Folding State Research Articles

Miura origami based reconfigurable polarization converter for multifunctional control of electromagnetic waves

Polarization is one of the basic characteristics of electromagnetic (EM) waves, and its flexible control is very important in many practical applications. At present, most of the multifunction polarization metasurfaces are electrically tunable based on PIN and varactor diodes, which are easy to operate and have strong real-time performance. However, there are still some problems in them, such as few degrees of freedom of planar structure control, complex circuit, bulky sample, and high cost. In view of these shortcomings, this paper proposes a Miura origami based reconfigurable polarization conversion metasurface for multifunctional control of EM waves. The interaction between the electric dipoles is changed by adjusting the folding angle θ, thereby tuning the operating frequency of the polarization conversion and the polarization state of the reflected wave. This mechanical control method brings more degrees of freedom to manipulate EM waves. And the processed sample is with lightweight and low cost. To verify the performance of the proposed origami polarization converter, a Miura origami structure loaded with metal split rings is designed and fabricated. The operating frequency of the structure can be tuned in different folding states. In addition, by controlling the folding angle θ, linear-to-linear and linear-to-circular polarization converters can be realized at different folding states. The proposed Miura origami polarization conversion metasurface provides a new idea for reconfigurable linear polarization conversion and multifunctional devices.

Conformational stability of peroxidase from the latex of Artocarpus lakoocha: influence of pH, chaotropes, and temperature.

The latex of the medicinal plant Artocarpus lakoocha (A. lakoocha), which has been shown to have potential anti-inflammatory and wound-healing capabilities, contains a novel heme-peroxidase. This protein was subjected to activity assays, fluorescence spectroscopy, and far-UV circular dichroism to investigate its structure, dynamics, and stability. The results demonstrated the presence of three folding states: the native state (N) at neutral pH, intermediate states including molten globule (MG) at pH 2 and acid-unfolded (UA) at pH 1.5 or lower, and acid-refolded (A) at pH 0.5, along with alkaline denatured (UB) at pH 8-12 and the third denatured state (D) at GuHCl concentrations exceeding 5 M. Absorbance studies indicated the presence of loosely associated form of heme in the pH range of 1-2. The protein showed stability and structural integrity across a wide pH range (3-10), temperature (70°C), and high concentrations of GuHCl (5 M) and urea (8 M). This study is the first to report multiple 'partially folded intermediate states' of A. lakoocha peroxidase, with varying amounts of secondary structure, stability, and compactness. These results demonstrate the high stability of A. lakoocha peroxidase and its potential for biotechnological and industrial applications, making it a valuable model system for further studies on its structure-function relationship.

Prediction of DNA i-motifs via machine learning.

i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of putative iMs vary dramatically. Much previous research on iM has focused on assessing the iM folding properties using biophysical experiments. However, there are no dedicated computational tools for predicting the folding status and strength of iM structures. Here, we introduce a machine learning pipeline, iM-Seeker, to predict both folding status and structural stability of DNA iMs. The programme iM-Seeker incorporates a Balanced Random Forest classifier trained on genome-wide iMab antibody-based CUT&Tag sequencing data to predict the folding status and an Extreme Gradient Boosting regressor to estimate the folding strength according to both literature biophysical data and our in-house biophysical experiments. iM-Seeker predicts DNA iM folding status with a classification accuracy of 81% and estimates the folding strength with coefficient of determination (R2) of 0.642 on the test set. Model interpretation confirms that the nucleotide composition of the C-rich sequence significantly affects iM stability, with a positive correlation with sequences containing cytosine and thymine and a negative correlation with guanine and adenine.

“Q-SLIP” determines the state of folding of individual amyloid oligomers in a lipid membrane

“Q-SLIP” determines the state of folding of individual amyloid oligomers in a lipid membrane

SonoTransformers: Transformable acoustically activated wireless microscale machines

Shape transformation, a key mechanism for organismal survival and adaptation, has gained importance in developing synthetic shape-shifting systems with diverse applications ranging from robotics to bioengineering. However, designing and controlling microscale shape-shifting materials remains a fundamental challenge in various actuation modalities. As materials and structures are scaled down to the microscale, they often exhibit size-dependent characteristics, and the underlying physical mechanisms can be significantly affected or rendered ineffective. Additionally, surface forces such as van der Waals forces and electrostatic forces become dominant at the microscale, resulting in stiction and adhesion between small structures, making them fracture and more difficult to deform. Furthermore, despite various actuation approaches, acoustics have received limited attention despite their potential advantages. Here, we introduce "SonoTransformer," the acoustically activated micromachine that delivers shape transformability using preprogrammed soft hinges with different stiffnesses. When exposed to an acoustic field, these hinges concentrate sound energy through intensified oscillation and provide the necessary force and torque for the transformation of the entire micromachine within milliseconds. We have created machine designs to predetermine the folding state, enabling precise programming and customization of the acoustic transformation. Additionally, we have shown selective shape transformable microrobots by adjusting acoustic power, realizing high degrees of control and functional versatility. Our findings open new research avenues in acoustics, physics, and soft matter, offering new design paradigms and development opportunities in robotics, metamaterials, adaptive optics, flexible electronics, and microtechnology.

Investigating lysozyme amyloid fibril formation and structural variability dependence on its initial folding state under different pH conditions.

Protein fibril formation and accumulation are associated with dozens of amyloidoses, including the widespread and yet-incurable Alzheimer's and Parkinson's diseases. Currently, there are still several aspects of amyloid aggregation that are not fully understood, which negatively contributes to the development of disease-altering drugs and treatments. One factor which requires a more in-depth analysis is the effect of the environment on both the initial state of amyloidogenic proteins and their aggregation process and resulting fibril characteristics. In this work, we examine how lysozyme's folding state influences its amyloid formation kinetics and resulting aggregate structural characteristics under several different pH conditions, ranging from acidic to neutral. We demonstrate that both the initial state of the protein and the solution's pH value have a significant combined effect on the variability of the resulting aggregate secondary structures, as well as their stabilities, interactions with amyloid-specific dye molecules, and self-replication properties.

Inkjet-printed flexible planar Zn-MnO2 battery on paper substrate

Energy storage devices (ESD) which are intended to power electronic devices, used in close contact of human skin, are desirable to be safe and non-toxic. In light of this requirement, Zn based energy storage devices seem to provide a viable pathway as they mostly employ aqueous based electrolytes which are safe and non-toxic in their functioning. Additionally, having a flexible ESD will play a crucial role as it will enable the ESD to conform to the varying shapes and sizes of wearable electronics which they energize. In this work, we have developed an inkjet-printed Zinc ion battery (IPZIB) with planar electrode configuration over bond paper substrate. Zn has been used as the negative electrode, MnO2 is used as the positive electrode with Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) as the active binder. Conducting tracks of reduced graphene oxide (rGO) are used to construct the current collector on the paper substrate. The fabricated IPZIB delivered a high discharge capacity of 300.14 mAh g−1 at a current density of 200 mA g−1. The energy density of the IPZIB is observed as 330.15 Wh kg−1 at a power density of 220 W kg−1 and retains an energy density of 94.36 Wh kg−1 at a high power density of 1650 W kg−1. Finally, we have demonstrated the capability of the IPZIB to power a LED at various bending and folding conditions which indicates its potential to be used in the next generation flexible and wearable electronic devices.

Monolithic Microparticles Facilitated Flower-Like TiO2 Nanowires for High Areal Capacity Flexible Li-Ion Batteries.

Flexible lithium-ion batteries (FLIBs) are intensively studied using free-standing transition metal oxides (TMOs)-based anode materials. However, achieving high areal capacity TMO-based anode materials is yet to be effectively elucidated owing to the poor adhesion of the active materials to the flexible substrate resulting in low active mass loading, and hence low areal capacity is realized. Herein, a novel monolithic rutile TiO2 microparticles on carbon cloth (ATO/CC) that facilitate the flower-like arrangement of TiO2 nanowires (denoted ATO/CC/OTO) is demonstrated as high areal capacity anode for FLIBs. The optimized ATO/CC/OTO anode exhibits high areal capacity (5.02 mAh cm-2@0.4mA cm-2) excellent rate capability (1.17 mAh cm-2@5.0mA cm-2) and remarkable cyclic stability (over 500 cycles). A series of morphological, kinetic, electrochemical, in situ Raman, and theoretical analyses reveal that the rational phase boundaries between the microparticles and nanowires contribute to promoting the Li storage activity. Furthermore, a 16.0 cm2 all-FLIB pouch cell assembled based on the ATO/CC/OTO anode and LiNiCoMnO2 cathode coated on ATO/CC (ATO/CC/LNCM) exhibits impressive flexibility under different folding conditions, creating opportunity for the development of high areal capacity anodes in future flexible energy storage devices.

Fluorogenic Hyaluronan Nanogels Track Individual Early Protein Aggregates Originated under Oxidative Stress.

Proteins are broadly versatile biochemical materials, whose functionality is tightly related to their folding state. Native folding can be lost to yield misfolded conformations, often leading to formation of protein oligomers, aggregates, and biomolecular phase condensates. The fluorogenic hyaluronan HA-RB, a nonsulfonated glycosaminoglycan with a combination of polyanionic character and of hydrophobic spots due to rhodamine B dyes, binds to early aggregates of the model protein cytoplasmic glyceraldehyde-3-phosphate dehydrogenase 1 from Arabidopsis thaliana (AtGAPC1) since the very onset of the oligomeric phase, making them brightly fluorescent. This initial step of aggregation has, until now, remained elusive with other fluorescence- or scattering-based techniques. The information gathered from nanotracking (via light-sheet fluorescence microscopy) and from FCS in a confocal microscope converges to highlight the ability of HA-RB to bind protein aggregates from the very early steps of aggregation and with high affinity. Altogether, this fluorescence-based approach allows one to monitor and track individual early AtGAPC1 aggregates in the size range from 10 to 100 nm with high time (∼10-2 s) and space (∼250 nm) resolution.

Artificial intelligence-driven design of the assembled major cat allergen Fel d 1 to improve its spatial folding and IgE-reactivity

BackgroundCat-derived allergens are considered as one of the most common causes of allergic diseases worldwide. Fel d 1 is a major cat allergen and plays an important role in immunoglobulin E (IgE)-reaction diagnosis. However, the two separate chains of Fel d 1 exhibited lower IgE-reactivity than its complete molecule of an assembled form, which makes it difficult to efficiently prepare and limits the application of Fel d 1 in molecular diagnosis of cat allergy. MethodsWe first applied artificial intelligence (AI) based tool AlphaFold2 to build the 3-dimensional structures of Fel d 1 with different connection modes between two chains, which were evaluated by ERRAT program and were expressed in Escherichia coli. We then calculated the expression ratios of soluble form/inclusion bodies form of optimized Fel d 1. The Circular Dichroism (CD), High Performance Liquid Chromatography-Size Exclusion Chromatography (HPLC-SEC) and reducing/non-reducing SDS-PAGE were performed to characterize the folding status and dimerization of the optimized fusion Fel d 1. The improvement of specific-IgE reactivity to optimized fusion Fel d 1 was investigated by enzyme linked immunosorbent assay (ELISA). ResultsAmong several linkers, 2 × GGGGS got the highest scores, with an overall quality factor of 100. The error value of the residues around the junction of 2 × GGGGS was lower than others. It exhibited highest proportion of soluble protein than other Fel d 1 constructs with ERRAT (GGGGS, KK as well as direct fusion Fel d 1). The results of CD and HPLC-SEC showed the consistent folding and dimerization of two fused subunits between the optimized fusion Fel d 1 and previously well-defined direct fusion Fel d 1. The overall IgE-binding absorbance of optimized fusion Fel d 1 tested by ELISA was improved compared with that of the direct fusion Fel d 1. ConclusionWe firstly provided an AI-design strategy to optimize the Fel d 1, which could spontaneously fold into its native-like structure without additional refolding process or eukaryotic folding factors. The improved IgE-binding activity and simplified preparation method could greatly facilitate it to be a robust allergen material for molecular diagnosis of cat allergy.

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.