Controlling Optical and Catalytic Activity of Genetically Engineered Proteins by Ultrasound

Sonogenetics for Monitoring and Modulating Biomolecular Function by Ultrasound

Ultrasound technology, synergistically harnessed with genetic engineering and chemistry concepts, has started to open the gateway to the remarkable realm of sonogenetics-a pioneering paradigm for remotely orchestrating cellular functions at the molecular level. This fusion not only enables precisely targeted imaging and therapeutic interventions, but also advances our comprehension of mechanobiology to unparalleled depths. Sonogenetic tools harness mechanical force within small tissue volumes while preserving the integrity of the surrounding physiological environment, reaching depths of up to tens of centimeters with high spatiotemporal precision. These capabilities circumvent the inherent physical limitations of alternative in vivo control methods such as optogenetics and magnetogenetics. In this review, we first discuss mechanosensitive ion channels, the most commonly utilized sonogenetic mediators, in both mammalian and non-mammalian systems. Subsequently, we provide a comprehensive overview of state-of-the-art sonogenetic approaches that leverage thermal or mechanical features of ultrasonic waves. Additionally, we explore strategies centered around the design of mechanochemically reactive macromolecular systems. Furthermore, we delve into the realm of ultrasound imaging of biomolecular function, encompassing the utilization of gas vesicles and acoustic reporter genes. Finally, we shed light on limitations and challenges of sonogenetics and present a perspective on the future of this promising technology.

Shape morphing of hydrogels by harnessing enzyme enabled mechanoresponse

Hydrogels have been designed to react to many different stimuli which find broad applications in tissue engineering and soft robotics. However, polymer networks bearing mechano-responsiveness, especially those displaying on-demand self-stiffening and self-softening behavior, are rarely reported. Here, we design a mechano-controlled biocatalytic system at the molecular level that is incorporated into hydrogels to regulate their mechanical properties at the material scale. The biocatalytic system consists of the protease thrombin and its inhibitor, hirudin, which are genetically engineered and covalently coupled to the hydrogel networks. The catalytic activity of thrombin is reversibly switched on by stretching of the hydrogels, which disrupts the noncovalent inhibitory interaction between both entities. Under cyclic tensile-loading, hydrogels exhibit self-stiffening or self-softening properties when substrates are present that can self-assemble to form new networks after being activated by thrombin or when cleavable peptide crosslinkers are constitutional components of the original network, respectively. Additionally, we demonstrate the programming of bilayer hydrogels to exhibit tailored shape-morphing behavior under mechanical stimulation. Our developed system provides proof of concept for mechanically controlled reversible biocatalytic processes, showcasing their potential for regulating hydrogels and proposing a biomacromolecular strategy for mechano-regulated soft functional materials.

Effects of sound energy on proteins and their complexes

Mechanical energy in the form of ultrasound and protein complexes intuitively have been considered as two distinct unrelated topics. However, in the past few years, increasingly more attention has been paid to the ability of ultrasound to induce chemical modifications on protein molecules that further change protein-protein interaction and protein self-assembling behavior. Despite efforts to decipher the exact structure and the behavior-modifying effects of ultrasound on proteins, our current understanding of these aspects remains limited. The limitation arises from the complexity of both phenomena. Ultrasound produces multiple chemical, mechanical, and thermal effects in aqueous media. Proteins are dynamic molecules with diverse complexation mechanisms. This review provides an exhaustive analysis of the progress made in better understanding the role of ultrasound in protein complexation. It describes in detail how ultrasound affects an aqueous environment and the impact of each effect separately and when combined with the protein structure and fold, the protein-protein interaction, and finally the protein self-assembly. It specifically focuses on modifying role of ultrasound in amyloid self-assembly, where the latter is associated with multiple neurodegenerative disorders.

Force-Triggered Atropisomerization of a Parallel Diarylethene to Its Antiparallel Diastereomers

This paper describes a mechanical approach to inducing the atropisomerization of a parallel diarylethene into its antiparallel diastereomers exhibiting distinct chemical reactivity. A congested parallel diarylethene mechanophore in the (R_a,S_a)-configuration with mirror symmetry is atropisomerized to its antiparallel diastereomers with C₂ symmetry under ultrasound-induced force field. The resulting stereochemistry-converted material gains symmetry-allowed reactivity toward conrotatory photocyclization.

Fracture Detection in Bio-Glues with Fluorescent-Protein-Based Optical Force Probes

Glues are being used to bond, seal, and repair in industry and biomedicine. The improvement of gluing performance is hence important for the development of new glues with better and balanced property spaces, which in turn necessitates a mechanistic understanding of their mechanical failure. Optical force probes (OFPs) allow the observation of mechanical material damage in polymers from the macro- down to the microscale, yet have never been employed in glues. Here, the development of a series of ratiometric OFPs based on fluorescent-protein-dye and protein-protein conjugates and their incorporation into genetically engineered bio-glues is reported. The OFPs are designed to efficiently modulate Förster resonance energy transfer upon force application thereby reporting on force-induced molecular alterations independent of concentration and fluorescence intensity both spectrally and through their fluorescence lifetime. By fluorescence spectroscopy in solution and in the solid state and by fluorescence lifetime imaging microscopy, stress concentrations are visualized and adhesive and cohesive failure in the fracture zone is differentiated.

Nanopore Detection Using Supercharged Polypeptide Molecular Carriers

The analysis at the single-molecule level of proteins and their interactions can provide critical information for understanding biological processes and diseases, particularly for proteins present in biological samples with low copy numbers. Nanopore sensing is an analytical technique that allows label-free detection of single proteins in solution and is ideally suited to applications, such as studying protein-protein interactions, biomarker screening, drug discovery, and even protein sequencing. However, given the current spatiotemporal limitations in protein nanopore sensing, challenges remain in controlling protein translocation through a nanopore and relating protein structures and functions with nanopore readouts. Here, we demonstrate that supercharged unstructured polypeptides (SUPs) can be genetically fused with proteins of interest and used as molecular carriers to facilitate nanopore detection of proteins. We show that cationic SUPs can substantially slow down the translocation of target proteins due to their electrostatic interactions with the nanopore surface. This approach enables the differentiation of individual proteins with different sizes and shapes via characteristic subpeaks in the nanopore current, thus facilitating a viable route to use polypeptide molecular carriers to control molecular transport and as a potential system to study protein-protein interactions at the single-molecule level.

Recent advances in mechanical force-responsive drug delivery systems

Mechanical force responsive drug delivery systems (in terms of mechanical force induced chemical bond breakage or physical structure destabilization) have been recently explored to exhibit a controllable pharmaceutical release behaviour at a molecular level. In comparison with chemical or biological stimulus triggers, mechanical force is not only an external but also an internal stimulus which is closely related to the physiological status of patients. However, although this mechanical force stimulus might be one of the most promising and feasible sources to achieve on-demand pharmaceutical release, current research in this field is still limited. Hence, this tutorial review aims to comprehensively evaluate the recent advances in mechanical force-responsive drug delivery systems based on different types of mechanical force, in terms of direct stimulation by compressive, tensile, and shear force, or indirect/remote stimulation by ultrasound and a magnetic field. Furthermore, the exciting developments and current challenges in this field will also be discussed to provide a blueprint for potential clinical translational research of mechanical force-responsive drug delivery systems.

Accelerated Mechanochemistry in Helical Polymers

Polymer chains, if long enough, are known to undergo bond scission when mechanically stressed. While the mechanochemical response of random coils is well understood, biopolymers and some key synthetic chains adopt well-defined secondary structures such as helices. To understand covalent mechanochemistry in such structures, poly(γ-benzyl glutamates) are prepared while regulating the feed-monomer chirality, producing chains with similar molecular weights and backbone chemistry but different helicities. Such chains are stressed in solution and their mechanochemistry rates compared by following molecular weight change and using a rhodamine mechanochromophore. Results reveal that while helicity itself is not affected by the covalent bond scissions, chains with higher helicity undergo faster mechanochemistry. Considering that the polymers tested differ only in conformation, these results indicate that helix-induced chain rigidity improves the efficiency of mechanical energy transduction.

Ultrasound-Responsive Systems as Components for Smart Materials

Smart materials can respond to stimuli and adapt their responses based on external cues from their environments. Such behavior requires a way to transport energy efficiently and then convert it for use in applications such as actuation, sensing, or signaling. Ultrasound can carry energy safely and with low losses through complex and opaque media. It can be localized to small regions of space and couple to systems over a wide range of time scales. However, the same characteristics that allow ultrasound to propagate efficiently through materials make it difficult to convert acoustic energy into other useful forms. Recent work across diverse fields has begun to address this challenge, demonstrating ultrasonic effects that provide control over physical and chemical systems with surprisingly high specificity. Here, we review recent progress in ultrasound-matter interactions, focusing on effects that can be incorporated as components in smart materials. These techniques build on fundamental phenomena such as cavitation, microstreaming, scattering, and acoustic radiation forces to enable capabilities such as actuation, sensing, payload delivery, and the initiation of chemical or biological processes. The diversity of emerging techniques holds great promise for a wide range of smart capabilities supported by ultrasound and poses interesting questions for further investigations.

Unraveling Ultrasonic Stress Response of Nanovesicles by the Mechanochromism of Self-Assembled Polydiacetylene

The force response of nanosized vesicles shows substantial applications in drug delivery, cancer therapies, and so on. Conventional methods in mechanical studies on vesicles rely on a camera and an optical microscope, which can hardly work for nanosized particles. Herein, we use self-assembled polydiacetylene (PDA) as a chromic mechanoresponsive group to study the responsiveness of nanovesicles under sonication. The sonication-induced deformation of the PDA backbone and reduction in its conjugation length leads to a color transition from blue to red. Three internal and external factors, including greater shear stress, lower polymerization degree, and higher viscosity of the continue phase, have been found to promote the mechanochromism of the vesicles. These results, for the first time, reveal that the force response of vesicles depends on the actual capillary number (correlated with the three explored factors), even at the nanoscale level, which opens a new avenue to mechanical modulation of nanovesicles for the development of vesicle-based bio- and nanotechniques.

Mechanoresponsive diselenide-crosslinked microgels with programmed ultrasound-triggered degradation and radical scavenging ability for protein protection

In the context of controlled delivery and release, proteins constitute a delicate class of cargo requiring advanced delivery platforms and protection. We here show that mechanoresponsive diselenide-crosslinked microgels undergo controlled ultrasound-triggered degradation in aqueous solution for the release of proteins. Simultaneously, the proteins are protected from chemical and conformational damage by the microgels, which disintegrate to water-soluble polymer chains upon sonication. The degradation process is controlled by the amount of diselenide crosslinks, the temperature, and the sonication amplitude. We demonstrate that the ultrasound-mediated cleavage of diselenide bonds in these microgels facilitates the release and activates latent functionality preventing the oxidation and denaturation of the encapsulated proteins (cytochrome C and myoglobin) opening new application possibilities in the targeted delivery of biomacromolecules.

Mechanoresponsive diselenide-crosslinked microgels undergo controlled ultrasound-triggered degradation and can be used for protein delivery due to their dual protection properties acting as radical scavengers and conformation stabilizers.

Ultrasound-controlled drug release and drug activation for cancer therapy

Traditional chemotherapy suffers from severe toxicity and side effects that limit its maximum application in cancer therapy. To overcome this challenge, an ideal treatment strategy would be to selectively control the release or regulate the activity of drugs to minimize the undesirable toxicity. Recently, ultrasound (US)-responsive drug delivery systems (DDSs) have attracted significant attention due to the non-invasiveness, high tissue penetration depth, and spatiotemporal controllability of US. Moreover, the US-induced mechanical force has been proven to be a robust method to site-selectively rearrange or cleave bonds in mechanochemistry. This review describes the US-activated DDSs from the fundamental basics and aims to present a comprehensive summary of the current understanding of US-responsive DDSs for controlled drug release and drug activation. First, we summarize the typical mechanisms for US-responsive drug release and drug activation. Second, the main factors affecting the ultrasonic responsiveness of drug carriers are outlined. Furthermore, representative examples of US-controlled drug release and drug activation are discussed, emphasizing their novelty and design principles. Finally, the challenges and an outlook on this promising therapeutic strategy are discussed.

Tailoring the Properties of Optical Force Probes for Polymer Mechanochemistry

The correlation of mechanical properties of polymer materials with those of their molecular constituents is the foundation for their holistic comprehension and eventually for improved material designs and syntheses. Over the last decade, optical force probes (OFPs) were developed, shedding light on various unique mechanical behaviors of materials. The properties of polymers are diverse, ranging from soft hydrogels to ultra‐tough composites, from purely elastic rubbers to viscous colloidal solutions, and from transparent glasses to super black dyed coatings. Only very recently, researchers started to develop tailored OFP solutions that account for such material requirements in energy (both light and force), in time, and in their spatially detectable resolution. We here highlight notable recent examples and identify future challenges in this emergent field.

Force-Induced Near-Infrared Chromism of Mechanophore-Linked Polymers

A near-infrared (NIR) mechanophore was developed and incorporated into a poly(methyl acrylate) chain to showcase the first force-induced NIR chromism in polymeric materials. This mechanophore, based on benzo[1,3]oxazine (OX) fused with a heptamethine cyanine moiety, exhibited NIR mechanochromism in solution, thin-film, and bulk states. The mechanochemical activity was validated using UV-vis-NIR absorption/fluorescence spectroscopies, gel permeation chromatography (GPC), NMR, and DFT simulations. Our work demonstrates that NIR mechanochromic polymers have considerable potential in mechanical force sensing, damage detection, bioimaging, and biomechanics.

Reversible regulation of metallo-base-pair interactions for DNA dehybridization by ultrasound

Mechanical force applied by ultrasound in solution leads to the dissociation of DNA metallo-base-pair interactions when these motifs are functionalized with oligodeoxynucleotide sequences of sufficient length. The annealing and force-induced denaturing process is followed by the attachment of distance-sensitive fluorescent probes and is found to be reversible.

Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound

The regulation of enzyme activity is a method to control biological function. We report two systems enabling the ultrasound-induced activation of thrombin, which is vital for secondary hemostasis. First, we designed polyaptamers, which can specifically bind to thrombin, inhibiting its catalytic activity. With ultrasound generating inertial cavitation and therapeutic medical focused ultrasound, the interactions between polyaptamer and enzyme are cleaved, restoring the activity to catalyze the conversion of fibrinogen into fibrin. Second, we used split aptamers conjugated to the surface of gold nanoparticles (AuNPs). In the presence of thrombin, these assemble into an aptamer tertiary structure, induce AuNP aggregation, and deactivate the enzyme. By ultrasonication, the AuNP aggregates reversibly disassemble releasing and activating the enzyme. We envision that this approach will be a blueprint to control the function of other proteins by mechanical stimuli in the sonogenetics field.

The many flavours of mechanochemistry and its plausible conceptual underpinnings

Mechanochemistry describes diverse phenomena in which mechanical load affects chemical reactivity. The fuzziness of this definition means that it includes processes as seemingly disparate as motor protein function, organic synthesis in a ball mill, reactions at a propagating crack, chemical actuation, and polymer fragmentation in fast solvent flows and in mastication. In chemistry, the rate of a reaction in a flask does not depend on how fast the flask moves in space. In mechanochemistry, the rate at which a material is deformed affects which and how many bonds break. In other words, in some manifestations of mechanochemistry, macroscopic motion powers otherwise endergonic reactions. In others, spontaneous chemical reactions drive mechanical motion. Neither requires thermal or electrostatic gradients. Distinct manifestations of mechanochemistry are conventionally treated as being conceptually independent, which slows the field in its transformation from being a collection of observations to a rigorous discipline. In this Review, we highlight observations suggesting that the unifying feature of mechanochemical phenomena may be the coupling between inertial motion at the microscale to macroscale and changes in chemical bonding enabled by transient build-up and relaxation of strains, from macroscopic to molecular. This dynamic coupling across multiple length scales and timescales also greatly complicates the conceptual understanding of mechanochemistry.

Controlling Optical and Catalytic Activity of Genetically Engineered Proteins by Ultrasound

Ultrasound (US) produces cavitation-induced mechanical forces stretching and breaking polymer chains in solution. This type of polymer mechanochemistry is widely used for synthetic polymers, but not biomacromolecules, even though US is biocompatible and commonly used for medical therapy as well as in vivo imaging. The ability to control protein activity by US would thus be a major stepping-stone for these disciplines. Here, we provide the first examples of selective protein activation and deactivation by means of US. Using GFP as a model system, we engineer US sensitivity into proteins by design. The incorporation of long and highly charged domains enables the efficient transfer of force to the protein structure. We then use this principle to activate the catalytic activity of trypsin by inducing the release of its inhibitor. We expect that this concept to switch "on" and "off" protein activity by US will serve as a blueprint to remotely control other bioactive molecules.

Mechanochemical activation of disulfide-based multifunctional polymers for theranostic drug release

Drug delivery systems responsive to physicochemical stimuli allow spatiotemporal control over drug activity to overcome limitations of systemic drug administration. Alongside, the non-invasive real-time tracking of drug release and uptake remains challenging as pharmacophore and reporter function are rarely unified within one molecule. Here, we present an ultrasound-responsive release system based on the mechanochemically induced 5-exo-trig cyclization upon scission of disulfides bearing cargo molecules attached via β-carbonate linker within the center of a water soluble polymer. In this bifunctional theranostic approach, we release one reporter molecule per drug molecule to quantitatively track drug release and distribution within the cell in real-time. We use N-butyl-4-hydroxy-1,8-naphthalimide and umbelliferone as fluorescent reporter molecules to accompany the release of camptothecin and gemcitabine as clinically employed anticancer agents. The generality of this approach paves the way for the theranostic release of a variety of probes and drugs by ultrasound.

A theranostic approach for the mechanochemically induced release of drugs is presented to track drug release and uptake in real-time.