Biomolecular Self-assembly Research Articles

Biomolecular self-assembly under extreme Martian mimetic conditions

The recent discovery of subsurface water on Mars has challenged our understanding of the natural limits of life. The presence of magnesium perchlorate (Mg(ClO4)2) on the Martian surface raises the possibility that it may also be present in this subsurface lake. Given that the subsurface lakes on Earth, such as Lake Vostok and Lake Whillans, are capable of harbouring surprising amounts of life, these new findings raise interesting possibilities for how biomolecules might self-assemble in this environment on Mars. Here we investigate the self-association and hydration of the amino acid glycine in aqueous Mg(ClO4)2 at 25°C and −20°C using neutron diffraction with hydrogen isotope substitution and subsequent analysis with empirical potential structure refinement to yield a simulated box of atoms consistent with the scattering data. We find that although the highly chaotropic properties of Mg(ClO4)2 disrupt the hydration and hydrogen bonding ability of the amino acid, as well as the bulk water structure, glycine molecules are nonetheless still able to self-associate. This occurs more readily at lower temperature, where clusters of up to three molecules are observed, allowing us to speculate that the formation of biological molecules is possible in the Martian environment.

Active Self-Assembly of Train-Shaped DNA Nanostructures via Catalytic Hairpin Assembly Reactions.

Biomolecular self-assembly is a powerful approach for fabricating supramolecular architectures. Over the past decade, a myriad of biomolecular assemblies, such as self-assembly proteins, lipids, and DNA nanostructures, have been used in a wide range of applications, from nano-optics to nanoelectronics and drug delivery. The method of controlling when and where the self-assembly starts is essential for assembly dynamics and functionalization. Here, train-shaped DNA nanostructures are actively self-assembled using DNA tiles as artificial "carriages," hairpin structures as "couplers," and initiators of catalytic hairpin assembly (CHA) reactions as "wrenches." The initiator wrench can selectively open the hairpin couplers to couple the DNA tile carriages with high product yield. As such, DNA nanotrains are actively prepared with two, three, four, or more carriages. Furthermore, by flexibly modifying the carriages with "biotin seats" (biotin-modified DNA tiles), streptavidin "passengers" are precisely arranged in corresponding seats. The applications of the CHA-triggered self-assembly mechanism are also extended for assembling the large DNA origami dimer. With the creation of 1D architectures established, it is thought that this CHA-triggered self-assembly mechanism may provide a new element of control for complex autonomous assemblies from a variety of starting materials with specific sites and times.

Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review.

Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π–π stacking, DNA base pairing, and ligand–receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

Hierarchical nanomaterials via biomolecular self-assembly and bioinspiration for energy and environmental applications.

Bioinspired synthesis offers potential green strategies to build highly complex nanomaterials by utilizing the unique nanostructures, functions, and properties of biomolecules, in which the biomolecular recognition and self-assembly processes play important roles in tailoring the structures and functions of bioinspired materials. Further understanding of biomolecular self-assembly for inspiring the formation and assembly of nanoparticles would promote the design and fabrication of functional nanomaterials for various applications. In this review, we focus on recent advances in bioinspired synthesis and applications of hierarchical nanomaterials based on biomolecular self-assembly. We first discuss biomolecular self-assembly towards biological nanomaterials, in which the mechanisms and ways of biomolecular self-assembly as well as various self-assembled biomolecular nanostructures are demonstrated. Secondly, the bioinspired synthesis strategies including molecule-molecule interaction, molecule-material recognition, molecule-mediated nucleation and growth, and molecule-mediated reduction/oxidation are introduced and discussed. Meanwhile, typical examples and discussions on how biomolecular self-assembly inspires the formation of hierarchical hybrid nanomaterials are presented. Finally, the applications of bioinspired nanomaterials in biofuel cells, light-harvesting systems, batteries, supercapacitors, catalysis, water/air purification, and environmental monitoring are presented and discussed. We believe that this review will be very helpful for readers to understand the self-assembly of biomolecules and the biomimetic/bioinspired strategies for synthesizing hierarchical nanomaterials on the one hand, and on the other hand to design novel materials for extended applications in nanotechnology, materials science, analytical science, and biomedical engineering.

2D bio-nanostructures fabricated by supramolecular self-assembly of protein, peptide, or peptoid

Biomolecular self-assembly is a promising strategy for fabricating two-dimensional (2D) nanostructures such as sheets, films, lattices, or membranes. In this paper, we summarize the recent development of 2D bio-nanostructures that are formed by supramolecular self-assembly of protein, peptide, or peptoid, respectively. Specific focus is given on the formation mechanisms and the structures as well as functionality of the 2D bio-nanostructures. Besides, some typical applications of 2D bio-nanostructures have been listed. At last, the potential research direction of 2D bio-nanostructures is discussed.

Engineering Aspects of Protein Interactions and Self-assembly.

In the new Laboratory for Biochemical Engineering (LBCE) at ETH Zurich researchers combine principles of chemical engineering with microfluidic technology and biophysical methods to investigate the physical determinants of biomolecular self-assembly in living organisms. In this account, we show the impact of this activity on concrete applications in biomedical sciences and biotechnology. We focus in particular on the field of protein aggregation and phase separation, and we highlight examples in the context of diagnosis and treatment of Alzheimer's disease and neurodegenerative disorders, cell compartmentalization as well as manufacturing and delivery of therapeutic proteins.

Macromolecular crowding for materials-directed controlled self-assembly.

Macromolecular crowding refers to intracellular environments where various macromolecules, including proteins and nucleic acids, are present at high total concentrations. Its influence on biological processes has been investigated using a highly concentrated in vitro solution of water-soluble polymers as a model. Studies have revealed significant effects of macromolecular crowding on the thermodynamic equilibria and dynamics of biomolecular self-assembly in vivo. Recently, macromolecular crowding has attracted materials scientists, especially those in bio-related areas, as a tool to control molecular/colloidal self-assembly. Macromolecular crowding has been exploited to control the structure of supramolecular materials, assemble nanomaterials, and improve the performance of polymeric materials. Furthermore, nanostructured materials have been shown to be an interesting alternative to water-soluble polymers for creating crowded environments for controlled self-assembly. In this review article, we summarize recent progress in research on macromolecular crowding for controlled self-assembly in bio-related materials chemistry.

Buffers Strongly Modulate Fibrin Self-Assembly into Fibrous Networks

Fibrin is a plasma protein with a central role in blood clotting and wound repair. Upon vascular injury, fibrin forms resilient fibrillar networks (clots) via a multistep self-assembly process, from monomers, to double-stranded protofibrils, to a branched network of thick fibers. In vitro, fibrin self-assembly is sensitive to physicochemical conditions like the solution pH and ionic strength, which tune the strength of the noncovalent driving forces. Here we report a surprising finding that the buffer—which is necessary to control the pH and is typically considered to be inert—also significantly influences fibrin self-assembly. We show by confocal microscopy and quantitative light scattering that various common buffering agents have no effect on the initial assembly of fibrin monomers into protofibrils but strongly hamper the subsequent lateral association of protofibrils into thicker fibers. We further find that the structural changes are independent of the molecular structure of the buffering agents as well as of the activation mechanism and even occur in fibrin networks formed from platelet-poor plasma. This buffer-mediated decrease in protofibril bundling results in a marked reduction in the permeability of fibrin networks but only weakly influences the elastic modulus of fibrin networks, providing a useful tuning parameter to independently control the elastic properties and the permeability of fibrin networks. Our work raises the possibility that fibrin assembly in vivo may be regulated by variations in the acute-phase levels of bicarbonate and phosphate, which act as physiological buffering agents of blood pH. Moreover, our findings add a new example of buffer-induced effects on biomolecular self-assembly to recent findings for a range of proteins and lipids.

Construction of Functional Biomaterials by Biomolecular Self-Assembly

Abstract This account discusses construction strategies for various functional biomaterials based on the designed self-assembly of biomolecules. Novel glycoclusters with regular intervals were developed by self-assembly of carbohydrate-conjugated oligodeoxyribonucleotides (ODNs) with the half-sliding complementary ODNs. Complexes of carbohydrate-modified DNA and lectin afforded a new regulation system for gene expression. DNA three-way junctions bearing self-complementary sticky-ends were self-assembled into nanometer-to-micrometer-sized spherical structures depending on the concentration. The three-way component design was extended to the design of an artificial trigonal peptide conjugate. The trigonal peptide conjugates bearing β-sheet-forming peptides or glutathione self-assembled into nano-sized spherical assemblies. Self-assembly of β-annulus peptide derived from tomato bushy stunt virus afforded artificial viral capsids, which can encapsulate and be modified with various molecules.

Assembly and application of diphenylalanine dipeptide nanostructures

The self-assembly of biomaterials to form well-ordered hierarchical structures provides great opportunities in biomedical applications. In the past decades, a great many of researches have been focused on self-assembly of peptide molecules owing to their structural simplicity, chemical versatility, biocompatibility, facile synthesis, and widespread applications. Well defined peptide assemblies could be effectively achieved by hydrogen bonding, electrostatic, hydrophobic and π - π stacking interactions. One well-known and the simplest peptide building block is diphenylalanine (FF), the core recognition motif of the Alzheimer’s β -amyloid polypeptide. It is a major building block for the preparation of biological functional nanomaterials. So far, researchers have developed a variety of FF-based micro/nanostructures, such as nanotubes, microtubes, microrods, nanowires, and nanovesicles, etc. However, how to effectively control the shape and size of the self-assembled materials has always been the key concern of the research. In recent years, our group has conducted substantial researches on controlled assembly of FF and its derivatives by simply changing the assembly condition (solvents, peptide concentrations, ultrasonic) or introduction of exogenous small molecules (polyoxometalates, sulfonic azobenzenes, aldehydes). For example, our group obtained hexagonal FF microtubes in water and peony- lower-like mesocrystal in the organic solvent tetrahydrofuran. When the organic solvent was changed to chloroform or toluene, FF organogels were obtained. Moreover, the structural transition from organogels to flower-like microcrystals were observed by changing the components of solvent. Similarly, upon a change in the peptide concentration, reversible shape transition between self-assembled dipeptide nanotubes and vesicle-like structures is achieved. In view of positive charge of cationic dipeptide, negatively charged small molecules (polyoxometalates and sulfonic azobenzenes) were added into the assembly system and colloidal spheres, urchin-like, flower-like and plate-like structures were obtained, respectively. Apart from non-covalent interactions, our group also exploited covalent Schiff’s reaction between the aldehyde group and the primary amine of peptide in the self-assembly of peptides by introducing aldehyde molecules, yielding peptides nanospheres and crystalline platelet structures. These peptide assemblies with diverse structures were successfully applied in drug delivery, optical waveguiding and SERS substrates. These researches not only enrich the FF-based nanomaterials, but also provide new strategy and important experimental basis for the preparation of other peptides-based nanomaterials and biological function materials. With the development of biology and nanotechnology, especially the establishment of the new assemblies or hybrid systems, higher requirements for the experiment, theory and application of biomolecular self-assembly are put forward. Therefore, further study on the assembly structure, the assembly dynamics and effectively control the assembly of peptides and other biological molecules are highly demanded. At the same time, in order to make the materials not only possess academic research significance, but also ultimately realize the social value, the exploitation of the functionalization and application of the materials will also be the focus of future research issues.

Peptide Supramolecular Self-Assembly:Structural Precise Regulation and Functionalization

Biomolecular self-assembly plays a significant role for physiological function. Inspired by this, the construction of functional structures and architectures by biomolecular self-assembly has attracted tremendous attentions. Peptides can be assembled into diverse nanostructures, exhibiting important potential for biomedical and green-life technology applications. How to achieve the structural precise regulation of various nanostructures and functionalization by precise control of structures is the two key challenges in the field of peptide self-assembly. As the assembly process is a spontaneous thermodynamic and kinetic driven process, and is determined by the cooperation of various intermolecular non-covalent interactions, including hydrogen-bonding, electrostatic, p-p stacking, hydrophobic, and van der Waals interactions, the reasonable regulation of these non-covalent interactions is a critical pathway to achieve the two goals. To modulate these non-covalent interactions, one of the common used methods is to change the kinetic factors/external environment, including pH, ionic strength, and temperature, etc. These kinetic factors can effectively influence the interactions between peptides and solvents, resulting in dynamic and responsive variations in structures through multiple length scales and ultimate morphologies. However, the fatal disadvantage is the lacking of the precise regulation of assembled structures in the molecular level with consideration of both thermodynamics and kinetics. Compared with changing the external environment, the specific and precise molecular design is more favorable to achieve the structural precise regulation. The molecular structures and the component of building blocks can be rationally designed. For example, one can modulate the interactions between two or more than two building blocks by changing the physicochemical properties of each building block, enabling self-assembly and structural diversity of the final nanostructures. Furthermore, by combining peptides and other functional biomolecules (such as porphyrins), the functionalization of assembled nanostructures and architectures can be achieved more easily and flexibly. In this review, we will focus on the structural precise regulation and the functionalization of assembled peptide nanostructures. It is believed that the precise regulation of nanostructures is promising to promote the development of peptide-based materials towards green-life technology applications.

X-ray Crystallographic Structure and Solution Behavior of an Antiparallel Coiled-Coil Hexamer Formed by de Novo Peptides.

The self-assembly of peptides and proteins into higher-ordered structures is encoded in the amino acid sequence of each peptide or protein. Understanding the relationship among the amino acid sequence, the assembly dynamics, and the structure of well-defined peptide oligomers expands the synthetic toolbox for these structures. Here, we present the X-ray crystallographic structure and solution behavior of de novo peptides that form antiparallel coiled-coil hexamers (ACC-Hex) by an interaction motif neither found in nature nor predicted by existing peptide design software. The 1.70 Å X-ray crystallographic structure of peptide 1a shows six α-helices associating in an antiparallel arrangement around a central axis comprising hydrophobic and aromatic residues. Size-exclusion chromatography studies suggest that peptides 1 form stable oligomers in solution, and circular dichroism experiments show that peptides 1 are stable to relatively high temperatures. Small-angle X-ray scattering studies of the solution behavior of peptide 1a indicate an equilibrium of dimers, hexamers, and larger aggregates in solution. The structures presented here represent a new motif of biomolecular self-assembly not previously observed for de novo peptides and suggest supramolecular design principles for material scaffolds based on coiled-coil motifs containing aromatic residues.

Peptide interfaces with graphene: an emerging intersection of analytical chemistry, theory, and materials.

Because noncovalent interface functionalization is frequently required in graphene-based devices, biomolecular self-assembly has begun to emerge as a route for controlling substrate electronic structure or binding specificity for soluble analytes. The remarkable diversity of structures that arise in biological self-assembly hints at the possibility of equally diverse and well-controlled surface chemistry at graphene interfaces. However, predicting and analyzing adsorbed monolayer structures at such interfaces raises substantial experimental and theoretical challenges. In contrast with the relatively well-developed monolayer chemistry and characterization methods applied at coinage metal surfaces, monolayers on graphene are both less robust and more structurally complex, levying more stringent requirements on characterization techniques. Theory presents opportunities to understand early binding events that lay the groundwork for full monolayer structure. However, predicting interactions between complex biomolecules, solvent, and substrate is necessitating a suite of new force fields and algorithms to assess likely binding configurations, solvent effects, and modulations to substrate electronic properties. This article briefly discusses emerging analytical and theoretical methods used to develop a rigorous chemical understanding of the self-assembly of peptide-graphene interfaces and prospects for future advances in the field.

A bioscaffolding strategy for hierarchical zeolites with a nanotube-trimodal network.

Hierarchical zeolite monoliths with multimodal porosity are of paramount importance as they open up new horizons for advanced applications. So far, hierarchical zeolites based on nanotube scaffolds have never been reported. Inspired by the organization of biominerals, we have developed a novel precursor scaffolding-solid phase crystallization strategy for hierarchical zeolites with a unique nanotube scaffolding architecture and nanotube-trimodal network, where biomolecular self-assembly (BSA) provides a scaffolding blueprint. By vapor-treating Sil-1 seeded precursor scaffolds, zeolite MFI nanotube scaffolds are self-generated, during which evolution phenomena such as segmented voids and solid bridges are observed, in agreement with the Kirkendall effect in a solid-phase crystallization system. The nanotube walls are made of intergrown single crystals rendering good mechanical stability. The inner diameter of the nanotube is tunable between 30 and 90 nm by varying the thickness of the precursor layers. Macropores enclosed by cross-linked nanotubes can be modulated by the choice of BSA. Narrow mesopores are formed by intergrown nanocrystals. Hierarchical ZSM-5 monoliths with nanotube (90 nm), micropore (0.55 nm), mesopore (2 nm) and macropore (700 nm) exhibit superior catalytic performance in the methanol-to-hydrocarbon (MTH) conversion compared to conventional ZSM-5. BSA remains intact after crystallization, allowing a higher level of organization and functionalization of the zeolite nanotube scaffolds. The current work may afford a versatile strategy for hierarchical zeolite monoliths with nanotube scaffolding architectures and a nanotube-multimodal network leading to self-supporting and active zeolite catalysts, and for applications beyond.

3D interconnected hierarchically macro-mesoporous TiO2 networks optimized by biomolecular self-assembly for high performance lithium ion batteries

A 3D interconnected hierarchically macro-mesoporous TiO2 network optimized by the mediation of biomolecular self-assembly has been used for high performance lithium storage.

A Single Stereodynamic Center Modulates the Rate of Self-Assembly in a Biomolecular System.

Chirality is a property of asymmetry important to both physical and abstract systems. Understanding how molecular systems respond to perturbations in their chiral building blocks can provide insight into diverse areas such as biomolecular self-assembly, protein folding, drug design, materials, and catalysis. Despite the fundamental importance of stereochemical preorganization in nature and designed materials, the ramifications of replacing chiral centers with stereodynamic atomic mimics in the context of biomolecular systems is unknown. Herein, we demonstrate that replacement of a single amino acid stereocenter with a stereodynamic nitrogen atom has profound consequences on the self-assembly of a biomolecular system. Our results provide insight into how the fundamental biopolymers of life would behave if their chiral centers were not configurationally stable, highlighting the vital importance of stereochemistry as a pre-organizing element in biomolecular folding and assembly events.

Capturing Conformation-Dependent Molecule-Surface Interactions When Surface Chemistry Is Heterogeneous.

Molecular building blocks, such as carbon nanotubes and DNA origami, can be fully integrated into electronic and optical devices if they can be assembled on solid surfaces using biomolecular interactions. However, the conformation and functionality of biomolecules depend strongly on the local chemical environment, which is highly heterogeneous near a surface. To help realize the potential of biomolecular self-assembly, we introduce here a technique to spatially map molecular conformations and adsorption, based on single-molecule fluorescence microscopy. On a deliberately patterned surface, with regions of varying hydrophobicity, we characterized the conformations of adsorbed helicogenic alanine-lysine copeptides using Förster resonance energy transfer. The peptides adopted helical conformations on hydrophilic regions of the surface more often than on hydrophobic regions, consistent with previous ensemble-averaged observations of α-helix surface stability. Interestingly, this dependence on surface chemistry was not due to surface-induced unfolding, as the apparent folding and unfolding dynamics were usually much slower than desorption. The most significant effect of surface chemistry was on the adsorption rate of molecules as a function of their initial conformational state. In particular, regions with higher adsorption rates attracted more molecules in compact, disordered coil states, and this difference in adsorption rates dominated the average conformation of the ensemble. The correlation between adsorption rate and average conformation was also observed on nominally uniform surfaces. Spatial variations in the functional state of adsorbed molecules would strongly affect the success rates of surface-based molecular assembly and can be fully understood using the approach developed in this work.

Isothermal DNA origami folding: avoiding denaturing conditions for one-pot, hybrid-component annealing.

The DNA origami technique offers great potential for nanotechnology. Using biomolecular self-assembly, defined 2D and 3D nanoscale DNA structures can be realized. DNA origami allows the positioning of proteins, fluorophores or nanoparticles with an accuracy of a few nanometers and enables thereby novel nanoscale devices. Origami assembly usually includes a thermal denaturation step at 90 °C. Additional components used for nanoscale assembly (such as proteins) are often thermosensitive, and possibly damaged by such harsh conditions. They have therefore to be attached in an extra second step to avoid defects. To enable a streamlined one-step nanoscale synthesis - a so called one-pot folding - an adaptation of the folding procedures is required. Here we present a thermal optimization of this process for a 2D DNA rectangle-shaped origami resulting in an isothermal assembly protocol below 60 °C without thermal denaturation. Moreover, a room temperature protocol is presented using the chemical additive betaine, which is biocompatible in contrast to chemical denaturing approaches reported previously.

Differentially Instructive Extracellular Protein Micro-nets

An ability to construct biological matter from the molecule up holds promise for applications ranging from smart materials to integrated biophysical models for synthetic biology. Biomolecular self-assembly is an efficient strategy for biomaterial construction which can be programmed to support desired function. A challenge remains in replicating the strategy synthetically, that is at will, and differentially, that is for a specific function at a given length scale. Here we introduce a self-assembly topology enabling a net-like architectural mimetic of native extracellular matrices capable of differential responses to cell adhesion--enhanced mammalian cell attachment and proliferation, and enhanced resistance to bacterial colonization--at the native sub-millimeter length scales. The biological performance of such protein micro-nets directly correlates with their morphological and chemical properties, offering thus an application model for differential extracellular matrices.

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

Molecular dynamics simulations can provide valuable atomistic insights into biomolecular function. However, the accuracy of molecular simulations on general-purpose computers depends on the time scale of the events of interest. Advanced simulation methods, such as accelerated molecular dynamics, have shown tremendous promise in sampling the conformational dynamics of biomolecules, where standard molecular dynamics simulations are nonergodic. Here we present a sampling method based on accelerated molecular dynamics in which rotatable dihedral angles and nonbonded interactions are boosted separately. This method (RaMD-db) is a different implementation of the dual-boost accelerated molecular dynamics, introduced earlier. The advantage is that this method speeds up sampling of the conformational space of biomolecules in explicit solvent, as the degrees of freedom most relevant for conformational transitions are accelerated. We tested RaMD-db on one of the most difficult sampling problems - protein folding. Starting from fully extended polypeptide chains, two fast folding α-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed β-hairpin (Chignolin) were completely folded to their native structures in very short simulation time. Multiple folding/unfolding transitions could be observed in a single trajectory. Our results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent. RaMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.