicomponent system, affording an excellent paradigm for developing novel biomaterials.

Oxidase-Mimetic Nanocatalyst Based on Geometry-Dependent Biomolecular Self-Assembly

Oxidase-Mimetic Nanocatalyst Based on Geometry-Dependent Biomolecular Self-Assembly

Tuning rheology and fire-fighting performance of protein-stabilized foam by actively switching the interfacial state of the liquid film

Biomolecular self-assembly has lately emerged as an intriguing method for creating stable gas-liquid dispersions with unique functional characteristics. In this work, protein-metal coordination complexes were designed as the stabilizer for generating ultrastable fire-fighting foam and creating interfacial architectures that were actively switched between “rigid” and “mobile” interfacial states of liquid films in response to changes in pH and bulk solution compositions (metal ions or alkyl polyglycosides). The reflected light interferometric technique was used to check interfacial states, and the foaming kinetics and rheological response of aqueous solution and liquid foam were investigated by dynamic surface tension tests and oscillatory rheology analysis. The results showed that liquid foams with mobile films with lower yield limits had a faster spreading rate to cover the burning oil, liquid foams with semi-rigid films cannot extinguish fires due to interfacial instability, and the enhanced rheology of the foam with rigid films established a robust and impenetrable barrier to effectively suppress fuel evaporation and combustion. A new correlation between interfacial properties and the fire-fighting performance of foam was proposed, which showed that the fire-extinguishing time of foam could be well correlated by the interfacial states or film lifetime rather than classical thermodynamics entry, spreading, and bridging coefficients (ESB coefficients).

Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics.

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

Molecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions.

A comprehensive understanding of protein folding and biomolecular self-assembly in the intracellular environment requires obtaining a microscopic view of the crowding effects. The classical view of crowding explains biomolecular collapse in such an environment in terms of the entropic solvent excluded volume effects subjected to hard-core repulsions exerted by the inert crowders, neglecting their soft chemical interactions. In this study, the effects of nonspecific, soft interactions of molecular crowders in regulating the conformational equilibrium of hydrophilic (charged) polymers are examined. Using advanced molecular dynamics simulations, collapse free energies of an uncharged, a negatively charged, and a charge-neutral 32-mer generic polymer are computed. The strength of the polymer-crowder dispersion energy is modulated to examine its effect on polymer collapse. The results show that the crowders preferentially adsorb and drive the collapse of all three polymers. The uncharged polymer collapse is opposed by the change in solute-solvent interaction energy but is overcompensated by the favorable change in the solute-solvent entropy as observed in hydrophobic collapse. However, the negatively charged polymer collapses with a favorable change in solute-solvent interaction energy due to reduction in the dehydration energy penalty as the crowders partition to the polymer interface and shield the charged beads. The collapse of a charge-neutral polymer is opposed by the solute-solvent interaction energy but is overcompensated by the solute-solvent entropy change. However, for the strongly interacting crowders, the overall energetic penalty decreases since the crowders interact with polymer beads via cohesive bridging attractions to induce polymer collapse. These bridging attractions are found to be sensitive to the binding sites of the polymer, since they are absent in the negatively charged or uncharged polymers. These interesting differences in thermodynamic driving forces highlight the crucial role of the chemical nature of the macromolecule as well as of the crowder in determining the conformational equilibria in a crowded milieu. The results emphasize that the chemical interactions of the crowders should be explicitly considered to account for the crowding effects. The findings have implications in understanding the crowding effects on the protein free energy landscapes.

Review on Recent Developments in Bioinspired-Materials for Sustainable Energy and Environmental Applications

Nature has always inspired innovative minds for development of new designs. Animals and plants provide various structures with lower density, more strength and high energy sorption abilities that can incite the development of new designs with significant properties. By observing the important functions of biological structures found in nature, scientists have fabricated structures by bio-inspiration that have been proved to exhibit a significant improvement over traditional structures for their applications in the environmental and energy sector. Bio-fabricated materials have shown many advantages due to their easy synthesis, flexible nature, high performance and multiple functions as these can be used in light harvesting systems, batteries, biofuels, catalysis, purification of water, air and environmental monitoring. However, there is an urgent need for sensitive fabrication instruments that can synthesize bio-inspired structures and convert laboratory scale synthesis into large scale production. The present review highlights recent advances in synthesis of bio-inspired materials and use of hierarchical nanomaterials generated through biomolecular self-assembly for their use in removal of environmental contaminants and sustainable development.

Exploring Biomolecular Self-Assembly with Far-Infrared Radiation.

Physical engineering technology using far-infrared radiation has been gathering attention in chemical, biological, and material research fields. In particular, the high-power radiation at the terahertz region can give remarkable effects on biological materials distinct from a simple thermal treatment. Self-assembly of biological molecules such as amyloid proteins and cellulose fiber plays various roles in medical and biomaterials fields. A common characteristic of those biomolecular aggregates is a sheet-like fibrous structure that is rigid and insoluble in water, and it is often hard to manipulate the stacking conformation without heating, organic solvents, or chemical reagents. We discovered that those fibrous formats can be conformationally regulated by means of intense far-infrared radiations from a free-electron laser and gyrotron. In this review, we would like to show the latest and the past studies on the effects of far-infrared radiation on the fibrous biomaterials and to suggest the potential use of the far-infrared radiation for regulation of the biomolecular self-assembly.

Biomolecular Self-Assembly of Nanorings on a Viral Protein Template.

Although there have been many advances in synthesizing nanoparticles, their assembly into deterministic and controllable patterns remains a major challenge. Biological systems operate at the nanoscale, building structural components with great chemical specificity that enable the processes of life. By adapting them to our needs, it is possible to utilize well-defined and well-controlled scaffolds to produce materials with novel properties resulting from precise ordering on the nanoscale. This approach uses spatial arrangement instead of nanoparticle size, shape, or composition to control material properties through the collective interactions between neighboring nanoparticles. Here, we demonstrate the use of tobacco mosaic virus (TMV) coat protein as a template to self-assemble plasmonic nanoparticles. Surface plasmons are resonant oscillations in the free electrons of a metal that are excited through interaction with light. These plasmonic oscillations can couple together, giving rise to more complex modes like plasmonic ring resonances that can be used to tune the response to incident light. By exploiting the self-assembling properties and chemical addressability of TMV coat protein, we can utilize site-directed mutagenesis and bioconjugation strategies to produce highly symmetrical plasmonic nanorings, as evidenced by transmission electron microscopy (TEM). Thus, we show the utility of viral proteins in designing and assembling nanostructured building blocks for advanced materials.

Correlation between Electrostatic and Hydration Forces on Silica and Gibbsite Surfaces: An Atomic Force Microscopy Study.

The balance between hydration and Derjaguin–Landau–Verwey–Overbeek (DLVO) forces at solid–liquid interfaces controls many processes, such as colloidal stability, wetting, electrochemistry, biomolecular self-assembly, and ion adsorption. Yet, the origin of molecular scale hydration forces and their relation to the surface charge density that controls the continuum scale electrostatic forces is poorly understood. We argue that these two types of forces are largely independent of each other. To support this hypothesis, we performed atomic force microscopy experiments using intermediate-sized tips that enable the simultaneous detection of DLVO and molecular scale oscillatory hydration forces at the interface between composite gibbsite:silica–aqueous electrolyte interfaces. We extract surface charge densities from forces measured at tip–sample separations of 1.5 nm and beyond using DLVO theory in combination with charge regulation boundary conditions for various pH values and salt concentrations. We simultaneously observe both colloidal scale DLVO forces and oscillatory hydration forces for an individual crystalline gibbsite particle and the underlying amorphous silica substrate for all fluid compositions investigated. While the diffuse layer charge varies with pH as expected, the oscillatory hydration forces are found to be largely independent of pH and salt concentration, supporting our hypothesis that both forces indeed have a very different origin. Oscillatory hydration forces are found to be distinctly more pronounced on gibbsite than on silica. We rationalize this observation based on the distribution of hydroxyl groups available for H bonding on the two distinct surfaces.

(Invited) DNA-Directed High-Precision Assembly of High-Performance CNT FETs

Precise fabrication of semiconducting channel materials into densely-aligned uniform arrays is one prerequisite towards the high-performance ultra-scaled technology nodes, in particular for carbon nanotubes (CNTs). Traditional thin-film approaches generally yield CNTs in irregularly-spaced bundles or with wide orientation distribution, and lack a mechanism to effectively eliminate the mis-aligned CNTs from the ultra-scaled channel area. Therefore, the averaged pitch value and precision of CNT arrays, the key parameters defining lateral CNT spacing, fail to simultaneously meet all of the patterning requirements for the ultra-scaled technology nodes. Bio-fabrication is promising for patterning CNTls at a resolution beyond the existing lithographic limit. However, impacted by surface charges and sub-micron dimensions of typical bio-templates, current bio-templated electronics exhibit both poor transport performance and array uniformity smaller than 1 micron.We report precise scaling of inter-CNT pitch using a supramolecular assembly method called Spatially Hindered Integration of Nanowire Electronics (SHINE). Specifically, by using nano-trenches to align CNTs and DNA hybridization to stabilize them in place, we constructed parallel CNT arrays with uniform pitch as small as 10.4 nm, at an assembly yield over 95%. The pitch precision improves on that prepared from conventional thin-film approaches by more than two orders of magnitude. Compared to the lithography-patterned Si channels at 10 nm technology node, SHINE simultaneously provides both 70% smaller averaged pitch value and molecular-scale pitch precision in the channel area. By engineering the interfacial compositions, metal ions and surface charges that are destructive to FET performance have been excluded from the channel area without degrading CNT alignment. Under a source-to-drain voltage of -0.5 V, we demonstrate both transconductance more than 0.6 mS/μm with fast on/off switching. And the key FET performance metrics are improved by more than one order of magnitude than previous bio-templated FETs. Furthermore, we demonstrate centimeter-scale alignment of fixed-width CNT arrays. At the interface of high-performance electronics and bio-molecular self-assembly, precise bio-fabrication could provide ultra-scaled devices or circuits compatible with or sensitive to local biological environments.

Auxetic Two-Dimensional Nanostructures from DNA*.

Architectured materials exhibit negative Poisson's ratios and enhanced mechanical properties compared with regular materials. Their auxetic behaviors emerge from periodic cellular structures regardless of the materials used. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. There are also molecular auxetics including natural crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by biomolecular self-assembly. Herein, we demonstrate two-dimensional auxetic nanostructures using DNA origami. Structural reconfigurations are performed by two-step DNA reactions and complemented by mechanical deformation studies using molecular dynamics simulations. We find that the auxetic behaviors are mostly defined by geometrical designs, yet the properties of the materials also play an important role. From elasticity theory, we introduce design principles for auxetic DNA metamaterials.

Folic acid self-assembly synthesis of ultrathin N-doped carbon nanosheets with single-atom metal catalysts

The development of single-atom catalysts anchored on two-dimensional (2D) conductive matrix with well exposed active sites has great significance in electrocatalytic energy storage yet remains challenging. Inspired by the power of biomolecular self-assembly in making delicate nanostructures, we report a novel template-free folic acid (FA) self-assembly strategy to achieve the facile preparation of ultrathin N-doped carbon nanosheet confining single-metal-atom catalysts (M-N-C SAC, M = Co, Ni, Zn, Fe). The 2D association of FA is developed for the first time via the ribbon-like H bonding pattern and metal-FA coordination in a mixed solvent. A tunable metal loading content of the catalysts is facilely realized through a pH-tuned FA partial dissociation chemistry. As a proof of demonstration, Co-N-C SAC shows an excellent performance for lean electrolyte lithium-sulfur battery. Our findinging suggest a new and potentially scalable route for facile fabrication of M-N-C SACs for broad energy storage applications.

Nonreciprocal interactions induced by water in confinement

Water mediates electrostatic interactions via the orientation of its dipoles around ions, molecules, and interfaces. This induced water polarization consequently influences multiple phenomena. In particular, water polarization modulated by nanoconfinement affects ion adsorption and transport, biomolecular self-assembly, and surface chemical reactions. Therefore, it is of paramount importance to understand how water-mediated interactions change at the nanoscale. Here we show that near the graphene surface anion-cation interactions do not obey the translational and isotropic symmetries of Coulomb's law. We identify a new property, referred to as non-reciprocity, which describes the non-equivalent and directional interaction between two oppositely charged ions near the confining surface when their positions with respect to the interface are exchanged. Specifically, upon exchange of the two ions' positions along the surface normal direction the interaction energy changes by about 5$k_BT$. In both cases, confinement enhances the attraction between two oppositely charged ions near the graphene surface, while intercalation of one ion into the graphene layers shifts the interaction to repulsive. While the water permittivity in confinement is different from that in bulk, the effects observed here via molecular dynamics simulations and X-ray reflectivity experiments cannot be accounted for by current permittivity models. Our work shows that the water structure is not enough to infer electrostatic interactions near interfaces.

Engineering Biomolecular Self-Assembly at Solid-Liquid Interfaces.

Biomolecular self-assembly is a key process used by life to build functional materials from the "bottom up." In the last few decades, bioengineering and bionanotechnology have borrowed this strategy to design and synthesize numerous biomolecular and hybrid materials with diverse architectures and properties. However, engineering biomolecular self-assembly at solid-liquid interfaces into predesigned architectures lags the progress made in bulk solution both in practice and theory. Here, recent achievements in programming self-assembly of peptides, proteins, and peptoids at solid-liquid interfaces are summarized and corresponding applications are described. Recent advances in the physical understandings of self-assembly pathways obtained using in situ atomic force microscopy are also discussed. These advances will lead to novel strategies for designing biomaterials organized at and interfaced with inorganic surfaces.

DNA-directed nanofabrication of high-performance carbon nanotube field-effect transistors.

Biofabricated semiconductor arrays exhibit smaller channel pitches than those created using existing lithographic methods. However, the metal ions within biolattices and the submicrometer dimensions of typical biotemplates result in both poor transport performance and a lack of large-area array uniformity. Using DNA-templated parallel carbon nanotube (CNT) arrays as model systems, we developed a rinsing-after-fixing approach to improve the key transport performance metrics by more than a factor of 10 compared with those of previous biotemplated field-effect transistors. We also used spatially confined placement of assembled CNT arrays within polymethyl methacrylate cavities to demonstrate centimeter-scale alignment. At the interface of high-performance electronics and biomolecular self-assembly, such approaches may enable the production of scalable biotemplated electronics that are sensitive to local biological environments.

(Invited) DNA-Directed High-Precision Assembly of CNT FETs

Precise fabrication of semiconducting channel materials into densely-aligned uniformly parallel arrays is one prerequisite to the high-performance ultra-scaled technology nodes, in particular for carbon nanotubes (CNTs). Traditional thin-film-based approaches generally yield CNTs in irregularly-spaced bundles or with wide orientation distribution, and lack a mechanism to effectively eliminate mis-aligned CNTs from the ultra-scaled channel area. Therefore, the averaged pitch value and precision of CNT arrays, the key parameters defining lateral CNT spacing, fail to simultaneously meet all of the patterning requirements for the ultra-scaled technology nodes. Bio-fabrication is promising for patterning CNTls at a resolution beyond the existing lithographic limit. However, impacted by surface charges and sub-micron dimensions of typical bio-templates, current bio-templated electronics exhibit both poor transport performance and array uniformity smaller than 1 micron.We report precise scaling of inter-CNT pitch using a supramolecular assembly method called Spatially Hindered Integration of Nanowire Electronics (SHINE). Specifically, by using nano-trenches to align CNTs and DNA hybridization to stabilize them in place, we constructed parallel CNT arrays with uniform pitch as small as 10.4 nm, at an assembly yield over 95%. The pitch precision improves on that prepared from conventional thin-film approaches by more than two orders of magnitude. Compared to the lithography-patterned Si channels at 10 nm technology node, SHINE simultaneously provides both 70% smaller averaged pitch value and molecular-scale pitch precision in the channel area. By engineering the interfacial compositions, metal ions and surface charges that are destructive to FET performance have been excluded from the channel area without degrading CNT alignment. Under a source-to-drain voltage of -0.5 V, we demonstrate both transconductance more than 0.6 mS/μm with fast on/off switching. And the key FET performance metrics are improved by more than one order of magnitude than previous bio-templated FETs. Furthermore, we demonstrate centimeter-scale alignment of fixed-width CNT arrays. At the interface of high-performance electronics and bio-molecular self-assembly, precise bio-fabrication could provide ultra-scaled devices or circuits compatible with or sensitive to local biological environments.

Silk Protein Solution: A Natural Example of Sticky Reptation.

Silk is one of the most intriguing examples of biomolecular self-assembly, yet little is understood of molecular mechanisms behind the flow behavior generating these complex high-performance fibers. This work applies the polymer physics of entangled solution rheology to present a first microphysical understanding of silk in the linear viscoelastic regime. We show that silk solutions can be approximated as reptating polymers with “sticky” calcium bridges whose strength can be controlled through the potassium concentration. This approach provides a new window into critical microstructural parameters, in particular identifying the mechanism by which potassium and calcium ions are recruited as a powerful viscosity control in silk. Our model constitutes a viable starting point to understand not only the “flow-induced self-assembly” of silk fibers but also a broader range of phenomena in the emergent field of material-focused synthetic biology.

Bottom-up synthesis of protein-based nanomaterials from engineered β-solenoid proteins.

Biomolecular self-assembly is an emerging bottom-up approach for the synthesis of novel nanomaterials. DNA and viruses have both been used to create scaffolds but the former lacks chemical diversity and the latter lack spatial control. To date, the use of protein scaffolds to template materials on the nanoscale has focused on amyloidogenic proteins that are known to form fibrils or two-protein systems where a second protein acts as a cross-linker. We previously developed a unique approach for self-assembly of nanomaterials based on engineering β-solenoid proteins (BSPs) to polymerize into micrometer-length fibrils. BSPs have highly regular geometries, tunable lengths, and flat surfaces that are amenable to engineering and functionalization. Here, we present a newly engineered BSP based on the antifreeze protein of the beetle Rhagium inquisitor (RiAFP-m9), which polymerizes into stable fibrils under benign conditions. Gold nanoparticles were used to functionalize the RiAFP-m9 fibrils as well as those assembled from the previously described SBAFP-m1 protein. Cysteines incorporated into the sequences provide site-specific gold attachment. Additionally, silver was deposited on the gold-labelled fibrils by electroless plating to create nanowires. These results bolster prospects for programable self-assembly of BSPs to create scaffolds for functional nanomaterials.

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins' sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins' sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.

Enzyme-instructed self-assembly of peptides: Process, dynamics, nanostructures, and biomedical applications

Biomolecular self-assembly provides a potential way for the design and synthesis of functional biomaterials with uniform structure and unique properties, in which the self-assembly of peptide molecules is especially important ascribed to the controllable structural design and functional tailoring of peptide motifs. The self-assembly of peptides can be instructed by internal and external physical, chemical, and biological stimulations. Compared to both physical and chemical stimulations including light/thermal treatment, pH/ionic strength adjustment, and others, the biological mediation with enzymes exhibited great advantages due to its high bioactivity, excellent biocompatibility, high specificity, and in vivo reaction. Herein we summarize the advance in the enzyme-instructed peptide self-assembly for biomedical applications. For this aim, we introduce and discuss the self-assembly of peptide that controlled by both kinetics and dynamics, and then demonstrate the enzyme-induced preparation of peptide nanostructures such as nanofibers, nanotubes, vesicles, networks, and hydrogels. Finally, the biomedical applications of enzyme-induced self-assembled peptide nanomaterials for cancer diagnostics, cancer therapy, bioelectronic devices, and biosensors are presented. It is expected this work will inspire more studies on the using of bioactive enzymes for triggering the self-assembly of peptides to create various novel bionanomaterials, which could extend this interesting research field to others such as tissue engineering, biocatalysis, energy storage, and environmental science.