Folding State Research Articles

Highly improved photocurrent of a flexible MoS2 photodetector via a backside Al metal mirror and its in- and outward folding states.

High-performance foldable and flexible photodetectors have been extensively studied for next-generation hinged electronics and AR/VR technology. The need to maintain efficiency in the folded state restricts the development of strategies aimed at further improving the efficiency of photodetectors. For the first time, we introduce a simple and effective method for the photocurrent improvement of a molybdenum disulfide (MoS2) flexible photodetector by attaching a backside Al metal mirror and folding it in- and outward. Under light illumination, the Al film underneath the MoS2 photodetector acts as a flat reflective metal mirror and further functions as a concave mirror under the inward folded state. In this state, the proposed device with the backside Al metal mirror improved photocurrent from 4.04 μA to 8.53 μA under illumination (a λ ex of 405 nm with a P inc of 0.3 mW cm-2) compared to the device on a flat polyimide (PI) substrate without the Al metal mirror. Our work provides new insights into high-performance flexible photodetectors in the inward and outward folded states, which will be beneficial for future foldable/hinged electronics and AR/VR devices.

From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding.

Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.

Dual-environment-sensitive probe to detect protein aggregation in stressed laryngeal carcinoma cells and tissues.

The interplay between protein folding and biological activity is crucial, with the integrity of the proteome being paramount to ensuring effective biological function execution. In this study, we report a dual-environment-sensitive probe A1, capable of selectively binding to protein aggregates and dynamically monitoring their formation and degradation. Through in vitro, cellular, and tissue assays, A1 demonstrated specificity in distinguishing aggregated from folded protein states, selectively partitioning into aggregated proteins. Thermal shift assays revealed A1 could monitor the process of protein aggregation upon binding to misfolded proteins and preceding to insoluble aggregate formation. In cellular models, A1 detected stress-induced proteome aggregation in TU212 cells (laryngeal carcinoma cells), revealing a less polar microenvironment within the aggregated proteome. Similarly, tissue samples showed more severe proteome aggregation in cancerous tissues compared to paracancerous tissues. Overall, A1 represents a versatile tool for probing protein aggregation with significant implications for both fundamental research and clinical diagnostics.

Förster resonance energy transfer within single chain nanoparticles.

Single chain nanoparticles (SCNPs) are a highly versatile polymer architecture consisting of single polymer chains that are intramolecularly crosslinked. Currently, SCNPs are discussed as powerful macromolecular architectures for catalysis, delivery and sensors. Herein, we introduce a methodology based on Förster Resonance Energy Transfer (FRET) to evidence the folding of single polymer chains into SCNPs via fluorescence readout. We initially introduce a molecular FRET pair based on a bimane and nitrobenzoxadiazole (NBD) moiety and study its fluorescence properties in different solvents. We subsequently construct a low dispersity polymer chain carrying NBD units, while exploiting the bimane units for intramolecular chain collapse. Upon chain collapse and SCNP formation - thus bringing bimane and NBD units into close proximity - the SCNPs report their folded state by a strong and unambiguous FRET fluorescence signal. The herein introduced reporting of the folding state of SCNPs solely relies on an optical readout, opening avenues to monitoring SCNP folding without recourse to complex analytical methodologies.

Foldable chromium vanadate cathodes for high-performance aqueous zinc ion batteries

A novel cathode material, CrV2.7O4.36·2.85H2O/CNT-rGO, composited with a CNT and rGO framework was developed. The flexible battery assembled with it still has stable electrochemical performance under different folding states.

Edge Detection and Defects Checking of Binder Clip and Welded Joint using a Python-Based Algorithm: Applications in Quality Inspection

Machine vision is a computer vision system that enables a computer to work on image-based inspection and analysis for different applications. In this computer vision, a camera and sensor were used to view an image for its analysis with the help of some sort of algorithms, then processed to infer the image-based data. Machine vision systems along with Python programs can be used for many interdisciplinary applications like weld inspection, online monitoring in manufacturing auto components etc. In this study, the “Edge detection python algorithm” was developed and run through “Google Colab” notebook to inspect the edges and the boundaries of samples like faying surface-modified friction welded dissimilar joints and a binder clip (paper clamp) to check any defects or cracks and straightness etc. With the help of this Python algorithm, the edge detection was done by Sobel, Scharr, and Prewit operators. An input image of the weld joint and the binder clip were converted into Otsu’s binary threshold image. The matrix vision camera and the CMOS sensor were used in the machine vision set-up to take the images. This written algorithm is helpful to trace the edges of any kind of solids components. The edges of the binder clips and the weld joint/zone were detected. The binder clips were inspected under two different cases namely the clip in folding condition (Case I) and the binder clip in unfolding condition (Case II). The results showed a defect that was identified in the weld zone and no bending was in the binder clips. This kind of study is useful in manufacturing industries for quality inspection purposes with a new machine vision set up for online inspection of fabricated components like nuts and bolts etc.

In Situ Gelled Covalent Organic Frameworks Electrolyte with Long-Range Interconnected Skeletons for Superior Ionic Conductivity.

Covalent organic frameworks (COFs) present an ideal platform for ion transport owing to their tunable and ordered nanochannels at the single-digit scale. However, achieving superior COF-based electrolytes remains challenging because of the mismatch between the intricate synthesis processes of COFs and the battery preparation environment, which makes it difficult to build continuous ion channels and low-impedance electrochemical interfaces for devices. Here, we present an in situ gelation method to produce COF gel electrolytes (CGEs) within liquid carbonate electrolyte, integrating COF synthesis with their applicability in batteries. This method leads to long-range interconnected and highly crystalline skeletons of COFs from a robust precoordination structure between lithium salts of liquid electrolyte and building blocks. By incorporating the lithium affinity groups in the COFs, the developed CGEs show a remarkable 3-fold enhancement in ionic conductivity, reaching up to 10.5 mS cm-1 compared to the corresponding liquid carbonate electrolytes. Furthermore, the CGEs exhibit a low activation energy of 0.068 eV, ensuring efficient ion transport, while demonstrating dendrite-free lithium deposition even after prolonged testing periods exceeding 1800 h. These CGEs exhibit excellent rate performance (reversible capacity up to 101 mAh g-1 at a current density of 3C, 1C = 170 mAh g-1) in Li-LiFePO4 coin cells and reversible cycling under extreme conditions (reversible capacity up to 158 mAh g-1 under folding state at 0.1C) in pouch cells. Importantly, our novel methodology extends beyond lithium-ion systems, as it can also be applied to the synthesis of CGEs utilizing potassium, magnesium, zinc, sodium, and calcium ions.

Sensitized Emission Imaging Allows Nanoscale Surface Polarity Mapping of α-Synuclein Amyloid Fibrils.

When misfolded, α-Synuclein (α-Syn), a natively disordered protein, aggregates to form amyloid fibrils responsible for the neurodegeneration observed in Parkinson's disease. Structural studies revealed distinct molecular packing of α-Syn in different fibril polymorphs and variations of interprotofilament connections in the fibrillar architecture. Fibril polymorphs have been hypothesized to exhibit diverse surface polarities depending on the folding state of the protein during aggregation; however, the spatial variation of surface polarity in amyloid fibrils remains unexplored. To map the local polarity (or hydrophobicity) along α-Syn fibrils, we visualized the spectral characteristics of two dyes with distinct polarities-hydrophilic Thioflavin T (ThT) and hydrophobic Nile red (NR)─when both are bound to α-Syn fibrils. Dual-channel fluorescence imaging reveals uneven partitioning of ThT and NR along individual fibrils, implying that relatively more polar/hydrophobic patches are spread over a few hundred nanometers. Remarkably, spectrally resolved sensitized emission imaging of α-Syn fibrils provides unambiguous evidence of energy transfer from ThT to NR, implying that dyes of dissimilar polarity are in close proximity. Furthermore, spatially resolved fluorescence spectroscopy of the solvatochromic probe NR allowed us to quantitatively map the range and variation of the polarity parameter ET30 along individual fibrils. Our results suggest the existence of interlaced polar and nonpolar nanoscale domains throughout the fibrils; however, the relative populations of these patches vary considerably over larger length scales likely due to heterogeneous packing of α-Syn during fibrilization and dissimilar exposed polarities of polymorphic segments. The employed method may provide a foundation for imaging modalities of other similar structurally unresolved systems with diverse hydrophobic-hydrophilic topology.

Self-Assembly and Conformational Change in the Oligomeric Structure of the Ectodomain of the TBEV E Protein Studied via X-ray, Small-Angle X-ray Scattering, and Molecular Dynamics

The determination of the three-dimensional structures of viral proteins is a necessary step both for understanding the mechanisms of virus pathogenicity and for developing methods to combat viral infections. This study aimed to explore the folding and oligomeric state of the major component of the virion surface of the tick-borne encephalitis virus (TBEV), the ectodomain of the envelope E protein (ectoE), which was expressed in E. coli in a soluble form and purified from inclusion bodies as a mixture of dimeric and monomeric forms. The time-dependent assembly of monomers into dimers was detected using size-exclusion chromatography. An X-ray diffraction study of the ectoE crystals grown at pH 4.5 confirmed the dimeric folding of the recombinant protein typical for ectoE. The ability of ectoE dimers to self-assemble into tetramers was detected via small-angle X-ray scattering (SAXS) in combination with molecular dynamics. Such self-assembly occurred at protein concentrations above 4 mg/mL and depended on the pH of the solution. In contrast to stable, specific dimers, we observed that tetramers were stabilized with weak intermolecular contacts and were sensitive to environmental conditions. We discovered the ability of ectoE tetramers to change conformation under crystallization conditions. These results are important for understanding the crystallization process of viral proteins and may be of interest for the development of virus-like particles.

Small-molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states.

Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small-molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase and demonstrated that CFTR-F508del ERAD is robust. Gene-drug interaction experiments illustrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.

Quantitative analytics for protein refolding states

Development and optimization of inclusion body (IB) refolding processes is often based on empirical strategies. Thus, generation of in-depth process understanding is crucial to shift towards more knowledge-driven approaches. Within this contribution the goal was to establish a systematic approach for the reliable quantification of process dynamics in protein refolding processes. Established offline- analytical tools like HPLC-based methods or photometric assays were analyzed regarding their specifications and consequent suitability to quantify protein states. An in-silico study was conducted to define requirements for state quantification by analyzing the influences of error, discrete sampling intervals and the pace of the reaction on signal quality. Refolding and aggregation reaction rates were calculated by finite difference approximation with errors propagated from the corresponding folding state. Application of the defined principles on two real Lactate dehydrogenase fed-batch refolding processes resulted in two individual sampling strategies. At reaction rates of up to 0.58 g h−1 description of the ongoing dynamics could be done accurately with high sampling intervals during the first few hours of processing as shown by comparison to a noise free simulation. The proposed method has the potential to be transferred to other proteins and to facilitate the development of model-based monitoring & control strategies.

Detection of hypersonic weak targets by high pulse repetition frequency radar based on multi‐hypothesis fuzzy‐matching radon transform

AbstractFor the integration detection of near space hypersonic weak targets by high pulse repetition frequency (PRF) radar, a novel method named Multi‐Hypothesis Fuzzy‐Matching Radon transform (MHFM‐RT) is proposed for the near space hypersonic target detection and tracking. For remote hypersonic target detection, to avoid range ambiguity, current radars always use a low PRF mode, which limit the number of pulse accumulations. Using the high PRF mode, the fuzzy folding will appear in the target range measurements when target trajectory crosses range fuzzy intervals. Therefore, there is a contradiction between range ambiguity and energy accumulation. The proposed method is used to match the fuzzy measurements, so as to realise the correct integration in the condition of range ambiguity. Firstly, considering the need of range ambiguity resolution, the mode of staggered PRF is used. Secondly, the first frame measurements are periodically extended for multiple‐fuzzy hypothesis. Finally, the weak target track is accumulated in MHFM‐RT domain, and the signal integration and ambiguity resolution can be realised simultaneously. The proposed method expands the Variable‐Diameter‐Arc‐Helix Radon transform (VDAH‐RT) method to fuzzy folding conditions. Compared with the existing methods, for 7‐scan measurements non‐coherent integration, the detection sensitivity of the proposed method is about 0.5–1 dB higher than that of the IMM hybrid filter algorithm, and about 1 dB higher than that of the RHT‐TBD approach, and it needs less storage space and has higher detection probability.

Contact Endoscopy – Narrow Band Imaging (CE-NBI) data set for laryngeal lesion assessment

The endoscopic examination of subepithelial vascular patterns within the vocal fold is crucial for clinicians seeking to distinguish between benign lesions and laryngeal cancer. Among innovative techniques, Contact Endoscopy combined with Narrow Band Imaging (CE-NBI) offers real-time visualization of these vascular structures. Despite the advent of CE-NBI, concerns have arisen regarding the subjective interpretation of its images. As a result, several computer-based solutions have been developed to address this issue. This study introduces the CE-NBI data set, the first publicly accessible data set that features enhanced and magnified visualizations of subepithelial blood vessels within the vocal fold. This data set encompasses 11144 images from 210 adult patients with pathological vocal fold conditions, where CE-NBI images are annotated using three distinct label categories. The data set has proven invaluable for numerous clinical assessments geared toward diagnosing laryngeal cancer using Optical Biopsy. Furthermore, given its versatility for various image analysis tasks, we have devised and implemented diverse image classification scenarios using Machine Learning (ML) approaches to address critical clinical challenges in assessing laryngeal lesions.

High internal phase emulsions stabilized by walnut protein amyloid-like aggregates and their application in food 3D printing

This study comparatively investigated the rheological properties of high internal phase emulsions (HIPEs) stabilized by walnut protein isolate (WPI) and its amyloid-like aggregate form (WPIA) in detail. WPIA was generated through combined acidic and thermal treatment. Transmission electron microscopy revealed a long rod-like fibrillar structure in WPIA. At pH 3.0, WPI effectively stabilized HIPEs by functioning as a soluble protein emulsifier, while WPIA stabilized Pickering-type HIPEs (HIPPEs) by functioning as solid particles. HIPEs stabilized by WPI at pH 3.0 displayed a slightly higher storage modulus but lower yield strain/stress and a higher loss factor compared to those stabilized by WPIA. Notably, WPIA-stabilized HIPEs showed more pronounced weak strain overshoot behavior. At pH 7.0, WPIA-stabilized HIPEs exhibited a lower storage modulus but higher yield strain compared to pH 3.0 preparations. WPI failed to stabilize HIPEs at pH 7.0 due to its poor solubility. HIPEs stabilized by WPIA at pH 3.0 exhibited good long-term storage stability and had relative resistance to heat treatment and high ionic strength. Furthermore, both WPI- and WPIA-stabilized HIPEs at pH 3.0 exhibited good 3D printability. These findings provide valuable insights into the effect of different folding states of the same protein (WPI and WPIA) on the properties of the resulting HIPEs and offer a novel strategy for expanding the use of walnut proteins in the food industry.

The influence of source-filter interaction on the voice source in a three-dimensional computational model of voice production.

The goal of this computational study is to quantify global effects of vocal tract constriction at various locations (false vocal folds, aryepiglottic folds, pharynx, oral cavity, and lips) on the voice source across a large range of vocal fold conditions. The results showed that while inclusion of a uniform vocal tract had notable effects on the voice source, further constricting the vocal tract only had small effects except for conditions of extreme constriction, at which constrictions at any location along the vocal tract decreased the mean and peak-to-peak amplitude of the glottal flow waveform. Although narrowing in the epilarynx increased the normalized maximum flow declination rate, vocal tract constriction in general slightly reduced the source strength and high-frequency harmonic production at the glottis, except for a limited set of vocal fold conditions (e.g., soft, long vocal folds subject to relatively high pressure). This suggests that simultaneous laryngeal and vocal tract adjustments are required to maximize source-filter interaction. While vocal tract adjustments are often assumed to improve voice production, our results indicate that such improvements are mainly due to changes in vocal tract acoustic response rather than improved voice production at the glottis.

Folding endurance and damage mechanisms of SiC fiber braided fabrics

Aiming at the issues of poor toughness, low folding endurance, and susceptibility to damage of silicon carbide (SiC) fiber tows during repeated folding process, two-dimensional (2D) SiC fiber braided fabrics with varying braiding angles were prepared in this study. The folding endurance and damage mechanisms of SiC fiber fabrics under different folding conditions were investigated through repeated folding tests, tensile tests, and optical microscope measurements. The results revealed that when the folding angle was (+180°, −180°), the SiC fiber braided fabric with a lower braiding angle (α = 37.8°) exhibited a folding endurance number of 1984 times, while the medium angle fabric (α = 41.2°) had a value of 761 times, and the high angle fabric (α = 43.1°) achieved 1733 times. During the folding process, both interlaced abrasion between fiber tows and external folding loads affected the mechanical properties of SiC fiber tows and their fabrics leading to material damage. Initially, the folding load played a major role in determining fold endurance when there were fewer number of folds; however, as the number of folds increased, the influence of interlaced abrasion became increasingly significant. Ultimately, these combined factors led to progressive damage evolution until failure occurred in the fabrics. Among all tested samples, the SiC fiber braided fabric with a higher braiding angle (α = 43.1°) demonstrated optimal fold endurance performance, and it had superior characteristics such as higher fold endurance numbers along with lower force loss rates for fiber tows after multiple folds and fabric force loss rates following repeated folds.

Reconfigurable High-Efficiency metadevice using Kirigami-Inspired phase gradient metasurfaces

Kirigami-inspired metasurface has attracted great attention in electromagnetic (EM) wave manipulations, due to its unprecedented and tailorable structural transformations via mechanical approaches. However, it is still challenging for wavefront control because of its unfeasibility in forming a phase gradient at different folding angle β. Here, we report a strategy of kirigami-inspired reconfigurable phase gradient metasurfaces to efficiently control beam steering of scattering wave through mechanically changing β, where the control range of β is theoretically derived based on EM diffraction and generalized Snell’s law. For demonstration, reconfigurable anomalous reflectors with high efficiency are demonstrated in both dual-element and tri-element tunable metadevices. In former case, the reflection angle varies within 37°∼47° under polarization along y axis by changing β within the range of 10°∼40°, whereas it varies within 36°∼50° under that along x axis when β is changed within 10°∼39°, and numerical and experimental results show measured efficiency of beam steering over 78.6%. In latter case, the reconfigurable tri-element metadevice with various folding states are also experimentally characterized to further verify our strategy. Compared with available metasurfaces, our reconfigurable strategy using maneuverable structures to control EM wave is more versatile and shows great potential in engineering applications.

Detecting Molecular Folding from Noise Measurements

Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We consider cases where Brownian force fluctuations are large, masking the force rips and jumps characteristics of conformational transitions. We compare unfolding and folding data for DNA hairpin systems of loop sizes 4, 8, and 20 and the 110-amino acid protein barnase, finding conditions that facilitate the detection of folding events at low forces where the signal-to-noise ratio is low. In particular, we discuss the role of temperature as a useful parameter to improve the detection of folding transitions in entropically driven processes where folding forces are temperature independent. The force variance approach might be extended to detect the elusive intermediate states in RNA and protein folding.

High durable aqueous zinc ion batteries by synergistic effect of V6O13/VO2 electrode materials

Vanadium oxides have attracted one’s wide attention due to their diverse valences and spatial structure as cathode for aqueous zinc ion batteries. However, a strong electrostatic interaction exists between Zn ions and host materials, which leads to their sluggish reaction kinetics and inferior structural stability. Herein, we design a kind of vanadium-based electrode materials with abundant phase boundaries and oxygen defects. The assembled Zn//V6O13/VO2 batteries deliver a specific capacity of 498.3 mA h g−1 at 0.2 A g−1 and retain a capacity of 485.8 mA h g−1 after 100 cycles. Moreover, they achieve a retention rate of 96.8% after 5000 cycles at 10 A g−1. The soft pack cells also show excellent mechanical stability at different folding conditions.

Optimisation of recombinant TNFα production in Escherichia coli using GFP fusions and flow cytometry.

Escherichia coli is commonly used industrially to manufacture recombinant proteins for biopharmaceutical applications, as well as in academic and industrial settings for R&D purposes. Optimisation of recombinant protein production remains problematic as many proteins are difficult to make, and process conditions must be optimised for each individual protein. An approach to accelerate process development is the use of a green fluorescent protein (GFP) fusions, which can be used to rapidly and simply measure the quantity and folding state of the protein of interest. In this study, we used GFP fusions to optimise production of recombinant human protein tumour necrosis factor (rhTNFα) using a T7 expression system. Flow cytometry was used to measure fluorescence and cell viability on a single cell level to determine culture heterogeneity. Fluorescence measurements were found to be comparable to data generated by subcellular fractionation and SDS-PAGE, a far more time-intensive technique. We compared production of rhTNFα-GFP with that of GFP alone to determine the impact of rhTNFα on expression levels. Optimised shakeflask conditions were then transferred to fed-batch high cell density bioreactor cultures. Finally, the expression of GFP from a paraBAD expression vector was compared to the T7 system. We highlight the utility of GFP fusions and flow cytometry for rapid process development.