Supramolecular Machines Research Articles

Self-assembly via hydrogen bonding of bis(18-crown-6)-1,3-distyrylbenzene and [2 + 2] photocycloaddition: Stereoselective synthesis of [2.2]metacyclophanes and butterfly-type thermal isomerization

The photochemistry of bis(18-crown-6)-containing 1,3-distyrylbenzene and its 2 : 2 bis-pseudo-sandwich complex with ethane-1,2-diammonium was studied. The UV irradiation of the supramolecular complex resulted in the formation of three geometric isomers of tetracrown-containing dicyclobutano[2.2]metacyclopane, differing in the orientation of the cyclobutane moieties, with the unsymmetrical isomer (>50 %) predominating. The diammonium cations used as the template could be removed after photolysis by simple extraction, and the product was obtained in high yield (82 %). The 1H NMR signals of a mixture of geometric isomers of [2.2]metacyclophane derivative were assigned resorting to quantum chemistry methods (DFT). The kinetic and thermodynamic parameters of thermal isomerization between the endo,endo- and exo,exo-isomers were measured. Tetracrown-containing dicyclobutano[2.2]metacyclophanes are homotetratopic ligands that contain four binding sites for metal and ammonium cations, which is of interest for the design of photo- and thermo-switchable supramolecular devices with a variable complex formation behavior and supramolecular machines owing to the butterfly-type thermal isomerization.

Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis.

DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.

Piezoelectric self-power supply driven by ferroelastic host–guest supramolecule with considerable electromechanical conversion capability

Crown ether supramolecules with host–guest structure bring the two most advanced application categories, namely information storage and energy conversion. The former was awarded the 2016 Nobel Prize in Chemistry, but the latter has thus far exhibited suboptimal electromechanical conversion properties. Enhancing the piezoelectric properties of such supramolecules has become a continuous and fascinating challenge. Here, we have made breakthrough progress in a crown ether-based ferroelastic supramolecular rotator [(N,N-dimethylethylenediammonium)(18-crown-6)]BF4 (MCBF) under the guidance of the crystallographic engineering. MCBF shows the record-high piezoelectric voltage coefficient (∼1000 × 10-3 V m N−1) and piezoelectric coefficient (∼46.1 pC N−1), which represent respectively improvements of 41.7% and 9.8% compared to the latest reported counterpart (J. Am. Chem. Soc. 145 (2023) 3187–3195). Notably, theoretical calculations elucidate that the ferroelasticity of MCBF contributes to its large piezoelectric response. In addition, an energy harvesting device is successfully achieved for the first time to evaluate its potential as a piezoelectric self-power supply, and LEDs are successfully lit by harvesting mechanical energy. This work takes an important step towards artificial supramolecular machines and arouses broad interest in self-powered flexible devices.

Cryo-Electron Microscopy Structure of the Mycobacterium tuberculosis Cytochrome bcc:aa3 Supercomplex and a Novel Inhibitor Targeting Subunit Cytochrome cI.

The mycobacterial cytochrome bcc:aa3 complex deserves the name "supercomplex" since it combines three cytochrome oxidases-cytochrome bc, cytochrome c, and cytochrome aa3-into one supramolecular machine and performs electron transfer for the reduction of oxygen to water and proton transport to generate the proton motive force for ATP synthesis. Thus, the bcc:aa3 complex represents a valid drug target for Mycobacterium tuberculosis infections. The production and purification of an entire M. tuberculosis cytochrome bcc:aa3 are fundamental for biochemical and structural characterization of this supercomplex, paving the way for new inhibitor targets and molecules. Here, we produced and purified the entire and active M. tuberculosis cyt-bcc:aa3 oxidase, as demonstrated by the different heme spectra and an oxygen consumption assay. The resolved M. tuberculosis cyt-bcc:aa3 cryo-electron microscopy structure reveals a dimer with its functional domains involved in electron, proton, oxygen transfer, and oxygen reduction. The structure shows the two cytochrome cIcII head domains of the dimer, the counterpart of the soluble mitochondrial cytochrome c, in a so-called "closed state," in which electrons are translocated from the bcc to the aa3 domain. The structural and mechanistic insights provided the basis for a virtual screening campaign that identified a potent M. tuberculosis cyt-bcc:aa3 inhibitor, cytMycc1. cytMycc1 targets the mycobacterium-specific α3-helix of cytochrome cI and interferes with oxygen consumption by interrupting electron translocation via the cIcII head. The successful identification of a new cyt-bcc:aa3 inhibitor demonstrates the potential of a structure-mechanism-based approach for novel compound development.

Construction of Artificial Cell as an Autonomous Supramolecular Machine

Construction of Artificial Cell as an Autonomous Supramolecular Machine

Evolution of Proliferative Model Protocells Highly Responsive to the Environment.

In this review, we discuss various methods of reproducing life dynamics using a constructive approach. An increase in the structural complexity of a model protocell is accompanied by an increase in the stage of reproduction of a compartment (giant vesicle; GV) from simple reproduction to linked reproduction with the replication of information molecules (DNA), and eventually to recursive proliferation of a model protocell. An encounter between a plural protic catalyst (C) and DNA within a GV membrane containing a plural cationic lipid (V) spontaneously forms a supramolecular catalyst (C@DNA) that catalyzes the production of cationic membrane lipid V. The local formation of V causes budding deformation of the GV and equivolume divisions. The length of the DNA strand influences the frequency of proliferation, associated with the emergence of a primitive information flow that induces phenotypic plasticity in response to environmental conditions. A predominant protocell appears from the competitive proliferation of protocells containing DNA with different strand lengths, leading to an evolvable model protocell. Recently, peptides of amino acid thioesters have been used to construct peptide droplets through liquid–liquid phase separation. These droplets grew, owing to the supply of nutrients, and were divided repeatedly under a physical stimulus. This proposed chemical system demonstrates a new perspective of the origins of membraneless protocells, i.e., the “droplet world” hypothesis. Proliferative model protocells can be regarded as autonomous supramolecular machines. This concept of this review may open new horizons of “evolution” for intelligent supramolecular machines and robotics.

Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures.

Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.

A unique bacterial secretion machinery with multiple secretion centers

The Porphyromonas gingivalis type IX secretion system (T9SS) promotes periodontal disease by secreting gingipains and other virulence factors. By in situ cryoelectron tomography, we report that the P. gingivalis T9SS consists of 18 PorM dimers arranged as a large, caged ring in the periplasm. Near the outer membrane, PorM dimers interact with a PorKN ring complex of ∼52 nm in diameter. PorMKN translocation complexes of a given T9SS adopt distinct conformations energized by the proton motive force, suggestive of different activation states. At the inner membrane, PorM associates with a cytoplasmic complex that exhibits 12-fold symmetry and requires both PorM and PorL for assembly. Activated motors deliver substrates across the outer membrane via one of eight Sov translocons arranged in a ring. The T9SSs are unique among known secretion systems in bacteria and eukaryotes in their assembly as supramolecular machines composed of apparently independently functioning translocation motors and export pores.

Dissolved xylan inhibits cellulosome-based saccharification by binding to the key cellulosomal component of Clostridium thermocellum

Polysaccharides derived from lignocellulose are promising sustainable carbon sources. Cellulosome is a supramolecular machine integrating multi-function enzymes for effective lignocellulose bio-saccharification. However, how various non-cellulose components of lignocellulose affect the cellulosomal saccharification is hitherto unclear. This study first investigated the stability and oxygen sensitivity of the cellulosome from Clostridium thermocellum during long-term saccharification process. Then, the differential inhibitory effects of non-cellulose components, including lignin, xylan, and arabinoxylan, on the cellulosome-based saccharification were determined. The results showed that lignin played inhibitory roles by non-productively adsorbing extracellular proteins of C. thermocellum. Differently, arabinoxylan preferred to bind with the cellulosomal components. Almost no adsorption of cellulosomal proteins on solid xylan was detected. Instead, xylan in water-dissolved form interacted with the cellulosomal proteins, especially the key exoglucanase Cel48S, leading to the xylan inhibitory effect. Compared to xylan, xylooligosaccharides influenced the cellulosome activity slightly. Hence, this work demonstrates that the timely hydrolysis or removal of dissolved xylan is important for cellulosome-based lignocellulose saccharification.

Formation of the various types of daisy chains constructed by modified cyclodextrin depending on the bond angle of the modified part linked to α-cyclodextrin

ABSTRACT Inclusion complexes (daisy chains) have been widely used in supramolecular chemistry and molecular machines. To develop new molecular machines, it is important to control the inclusion complex structures constructed using modified cyclodextrins (mCDs). To investigate the influence of the bond angle of the modified part linked to the CD on the inclusion complex structures, coarse-grained Brownian dynamics (BD) simulations were conducted. During the simulations, we observed the various types of inclusion complex structures (acyclic, cyclic, branched acyclic, and branched cyclic daisy chains). For the modified part linked to the outer direction of the CD, daisy chains of various sizes were constructed. However, for the modified part linked to the inner direction of the CD, cyclic dimers ([c2] daisy chain) were mainly constructed. To elucidate the formation difference in the daisy chain structures, depending on the bond angle of the modified part linked to the CD, the free energies of the [c2] daisy chain structures were estimated using the histogram reweighting method. It was observed that the formation of the various types of daisy chain structures was determined by the stability of the [c2] daisy chain.

Erratum to: Development of Photoactive Supramolecular Devices and Machines

Erratum to: Development of Photoactive Supramolecular Devices and Machines

Supramolecular Polymers and Materials Formed by Host-Guest Interactions

Abstract Supramolecular polymers and materials have been designed and prepared using macromolecular recognition by cyclodextrins as host parts. Polyrotaxanes, tubular polymers, supramolecular machines, artificial polymerases have been obtained by main-chain recognition. Macroscopic-self-assembly, self-healing materials, sol-gel transition, muscle-like materials have been achieved by side-chain recognition. End-group recognition leads to the construction of supramolecular polymers in narrow sense.

Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions.

The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G0, where G0 is the quantum of conductance, for 5 nm duplexes.

Light driven molecular lock comprises a Ru(bpy)2(hpip) complex and cucurbit[8]uril.

Here, complex 1 ([Ru(bpy)2(hpip)]2+–MV2+) and CB[8] can form a stable 1 : 1 inclusion complex in aqueous solution, resembling a U-shaped conformation. Upon light irradiation, two complex 1 were reversibly locked through the formation of a MV˙+ radical dimer that is stabilized in the cavity of CB[8] with Ru complexes as blockers, in which complex 1 was transformed from a U-shaped conformation to a interlocked complex. This study provided a feasible strategy for the fabrication of a photo-driven supramolecular machine resembling a “lock”.

Environment-Sensitive Intelligent Self-Reproducing Artificial Cell with a Modification-Active Lipo-Deoxyribozyme.

As a supramolecular micromachine with information flow, a giant vesicle (GV)-based artificial cell that exhibits a linked proliferation between GV reproduction and internal DNA amplification has been explored in this study. The linked proliferation is controlled by a complex consisting of GV membrane-intruded DNA with acidic amphiphilic catalysts, working overall as a lipo-deoxyribozyme. Here, we investigated how a GV-based artificial cell containing this lipo-deoxyribozyme responds to diverse external and internal environments, changing its proliferative dynamics. We observed morphological changes (phenotypic expression) in GVs induced by the addition of membrane precursors with different intervals of addition (starvation periods). First, we focused on a new phenotype, the “multiple tubulated” form, which emerged after a long starvation period. Compared to other forms, the multiple tubulated form is characterized by a larger membrane surface with a heavily cationic charge. A second consideration is the effect of the chain length of encapsulated DNA on competitive proliferation. The competitive proliferation among three different species of artificial cells containing different lengths of DNA was investigated. The results clearly showed a distinct intervention in the proliferation dynamics of the artificial cells with each other. In this sense, our GV-based artificial cell can be regarded as an intelligent supramolecular machine responding to external and internal environments, providing a new concept for developing molecular machines and robotics.

Bioinspired EVAL membrane modified with cilia-like structures showing simultaneously enhanced permeability and antifouling properties

A simple and effective strategy to simultaneously enhance the permeability and antifouling properties of ethylene vinyl alcohol (EVAL) membrane was developed based on the bioinspired natural cleaner, cilia. Taking clue from the self-cleaning effect of cilia, supramolecular polyrotaxanes (PRs) with sliding and rotating cyclic molecules along linear chains were synthesized using azide-alkyne click chemistry. Cilia-like PRs were incorporated into EVAL matrix in the fabrication of modified EVAL membranes. Cilia-like structures protruding from the membrane surface have been observed by SEM, TEM and AFM. By imitating natural ciliary movements, these structures provided a proactive self-cleaning system to remove the foulants. The introduction of cilia-like PRs enhanced the surface roughness and hydrophilicity, and significantly enhanced permeability by 55.3% compared to raw EVAL membrane. Moreover, the membrane modified with cilia-like PRs showed an excellent antifouling property with a lower water flux decline (12.6%) and higher water flux recovery (94%) in dynamic fouling tests. Furthermore, this modified membrane develops the scope of bioinspired membranes, inspiring more attractive potential applications in self-cleaning materials, dynamic membranes and supramolecular machines.

Molecular photoswitches mediating the strain-driven disassembly of supramolecular tubules

Chemists have created molecular machines and switches with specific mechanical responses that were typically demonstrated in solution, where mechanically relevant motion is dissipated in the Brownian storm. The next challenge consists of designing specific mechanisms through which the action of individual molecules is transmitted to a supramolecular architecture, with a sense of directionality. Cellular microtubules are capable of meeting such a challenge. While their capacity to generate pushing forces by ratcheting growth is well known, conversely these versatile machines can also pull microscopic objects apart through a burst of their rigid tubular structure. One essential feature of this disassembling mechanism is the accumulation of strain in the tubules, which develops when tubulin dimers change shape, triggered by a hydrolysis event. We envision a strategy toward supramolecular machines generating directional pulling forces by harnessing the mechanically purposeful motion of molecular switches in supramolecular tubules. Here, we report on wholly synthetic, water-soluble, and chiral tubules that incorporate photoswitchable building blocks in their supramolecular architecture. Under illumination, these tubules display a nonlinear operation mode, by which light is transformed into units of strain by the shape changes of individual switches, until a threshold is reached and the tubules unleash the strain energy. The operation of this wholly synthetic and stripped-down system compares to the conformational wave by which cellular microtubules disassemble. Additionally, atomistic simulations provide molecular insight into how strain accumulates to induce destabilization. Our findings pave the way toward supramolecular machines that would photogenerate pulling forces, at the nanoscale and beyond.

Disassembly/reassembly strategy for the production of highly pure GroEL, a tetradecameric supramolecular machine, suitable for quantitative NMR, EPR and mutational studies

GroEL, a prototypical member of the chaperonin class of chaperones, is a large supramocular machine that assists protein folding and plays an important role in proteostasis. GroEL comprises two heptameric rings, each of which encloses a large cavity that provides a folding chamber for protein substrates. Many questions remain regarding the mechanistic details of GroEL facilitated protein folding. Thus, data at atomic resolution of the type provided by NMR and EPR are invaluable. Such studies often require complete deuteration of GroEL, uniform or residue specific 13C and 15N isotope labeling, and the introduction of selective cysteine mutations for site-specific spin labeling. In addition, high purity GroEL is essential for detailed studies of substrate-GroEL interactions as quantitative interpretation is impossible if the cavities are already occupied and blocked by other protein substrates present in the bacterial expression system. Here we present a new purification protocol designed to provide highly pure GroEL devoid of non-specific protein substrate contamination.

Long-Lived Supramolecular Helices Promoted by Fluorinated Photoswitches.

Chiral azobenzenes can be used as photoswitchable dopants to control supramolecular helices in liquid crystals. However, the lack of thermal stability of the cis-isomer precludes envisioning the generation of long-lived supramolecular helices with light. Here, this study demonstrates thermally stable and axially chiral azobenzene switches that can be used as chiral dopants to create supramolecular helices from (achiral) nematic liquid crystals. Their trans-to-cis photoisomerization leads to a variation of helical twisting power that reaches up to 60%, and the helical superstructure that is engineered with light displays a relaxation time that reaches tens of hours. These results demonstrate that combining ortho-fluorination with axial chirality in molecular photoswitches constitutes an efficient strategy to promote long-lived helical states. Further, this approach shows potential to design supramolecular machines that are controlled by light entirely.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.