Reversible Conformational Change Research Articles

Fantastic [FeFe]-Hydrogenases and Where to Find Them.

[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.

Fluctuations in T cell receptor and pMHC interactions regulate T cell activation.

Adaptive immune responses depend on interactions between T cell receptors (TCRs) and peptide major histocompatibility complex (pMHC) ligands located on the surface of T cells and antigen presenting cells (APCs), respectively. As TCRs and pMHCs are often only present at low copy numbers their interactions are inherently stochastic, yet the role of stochastic fluctuations on T cell function is unclear. Here, we introduce a minimal stochastic model of T cell activation that accounts for serial TCR-pMHC engagement, reversible TCR conformational change and TCR aggregation. Analysis of this model indicates that it is not the strength of binding between the T cell and the APC cell per se that elicits an immune response, but rather the information imparted to the T cell from the encounter, as assessed by the entropy rate of the TCR-pMHC binding dynamics. This view provides an information-theoretic interpretation of T cell activation that explains a range of experimental observations. Based on this analysis, we propose that effective T cell therapeutics may be enhanced by optimizing the inherent stochasticity of TCR-pMHC binding dynamics.

Solid-state cooling by elastocaloric polymer with uniform chain-lengths

Although the elastocaloric effect was found in natural rubber as early as 160 years ago, commercial elastocaloric refrigeration based on polymer elastomers has stagnated owing to their deficient elastocaloric effects and large extension ratios. Herein, we demonstrate that polymer elastomers with uniform molecular chain-lengths exhibit enormous elastocaloric effects through reversible conformational changes. An adiabatic temperature change of −15.3 K and an isothermal entropy change of 145 J kg−1 K−1, obtained from poly(styrene-b-ethylene-co-butylene-b-styrene) near room temperature, exceed those of previously reported elastocaloric polymers. A rotary-motion cooling device is tailored to high-strains characteristics of rubbers, which effectively discharges the cooling energy of polymer elastomers. Our work provides a strategy for the enhancement of elastocaloric effects and could promote the commercialization of solid-state cooling devices based on polymer elastomers.

Unusual motion of the n-methoxypropyl moiety observed in the photochromic crystals of an organorhodium dithionite complex with n-methoxypropyltetramethylcyclopentadienyl ligands.

The crystalline-state photochromism of a new organorhodium dinuclear complex having n-methoxypropyltetramethylcyclopentadienyl (η5-C5Me4n-C3H6OCH3) and photoresponsive dithionite (μ-O2SSO2) ligands was investigated directly by performing single-crystal X-ray diffraction experiments; a reversible conformational change of the n-methoxypropyl moiety was intriguingly observed during the course of a thermal back-reaction.

Direct Color Observation of Light-Driven Molecular Conformation-Induced Stress.

Although usually complex to handle, nanomechanical sensors are exceptional, label-free tools for monitoring molecular conformational changes, which makes them of paramount importance in understanding biomolecular interactions. Herein, a simple and inexpensive mechanical imaging approach based on low-stiffness cantilevers with structural coloration (mechanochromic cantilevers (MMC)) is demonstrated, able to monitor and quantify molecular conformational changes with similar sensitivity to the classical optical beam detection method of cantilever-based sensors (≈4.6×10-3 Nm-1 ). This high sensitivity is achieved by using a white light and an RGB camera working in the reflection configuration. The sensor performance is demonstrated by monitoring the UV-light induced reversible conformational changes of azobenzene molecules coating. The trans-cis isomerization of the azobenzene molecules induces a deflection of the cantilevers modifying their diffracted color, which returns to the initial state by cis-trans relaxation. Interestingly, the mechanical imaging enables a simultaneous 2D mapping of the response thus enhancing the spatial resolution of the measurements. A tight correlation is found between the color output and the cantilever's deflection and curvature angle (sensitivities of 5×10-3 Hueµm-1 and 1.5×10-1 Hue(°)-1 ). These findings highlight the suitability of low-stiffness MMC as an enabling technology for monitoring molecular changes with unprecedented simplicity, high-throughput capability, and functionalities.

DNA-Scaffolded Synergistic Catalysis.

We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.

Freeze-thaw and solvent-exchange strategy to generate physically cross-linked organogels and hydrogels of curdlan with tunable mechanical properties

Physical gels from natural polysaccharides present the advantage of no toxic cross-linking agents and no chemical modification during preparation. Herein, novel physical gels, transparent organogels and opaque hydrogels from the microorganism-derived (1,3)-β-D-glucan of curdlan were prepared in dimethyl sulfoxide (DMSO) using the freeze-thaw technique, followed by a solvent-exchange strategy with water. The mechanical and structural properties of these gels were investigated by rheology, scanning electron microscopy, attenuated total reflection infrared spectroscopy, wide-angle X-ray diffraction and small-angle X-ray scattering. Gelation mechanisms and intermolecular interaction models have also been proposed. The good solvent DMSO serves as both a crosslinker and a pore-foaming agent in organogels. The reversible macromolecular conformation changes and phase separation of curdlan endow the gels with reversible transparency, volume change and tunable mechanical strength. The new design strategy of facile preparation and performance tuning provides a platform for developing new organogels and sterile hydrogels of curdlan.

Anthraquinodimethane Ring-Flip in Sterically Congested Alkenes: Isolation of Isomer and Elucidation of Intermediate through Experimental and Theoretical Approach

Abstract From the viewpoint of the development of molecular response systems, stimulus-induced switching of multi-conformational/multi-configurational overcrowded ethylenes are interesting, whose properties could be manipulated by understanding the detailed isomerization paths. Anthraquinodimethane (AQD) ring-flip is usually a very fast process, and thus less studied experimentally. Herein, we studied AQDs with dibenzo- and tribenzocycloheptatrienylidene units, which have large enough steric hindrance to retard the AQD ring-flip to allow determination of the ΔG≠ value experimentally. Their thermal isomerization was also scrutinized using the artificial force induced reaction method to elucidate the intermediates. Based on the structural unsymmetry in a newly prepared AQD, one of the isomers that undergoes a reversible conformational change via AQD ring-flip was isolated and analyzed by X-ray for the first time.

Desolvation–Solvation-Induced Reversible On–Off Switching of Two Memory Channels in a Cobalt(II) Coordination Polymer: Overlay of Spin Crossover and Structural Phase Transition

Desolvation–Solvation-Induced Reversible On–Off Switching of Two Memory Channels in a Cobalt(II) Coordination Polymer: Overlay of Spin Crossover and Structural Phase Transition

Photoswitchable Machine-Engineered Plasmonic Nanosystem with High Optical Response for Ultrasensitive Detection of microRNAs and Proteins Adaptively

Modulating optoelectronic properties of inorganic nanostructures tethered with light-responsive molecular switches by their conformational change in the solid state is fundamentally important for advanced nanoscale-device fabrication, specifically in biosensing applications. Herein, we present an entirely new solid-state design approach employing the light-induced reversible conformational change of spiropyran (SP)-merocyanine (MC) covalently attached to gold triangular nanoprisms (Au TNPs) via alkylthiolate self-assembled monolayers to produce a large localized surface plasmon resonance response (∼24 nm). This shift is consistent with the increase in thickness of the local dielectric shell-surrounded TNPs and perhaps short-range dipole-dipole (permanent and induced) interactions between TNPs and the zwitterionic MC form. Water contact angle measurement and Raman spectroscopy characterization unequivocally prove the formation of a stable TNP-MC structural motif. Utilizing this form, we fabricated the first adaptable nanoplasmonic biosensor, which uses an identical structural motif for ultrasensitive, highly specific, and programmable detection of microRNAs and proteins at attomolar concentrations in standard human plasma and urine samples, and at femtomolar concentrations from bladder cancer patient plasma (n = 10) and urine (n = 10), respectively. Most importantly, the TNP-MC structural motif displays a strong binding affinity with receptor molecules (i.e., single-stranded DNA and antibody) producing a highly stable biosensor. Taken together, the TNP-MC structural motif represents a multifunctional super biosensor with the potential to expand clinical diagnostics through simplifying biosensor design and providing highly accurate disease diagnosis.

Smart fluorescent tag based on amine response for non-contact and visual monitoring of seafood freshness

The method of monitoring the freshness of seafood is not satisfactory for ensuring food safety. Here, we develop a filter membrane-based smart fluorescent tag with excellent biogenic amine response, which can monitor the freshness of seafood in real time and visually. We use green fluorescent fluorescein as an indicator and red fluorescent carbon quantum dots (RQDs) with aggregation-induced emission property as an internal reference. After simple mixing, they are deposited on the commercial filter membrane by physical deposition method to prepare the fluorescent tag. When amine molecules are present, the molecular conformation of fluorescein changes and the fluorescence increases rapidly, while RQDs have no obvious response, thus achieving a clear fluorescence color response to biogenic amines. Under UV light of 254 nm and 365 nm, the fluorescent tag showed sensitive, rapid, and color-responsive to ammonia in a wide range of 250–2.5 × 104 ppm. To further verify the practical application potential, the fluorescent tag was used to monitor the freshness of shrimp and crab in situ in real time, and satisfactory results were achieved. More importantly, owing to the reversible conformational change of fluorescein, the fluorescent tag can be reused and manufactured at low cost, making it a more attractive platform for freshness monitoring in the field of food safety.

Self-cleaning electrochemical protein-imprinting biosensor with a dual-driven switchable affinity for sensing bovine serum albumin

A facile, universal and highly efficient approach for producing a self-cleaning electrochemical protein-imprinting biosensor based on dual stimuli-responsive memory hydrogels via free-radical polymerisation is described. As confirmed by static contact angle and scanning electron microscopy results, the imprinted hydrogels exhibited reversible conformational changes after being simulated by an external electric field and temperature. By exploring the properties of imprinted hydrogels for sensing applications, the electrochemical protein-imprinting biosensor was originally fabricated on a glassy carbon electrode using the drop-casting method. Because of the trigger gates of the temperature and electric field, the biosensor demonstrated excellent self-cleaning behaviours compared with other corresponding electric-field or thermo-responsive imprinting biosensors. Moreover, the prepared biosensor exhibited satisfactory selectivity, good biocompatibility, comparable limits of detection and linearity ranges as well as acceptable stability toward bovine serum albumin. Consequently, the biosensor was successfully employed to simultaneously enrich, detect and extract bovine serum albumin from complex biological samples; the process was dynamic, controllable and harmless to the template under the dual external stimuli. Thus, the proposed biosensor exhibited considerable potential in controlled drug/chemical delivery and smart sensing for bioanalyses involving dual stimuli-responsive behaviours.

Toward Convergence in Free Energy Calculations for Protein Conformational Changes: A Case Study on the Thin Gate of Mhp1 Transporter.

It has been challenging to obtain reliable free energies for protein conformational changes from all-atom molecular dynamics simulations, despite the availability of many enhanced sampling techniques. To alleviate the difficulties associated with the enormous complexity of the conformational space, here we propose a few practical strategies for such calculations, including (1) a stringent method to examine convergence by comparing independent simulations starting from different initial coordinates, (2) adoption of multistep schemes in which the complete conformational change consists of multiple transition steps, each sampled using a distinct reaction coordinate, and (3) application of boundary restraints to simplify the conformational space. We demonstrate these strategies on the conformational changes between the outward-facing and outward-occluded states of the Mhp1 membrane transporter, obtaining the equilibrium thermodynamics of the relevant metastable states, the kinetic rates between these states, and the reactive trajectories that reveal the atomic details of spontaneous transitions. Our approaches thus promise convergent and reliable calculations to examine intuition-based hypotheses and to eventually elucidate the underlying molecular mechanisms of reversible conformational changes in complex protein systems.

Double- to Single-Strand Transition Induces Forces and Motion in DNA Origami Nanostructures.

The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids.

Regulation of reversible conformational change, size switching, and immunomodulation of RNA nanocubes.

In biological systems, conformational changes and allosteric modulation play pivotal roles in regulating biological functions, such as the dynamic change of protein molecules, in response to binding or interacting with other factors such as pH, voltage, salt, light, or ligand. RNA can be manipulated and tuned with a level of simplicity that is characteristic of DNA or polymers, while displaying versatility in structure, diversity in function, and adaptability in a configuration similar to proteins. In the past, the work on the investigation of conformational change mainly focused on protein. The induced-fit and conformational capture in RNA have also been explored, such as in the study of riboswitches. Herein, we report the engineering of three-dimensional RNA nanocubes and demonstrated the operation and regulation for its configuration. We demonstrate the operation of reconfigurable RNA nanocubes whose shapes change precisely and reversibly in response to a specific trigger strand. The shape, size, and conformation can be regulated precisely and reversibly in response to the specific triggering signals. The shape and conformational conversion were observed by cryo-EM and gel electrophoresis, respectively. Harnessing the size, shape, conformation, and self-assembly capabilities of the RNA nanocube can provide a new potential use of this technology as nanocarriers for the treatment of various diseases.

Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding

Summary Because of proteins’ many degrees of conformational freedom, programming protein folding dynamics, overall elasticity, and motor functions remains an elusive objective. Instead, smaller and simpler objects, such as synthetic foldamers, may be amenable to design. However, little is known about their mechanical performance. Here, we show that reducing molecular size may not compromise mechanical properties. We report that helical aromatic oligoamides as small as 1 nm possess outstanding elasticity and outperform most natural helices. Using single-molecule force spectroscopy, we characterize their folding trajectories and intermediate states. We show that they cooperatively and reversibly unwind at high forces. They extend up to 3.8 times their original length and rewind against considerable forces on a timescale of 10 μs. Pulling and relaxing cycles follow the same trace up to a very high loading rate, indicating that the mechanical energy accumulated during the stretching does not dissipate and is immediately reusable.

Controlling pairing of \u03c0-conjugated electrons in 2D covalent organic radical frameworks via in-plane strain

Controlling the electronic states of molecules is a fundamental challenge for future sub-nanoscale device technologies. π-conjugated bi-radicals are very attractive systems in this respect as they possess two energetically close, but optically and magnetically distinct, electronic states: the open-shell antiferromagnetic/paramagnetic and the closed-shell quinoidal diamagnetic states. While it has been shown that it is possible to statically induce one electronic ground state or the other by chemical design, the external dynamical control of these states in a rapid and reproducible manner still awaits experimental realization. Here, via quantum chemical calculations, we demonstrate that in-plane uniaxial strain of 2D covalently linked arrays of radical units leads to smooth and reversible conformational changes at the molecular scale that, in turn, induce robust transitions between the two kinds of electronic distributions. Our results pave a general route towards the external control, and thus technological exploitation, of molecular-scale electronic states in organic 2D materials.

A predictive model for astringency based on in vitro interactions between salivary proteins and (−)-Epigallocatechin gallate

Astringency is an important quality attribute of green tea infusion, and (−)-Epigallocatechin gallate (EGCG) is the main contributor to astringency. Turbidity was used to predict the intensity of astringency for EGCG. The interactions between the selected proteins and EGCG, and the impacts of temperature, pH, protein structure, and EGCG concentration were studied. Mucin was selected as the protein in study for the prediction of EGCG astringency intensity. A predictive model (R2 = 0.994) was developed based on the relationship between the astringency of EGCG and the turbidity of EGCG/mucin mixtures at pH 5.0 and 37 °C. The fluorescence quenching analyses showed the interactions between EGCG and the selected proteins, which induced the reversible protein molecule conformational changes. The interactions were considered as the main reason that causes the astringency of tea infusions. The results provided a biochemical approach to explore the sensory qualities of green tea.

Chemical and Microstructural Characterization of pH and [Ca2+] Dependent Sol-Gel Transitions in Mucin Biopolymer

Mucus is responsible for controlling transport and barrier function in biological systems, and its properties can be significantly affected by compositional and environmental changes. In this study, the impacts of pH and CaCl2 were examined on the solution-to-gel transition of mucin, the primary structural component of mucus. Microscale structural changes were correlated with macroscale viscoelastic behavior as a function of pH and calcium addition using rheology, dynamic light scattering, zeta potential, surface tension, and FTIR spectroscopic characterization. Mucin solutions transitioned from solution to gel behavior between pH 4–5 and correspondingly displayed a more than ten-fold increase in viscoelastic moduli. Addition of CaCl2 increased the sol-gel transition pH value to ca. 6, with a twofold increase in loss moduli at low frequencies and ten-fold increase in storage modulus. Changing the ionic conditions—specifically [H+] and [Ca2+] —modulated the sol-gel transition pH, isoelectric point, and viscoelastic properties due to reversible conformational changes with mucin forming a network structure via non-covalent cross-links between mucin chains.

Silicon Microcantilever Sensors to Detect the Reversible Conformational Change of a Molecular Switch, Spiropyan.

The high sensitivity of silicon microcantilever sensors has expanded their use in areas ranging from gas sensing to bio-medical applications. Photochromic molecules also represent promising candidates for a large variety of sensing applications. In this work, the operating principles of these two sensing methods are combined in order to detect the reversible conformational change of a molecular switch, spiropyran. Thus, arrays of silicon microcantilever sensors were functionalized with spiropyran on the gold covered side and used as test microcantilevers. The microcantilever deflection response was observed, in five sequential cycles, as the transition from the spiropyran (SP) (CLOSED) to the merocyanine (MC) (OPEN) state and vice-versa when induced by UV and white light LED sources, respectively, proving the reversibility capabilities of this type of sensor. The microcantilever deflection direction was observed to be in one direction when changing to the MC state and in the opposite direction when changing back to the SP state. A tensile stress was induced in the microcantilever when the SP to MC transition took place, while a compressive stress was observed for the reverse transition. These different type of stresses are believed to be related to the spatial conformational changes induced in the photochromic molecule upon photo-isomerisation.