Β-sheet Structure Research Articles

One-pot fabrication of sodium deoxycholate based supramolecular self-healing antibacterial double network hydrogels

Double network (DN) hydrogels have emerged as a significant technology for enhancement of mechanical strength of weak supramolecular gels. In the present study, we report the one-pot route for design of a low molecular weight gelator based DN hydrogel wherein sodium deoxycholate (NaDC) forms the primary network entangled with agar matrix. Various compositions of the reported agar-NaDC hydrogels were examined through FTIR, sol-gel transition temperature (Tsg), XRD, circular dichroism (CD), scanning electron microscopy (SEM), hydrophobicity probe studies, Zeta potential studies and rheology measurements. Analysis of all studies together reveal that 1 mg/ml agar-NaDC DN hydrogel is the optimum composition that exhibits dense networking with primarily β-sheet like structure, highest mechanical strength as well as self-healing characteristics with reversed optical activity and highest Tsg. Antibacterial activity studied using inhibition zone method suggests that 1 mg/ml agar-NaDC gel demonstrates significant bactericidal effect unlike the pure gel with an inhibition zone of ∼25 mm against E.coli after 24 h and ∼32 mm after 48 h incubation. The antibacterial activity was unique for this composition of the DN hydrogel which is attributed to its reversal in optical activity exhibiting positive cotton effect resulting in stronger interaction with the bacterial cell wall. Additionally, nearly 2 times reduced water absorption capacity of the 1 mg/ml agar-NaDC DN hydrogel compared to pure NaDC hydrogel ensures the retention of its mechanical strength as well as other properties in high moisture containing environment. Hence, the 1 mg/ml agar-NaDC DN hydrogel holds appreciable potential as a novel strong supramolecular self-healing antibacterial hydrogel with sustained release characteristics primarily important for biomedical applications.

Application of infrared spectroscopy to study carbon-deuterium kinetics and isotopic spectral shifts at the single-cell level

Microbial communities play crucial roles in shaping natural ecosystems, impacting human well-being, and driving advancements in industrial biotechnology. However, associating specific metabolic functions with bacteria proves challenging due to the vast diversity of microorganisms within these communities. In the past decades stable isotope probing (SIP) approaches, coupled with vibrational spectroscopy, have emerged as a novel method for revealing microbial metabolic roles and interactions in complex communities. In this study, we employed various combinations of heavy stable isotopes (D, 13C, 15N, and 18O), to evaluate all possible isotopic spectral shifts in the mid-IR region using Fourier-Transform Infrared (FT-IR) and Optical Photothermal Infrared (O-PTIR) spectroscopy, at both bulk community and single-cell levels. Additionally, we conducted a time-course study to explore the kinetics of CD vibration in Escherichia coli bacteria, allowing time-based sampling and assessment of isotopic labeling kinetics. The FT-IR and O-PTIR, along with the second derivative spectra of E. coli cells cultured in minimal medium supplemented with various combinations of heavy isotopes exhibited notable similarities. Several spectral shifts in primary vibrational peaks were observed due to the incorporation of heavy isotopes into biomolecules. Remarkably, the incorporation of deuterium into amide groups, resulting in the formation of nitrogen-deuterium bonds, caused a shift in amide A and B into the silent region, overlapping with CD signature peaks. The incorporation of 18O into the ester group of lipids and the carbonyl group of proteins resulted in a notable shift to the lower wavenumber region. Additionally, the second derivative of FT-IR spectral data highlighted the integration of 18O into α-helix and β-sheet structures. Furthermore, the spectra, second derivative, and PC-DFA scores plot of FT-IR data collectively illustrated the practicality of monitoring 13C and D incorporation into E. coli bacterial cells within the first 30-min incubation period. Significance: The findings of this study suggest that FT-IR and O-PTIR can serve as efficient tools for monitoring the incorporation of heavy isotopes into bacteria at both the population and single-cell levels. Additionally, the SIP approach allowed us to assign two new deuterium-associated vibrational peaks to their corresponding functional groups, which to the best of our knowledge have not been reported previously.

Structure-function relationship of PE11 esterase of Mycobacterium tuberculosis with respect to its role in virulence

The lipolytic enzymes of Mycobacterium tuberculosis play a critical role in immunomodulation and virulence. Among these proteins, PE11 which also belongs to the PE/PPE family, is the smallest (∼10.8 kDa) and play a significant role in cell wall remodelling and virulence. PE11 is established to be an esterase, but its enzymatic and structural properties are not yet characterized. In this study, using homology modelling we deduced the putative structure which shows the presence of both α-helix and β-sheet structures which is in close agreement with that observed by CD spectra of the purified protein. PE11 was found to contain a Gx3Sx4G motif homologous to canonical ‘GxSxG’ motif present in many serin hydrolases. The catalytic triad appears to be located within this motif as substitution of Serine26 and Glycine31 residues abrogated its enzymatic activity. Gel-filtration chromatography data indicate that PE11 possibly exists as dimer and tetramer showing positive cooperativity for binding its substrates. In addition, PE11 esterase activity was found to be critical for cell wall remodelling, antibiotic resistance and conferring survival advantages to M. tuberculosis. Our data suggest that PE11 can be targeted for designing potential therapeutic strategies.

Improving the mechanical property of silk by feeding silkworm with chiral carbon dots

The influence of chiral materials on organisms is crucial. However, there is little research on the impact of chiral carbon dots (CDs), a kind of typical chiral materials, on biology. Herein, chiral CDs (L-/D-CDs) were synthesized using the thermal polymerization method from citric acid and chiral cysteine. The effect of chiral CDs on silkworms was explored through feeding silkworms with chiral CDs. The breaking strength of silk fibers (667.9 MPa) in D-CDs group exhibit a 71.4 % increase compared with control-silk (389.5 MPa), while the breaking strength of silk fibers in L-CDs group increases by 51.6 %. In addition, Fourier transform infrared spectra display CDs can prevent the transformation from random coil/α-helix structures to β-sheet structures. Furthermore, D-CDs group exhibit the highest percentage of four primary amino acids (glycine, alanine, serine, and tyrosine) relative to the total amino acids in silkworm hemolymph. This percentage is elevated by 70.5 % compared to the control group, thereby furnishing an ample supply of raw materials for the synthesis of silk proteins. In contrast, L-CDs group exhibits increase by 39.3 %. Our work provides new ideas and approaches for studying the effects of chiral materials on living organisms.

Unveiling molecular mechanism underlying inhibition of human islet amyloid polypeptide fibrillation by benzene carboxylic acid-peptide conjugate

Type 2 diabetes (T2D) is linked to the apoptosis of insulin-producing β-cells due to the aberrant fibrillation of the human islet amyloid polypeptide (hIAPP or amylin) to cytotoxic aggregates. Profit et al. generated conjugates (C1–C7) by appending benzene carboxylic acids of varying charges to the N-terminal of hIAPP22-29 fragment peptide NFGAILSS to modulate hIAPP fibrillation and cytotoxicity. C5 (4 µM) derived by conjugating low-cost, commercially available benzene-1,2,4,5-tetracarboxylic acid known as pyromellitic acid to NFGAILSS completely abolishes the hIAPP (40 µM) self-assembly as noted in the thioflavin T (ThT) fluorescence assay. The circular dichroism (CD) spectra highlighted that C5 stabilized hIAPP in a distinctive conformation and blocked its conformational switching to amyloidogenic β-sheet structure. C5 possessing a charge-dense pyromellitic acid moiety appended on the N-terminal region of self-recognition hIAPP fragment sequence NFGAILSS created significant interest as it effectively inhibited hIAPP fibrillation and possessed lower molecular mass, smaller size, and charge as compared to hIAPP aggregation inhibitor EEEENFGAILSS (P10). However, it remains unclear how C5 traps hIAPP into a unique conformation that abolishes its self-aggregation propensity. Thus, molecular dynamics (MD) simulations have been employed to illuminate the conformational transitions and structural changes in hIAPP on the inclusion of C5. C5 displayed high-affinity binding interactions to hIAPP (ΔGbinding = −37.11 ± 3.72 kcal/mol) with major contributions from the van der Waals and electrostatic interactions. Furthermore, residue-specific binding free energy analysis depicted high-affinity binding interactions of C5 with Phe15, His18, Asp21, and Tyr37 of hIAPP that play a crucial role in hIAPP fibrillation. The negatively charged carboxylate groups of pyromellitic acid moiety of C5 displayed interactions with the key residues of hIAPP as noted in the conformational clustering analysis. Notably higher sampling of helix from 24.00 ± 0.84 % in hIAPP to 34.20 ± 1.92 % in hIAPP–C5 is consistent with the CD studies, which depicted that C5 trapped hIAPP monomer in a conformation that blocked its self-association. MD simulations illuminated the molecular mechanism and atomistic details of the C5 interactions with hIAPP, which are responsible for its inhibitory activity against hIAPP fibrillation and alleviating hIAPP aggregates-induced cytotoxicity.

The synergistic enhancement or inhibition of different molecular weight components of mannoproteins after ultrafiltration on the encapsulation.

This study investigated the effects of molecular weight regulation on mannoproteins (MPs) in encapsulating both monomeric and oligomeric proanthocyanidins (MOPC). To achieve this, two different conformations of MPs were fractionated by ultrafiltration into two main molecular weight components. The results indicated that regulating molecular weight through ultrafiltration altered the conformation of MPs chains, which in turn affected the intermolecular forces with MOPC. Specifically, the interactions among the different molecular weight components of MPs formed a cross-linking network. High molecular weight components provided external support to this network, while low molecular weight components contributed to internal stabilization. The dense, flexible, and irregular coil structure of MPs facilitated the entry of MOPC into the internal spaces of the cross-linking network. Additionally, protein unfolding into a more stable β-sheet structure further stabilized MPs' cross-linking network, enhancing its capacity to encapsulate MOPC. The presence of more hydrophobic regions and positive charges within the proteins increased the number of binding sites for MOPC. This study aimed to identify the primary structural forms of MPs with potent initial bitter inhibition capabilities on MOPC, and a proposed ultrafiltration method was introduced to modify the triple helix structure of polysaccharide, offering a foundational theoretical framework for enhancing the functional attributes of current or prospective MPs. Additionally, the mixed regulation of polysaccharides with varying conformations was also beneficial for guiding the production of high-efficiency polysaccharide products.

A strategy for improving the mechanical properties of silk fibers through the combination of genetic manipulation and zinc ion crosslinking

Silk fiber is generally considered an excellent biological material due to its good biocompatibility, morphological plasticity and biodegradability. Previously, the construction of silkworm silk gland bioreactors based on the piggyBac transposon has been optimized. However, the inserted exogenous genes have problems such as position uncertainty, and expression is not strictly controlled. Here, we applied transcription activator-like effector nuclease (TALEN)-mediated homology-directed repair (HDR) to precisely insert histidine-rich cuticular protein (CP) into silkworm Sericin1 (Ser1) gene. The Ser1-CP fusion protein was successfully secreted into cocoon shell. Subsequently, based on the metal coordination ability of the histidine imidazole group, we crosslinked cocoon with metal ions in vitro. In this strategy, the mechanical properties of the fused silk fibers with crosslinked Zn2+ improved, and the maximum breaking stress of the crosslinked Zn2+-fused silk fibers was 23.5 % greater than that of the wild-type fibers. Analysis of the secondary structure of the silk protein showed that the fused silk fibers crosslinked with Zn2+ had more β-sheet structures. This study pioneered a method of improving the mechanical properties of silk fibers by crosslinking metal ions with fused exogenous proteins and expanded the application value of silk gland bioreactors in the development of novel biomaterials.

Effect of protease hydrolysis on the structure of acidic heating-induced soy protein amyloid fibrils

The effectiveness of using amyloid fibrillation to improve the functional qualities of soy protein had drawn growing attention. However, the relationship between protein subunits and the structural polymorphism of soy protein-derived amyloid fibrils (SAFs) was not yet completely understood. In this study, soy protein subunits were hydrolyzed to different degrees according to the different action sites of different proteases (Pepsin, Papain and Alcalase). The impact of subunits on the amyloid fibrillation of soy protein was investigated through various techniques including atomic force microscopy, thioflavin T fluorescence, 1-anililo-naphthalene-8-sulfonate, and Fourier transform infrared spectrometer. The findings showed that the α and α’ subunits were associated with the formation of fibril branch chains. The degree of hydrolysis of β subunits was found to be proportional to the number of fibrils. The presence of the 11S component was identified as a necessary condition for the formation of long-rigid fibrils. Furthermore, enzymatic hydrolysis unfolded the protein structure, exposing hydrophobic groups, loosening the protein structure, and altering the proportion of parallel and antiparallel β-sheet structures. This promoted the formation of amyloid fibrils and accelerated the development of stable SAFs gel. This study advances the knowledge of the function of subunits in amyloid fibrillation.

Unravelling the Complexity of Amyloid Peptide Core Interfaces.

Amyloids, large intermolecular sandwiched β-sheet structures, underlie several protein misfolding diseases but have also been shown to have functional roles and can be a basis for designing smart and responsive nanomaterials. Short segments of proteins, called aggregation-prone regions (APRs), have been identified that nucleate amyloid formation. Here we present the database of 173 APR crystal structures currently available in the PDB, and a tool, ACW, for analyzing their topologies and the 267 inter-β-sheet interfaces of zipper regions assigned in these structures. We defined a new descriptor of zipper interfaces, the surface detail index (SDi), which quantifies the intertwining between the side chains of both β-sheets of the zipper, an important factor for the molecular recognition and self-assembly of these mesostructures. This allowed a comparative analysis of the zipper interfaces and identification of 6 clusters with different intertwining, steric fit, and size characteristics using three complementary descriptors, SDi, shape complementarity, and buried surface area. 60% of the APR structures are formed by parallel β-sheets, of which 52% belong to the topological class 1. This could be explained by the better fit and a deeper entanglement of the zipper regions of the parallel structures than of the antiparallel structures, as the analysis showed that both their shape complementarity (0.79 vs 0.70) and SDi (1.53 vs 1.32) were higher. The higher abundance of certain residues (Asn and Gln in parallel and Leu and Ala in antiparallel β-sheets) can be explained by their ability to form different ladder-like secondary interaction patterns within β-sheets. Analogous to the hierarchy of protein structure, we interpreted the primary, secondary, tertiary, and quaternary structure levels of APRs revealing different characteristics of the zipper regions for both parallel and antiparallel β-sheet structures, which may provide clues to the structural conditions of amyloid core formation and the rational design of amyloid polymorphs.

3D printed conductive hydrogel based on silk fibroin and tetramer-grafted-polyethylenimine micelle for body-motion monitoring

Conductive hydrogels hold significant promise for applications in flexible wearable, soft robotics, implantable devices, and other fields, which offer distinct advantages due to their biomimetic structures, intrinsic properties, and biocompatibility. This study builds upon our previous research by fabricating a conductive hydrogel through the combination of 30 % Pluronic F127 and aniline tetramer-grafted-polyethyleneimine (AT-PEI) copolymers. To enhance the properties of hydrogels, we successfully engineered silk fibroin-based conductive hydrogels (SF-AD) by inducing the transition of silk fibroin from a random coil to a β-sheet structure using the F127 and AT-PEI/DNA complex (AD), endowing the hydrogels with dual ionic and electronic conductivity. The conductivity of all hydrogel exceeds 10−4 S/cm. Additionally, SEM was employed to characterize the pore size of the hydrogels, revealing a decrease with higher AD content. The swelling ratio ranged between 4.89 and 6.50, indicating the tunable nature of the hydrogels' structure. Utilizing 3D printing, we produced a 2 × 2 cm2 mesh active conductive layer that ensures a more uniform stress distribution—maximum sensitivity with a grid width of 4 mm. Our assembled hydrogel sensor demonstrated long-term stability in cycling tests over 1000 cycles and proved capable of recognizing various human movements. The SF-AD hydrogel, characterized by its unique combination of properties and potential for customization, presents broad prospects for future applications in flexible electronics.

Improving the Gelation Properties of Pea Protein Isolates Using Psyllium Husk Powder: Insight into the Underlying Mechanism.

The industrial application of pea protein is limited due to its poor gelation properties. This study aimed to evaluate the effects of psyllium husk powder (PHP) on improving the rheological, textural, and structural properties of heat-induced pea protein isolate (PPI) gel. Scanning electron microscopy (SEM), intermolecular forces analysis, the quantification of the surface hydrophobicity and free amino groups, and Fourier transform infrared spectroscopy (FTIR) were conducted to reveal the inner structures of PPI-PHP composite gels, conformational changes, and molecular interactions during gelation, thereby clarifying the underlying mechanism. The results showed that moderate levels of PHP (0.5-2.0%) improved the textural properties, water holding capacity (WHC), whiteness, and viscoelasticity of PPI gel in a dose-dependent manner, with the WHC (92.60 ± 1.01%) and hardness (1.19 ± 0.02 N) peaking at 2.0%. PHP significantly increased surface hydrophobicity and enhanced hydrophobic interactions, hydrogen bonding, and electrostatic interactions in PPI-PHP composite gels. Moreover, the electrostatic repulsion between anionic PHP and negatively charged PPI in a neutral environment prevented the rapid and random aggregation of proteins, thereby promoting the formation of a well-organized gel network with more β-sheet structures. However, the self-aggregation of excessive PHP (3.0%) weakened molecular interactions and disrupted the continuity of protein networks, slightly reducing the gel strength. Overall, PHP emerged as an effective natural gel enhancer for the production of pea protein gel products. This study provides technical support for the development of innovative plant protein-based foods with strong gel properties and enriched dietary fiber content.

Evaluation of bacterial anti-adhesion and sustained antimicrobial abilities of chlorhexidine gluconate-loaded phase-transited lysozyme nanoparticle suspension on dentine: An exvivo study.

To evaluate the effect of chlorhexidine gluconate-loaded phase-transited lysozyme (CHG@PTL) coating on inhibiting bacterial adhesion and biofilm formation in an exvivo root canal dentine model. The physicochemical and structural characteristics of CHG@PTL nanoparticle suspension and its coating formed on the dentine surface were analysed by thioflavin T fluorescence assay, transmission electron microscopy and confocal laser scanning microscopy (CLSM). The sustained chlorhexidine release profile of the CHG@PTL coating on the dentine surface was compared with that of the 2% CHG solution. By comparing with phosphate-buffered saline, 1% sodium hypochlorite and 2% CHG solutions, the sustained antibacterial ability of the CHG@PTL coating and its effects on adhesion and biofilm formation of three types of bacteria (E. faecalis, S. mutans, and A. viscous) were analysed in exvivo root canal dentine models using the serial plate transfer test (SPTT) and CLSM with live/dead bacterial staining, respectively. CHG promoted the lysozyme protein to form a higher proportion of β-sheet structure during phase transition. In the CHG@PTL nanoparticle suspension, characteristic drug-loaded nanospheres with a high concentration of CHG molecules inside and an outer PTL nanofilm were observed, and they formed a thinner and tighter coating on the dentine surface. The CHG@PTL coating on the dentine surface showed a significantly higher cumulative release amount of chlorhexidine than that of 2% CHG (p < .05). The results of SPTT showed that the CHG@PTL coating had a longer antibacterial duration than the control groups. After 12 h of incubation, a higher number of bacteria were agglutinated on the CHG@PTL coating surface compared to the control groups (p < .05). After 7 days of incubation, the number of agglutinated bacteria significantly decreased. At two time points, the percentage of dead bacteria on the CHG@PTL coating surface was the highest among all experimental groups based on CLSM observation (over 99.9% for all three bacteria, p < .001). CHG@PTL nanoparticle suspension could form an antimicrobial coating on the surface of dentine with a novel 'agglutinating bacteria and sterilizing' mode.

Isotope Reverse-Labeled Infrared Spectroscopy as a Probe of In-Cell Protein Structure.

While recent years have seen great progress in determining the three-dimensional structure of isolated proteins, monitoring protein structure inside live cells remains extremely difficult. Here, we examine the utility of Fourier transform infrared (FTIR) spectroscopy as a probe of protein structure in live bacterial cells. Selective isotope enrichment is used both to distinguish recombinantly expressed NuG2b protein from the cellular background and to examine the conformation of specific residues in the protein. To maximize labeling flexibility and to improve spectral resolution between label and main-band peaks, we carry out isotope-labeling experiments in "reverse-labeling" mode: cells are initially grown in 13C-enriched media, with specific 12C-labeled amino acids added when protein expression is induced. 1 Because FTIR measurements require only around 20 μL of sample and each measurement takes only a few minutes to complete, isotope-labeling costs are minimal, allowing us to label multiple different residues in parallel in simultaneously grown cultures. For the stable NuG2b protein, isotope difference spectra from live bacterial cultures are nearly identical to spectra from isolated proteins, confirming that the structure of the protein is unperturbed by the cellular environment. By combining such measurements with site-directed mutagenesis, we further demonstrate that the local conformation of individual amino acids can be monitored, allowing us to determine, for example, whether a specific site in the protein contributes to α-helix or β-sheet structures.

Interactions of the Biphenylene Network with α-Helical and β-Sheet Proteins: Molecular Dynamics Simulations.

In recent years, nanomaterials have been widely used in the biomedical field. The biphenylene network is a highly promising planar carbon nanomaterial. To better explore its biomedical applications, we need to understand the biological effects of the biphenylene network. To investigate the biological effects of the novel nanomaterial biphenylene network, we used molecular dynamics simulations to study the interactions of the novel planar carbon nanomaterial biphenylene network with α-helical and β-sheet proteins. We found that both types of proteins adsorb flatly on the surface of the biphenylene network; the strong van der Waals interaction is the main adsorption force, while π-π stacking also provides an auxiliary force for the adsorption. When the HP35 protein whose secondary structure is an α-helix was adsorbed on biphenylene network, the entire structure of α-helix 2 was disrupted and α-helix 3 partly recovered its helical structure after being disrupted. In contrast to the β-sheet YAP65 protein, only part of the structure of β-sheet 1 was disrupted. Therefore, the biocompatibility of the biphenylene network with the β-sheet YAP65 protein is better than that of the α-helical HP35 protein, which may be due to the different surface curvature of the protein's secondary structure. Our research promotes the application of the biphenylene network in biomedicine and provides a theoretical basis and experimental direction for practical experiments.

Phosphate-Driven Interfacial Self-Assembly of Silk Fibroin for Continuous Noncovalent Growth of Nanothin Defect-Free Coatings.

Silk fibroin is a fiber-forming protein derived from the thread of Bombyx mori silkworm cocoons. This biocompatible protein, under the kosmotropic influence of potassium phosphate, can undergo supramolecular self-assembly driven by a random coil to β-sheet secondary structure transition. By leveraging concurrent nonspecific adsorption and self-assembly of silk fibroin, we demonstrate an interfacial phenomenon that yields adherent, defect-free nanothin protein coatings that grow continuously in time, without observable saturation in mass deposition. This noncovalent growth of silk fibroin coatings is a departure from traditionally studied protein adsorption phenomena, which generally yield adsorbed layers that saturate in mass with time and often do not completely cover the surface. Here, we explore the fundamental mechanisms of coating growth by examining the effects of coating solution parameters that promote or inhibit silk fibroin self-assembly. Results show a strong dependence of coating kinetics and structure on solution pH, salt species, and salt concentration. Moreover, coating growth was observed to occur in two stages: an early stage driven by protein-surface interactions and a late stage driven by protein-protein interactions. To describe this phenomenon, we developed a kinetic adsorption model with Langmuir-like behavior at early times and a constant steady-state growth rate at later times. Structural analysis by FTIR and photoinduced force microscopy show that small β-sheet-rich structures serve as anchoring sites for absorbing protein nanoaggregates, which is critical for coating formation. Additionally, β-sheets are preferentially located at the interface between protein nanoaggregates in the coating, suggesting their role in forming stable, robust coatings.

Orientation Distribution of Crystalline β-Sheet Domains in Bombyx mori Silk Fiber Studied with Vibrational Sum Frequency Generation Spectroscopy.

Silk fibers have good biocompatibility and mechanical properties, which make them attractive in biomaterial applications as well as textile industries. It is believed that the superior mechanical property is associated with the crystalline β-sheet structure in the fiber; but a deeper understanding of the structure-property relationship is still needed for full exploitation of its physical properties. Especially, accurate information on hydrogen-bonding interactions within β-sheet domains at the nanoscale and their spatial distributions at the mesoscale are critically needed. In this study, we demonstrate the selective detection of crystalline β-sheet domains in Bombyx mori silk fiber using sum frequency generation (SFG) spectroscopy and its use to determine the angular distribution of the β-sheet crystallites with respect to the fiber axis. Numerical simulations of the SFG signal of the amide-I band were carried out using tensors based on the B2 symmetry of the D2 point group and compared with experimental data. This comparison found that the crystalline β-sheet domains are aligned along the fiber axis with a standard deviation of ∼27° and parallel to the fiber surface with a standard deviation of ∼5°. It was also found that the amide bands in the SFG spectra cannot be fully explained with the assumption that the crystalline β-sheet vibrations can be described with the D2 point group. Being able to monitor the amide group vibrations sensitive to both interchain hydrogen bonding and crystallite orientations, SFG analysis has a potential to unveil the structure-mechanical property relationship that may not be readily assessable with other characterization techniques.

Disruption of PHF6 Peptide Aggregation from Tau Protein: Mechanisms of Palmatine Chloride in Preventing Early PHF6 Aggregation.

The formation of neurofibrillary tangles (NFTs), composed of tau protein aggregates, is a hallmark of neurodegenerative diseases known as tauopathies, including Alzheimer's disease (AD). NFTs consist of paired helical filaments (PHFs) of tau protein with a dominant β-sheet secondary structure. Within these PHFs, the PHF6 hexapeptide (Val306-Gln-Ile-Val-Tyr-Lys311) has been commonly highlighted as a key site for tau protein nucleation. Palmatine chloride (PC) has been identified as an inhibitor of PHF6 aggregation, capable of reducing aggregation propensity at submicromolar concentrations. In pursuit of novel anti-AD drugs targeting early tau aggregation stages, we conducted an in silico study to elucidate PC's mechanism of action during PHF6 aggregation. Our observations suggest that while PHF6 can still initiate self-aggregation in the presence of PC, PC molecules subtly influence PHF6 aggregation dynamics, favoring smaller aggregates over larger complexes. The study underlined the key roles of aromatic rings in PC binding to different PHF6 aggregates by interacting through π-π stacking with the PHF6 Tyr310 side chain. The presence of aromatic rings in compounds to be able to inhibit the earlier complexation phase seems to be essential. These in silico findings lay a foundation for the design of compounds that could intervene in resolving the neurotoxicity of protein aggregates in AD.

Effect of β-sitosterol+γ-oryzanol-based oleogels on protein conformation and gel properties of Nemiperus virgatus surimi.

The impact of β-sitosterol+γ-oryzanol-based oleogels or peanut oil on the protein conformation and gel quality of Nemiperus virgatus surimi was evaluated. A significant reduction in gel strength, texture parameters and water holding capacity (WHC) of surimi was found as oil concentration increased (P < 0.05). However, compared with peanut oil, the gel strength, hydrophobic interaction and disulfide bond content of surimi gel containing oleogels increased by 6.919%, 32.635% and 12.409%, respectively, when the oil concentration was 10 g kg-1. Both oleogels and peanut oil could enhance the whiteness of surimi gel. Oleogels induced the unfolding of surimi proteins, and promoted the conformational shift from α-helix to β-sheet structure. Furthermore, oleogels filled the gaps of protein networks to make the microstructure of surimi gel more compact and uniform, improving the WHC and reducing the cooking loss. γ-Oryzanol+β-sitosterol-based oleogel alleviated the adverse influences of direct addition of peanut oil on the gel and textural properties of surimi products. © 2024 Society of Chemical Industry.

Modulation of SpyCatcher Ligation Kinetics by SpyTag Thioamide Substitution.

Thioamide substitutions have been shown to impart valuable properties on peptides for biophysical experiments as well as cell or in vivo studies, but a rational understanding of thioamide effects on protein structure and protein-protein interactions is lacking. To elucidate their effects in β-sheet structures, we have used SpyCatcher003-SpyTag003 as a host-guest system to study individual thioamide incorporation at eight different positions in the SpyTag peptide. We have demonstrated that incorporating thioamides into SpyTag at specific positions can result in a ∼2-fold faster ligating complex, as well as >2000-fold slower ligating complex. Biophysical analysis and structural modeling provide a reasonable explanation for most of the thioamide effects, altering hydrogen bond networks as well as modulating an n→π* interaction within the SpyTag peptide. Our findings have important implications for potential applications of thioamide SpyTag variants, where the thioamide could impart protease stability in cells while also controlling the rate of ligation to SpyCatcher. These SpyCatcher-SpyTag host-guest experiments will also help to build a database for predicting thioamide effects on protein structure and function.

Peptide programming of supramolecular vinylidene fluoride ferroelectric phases.

Ferroelectric structures have spontaneous macroscopic polarization that can be inverted using external electric fields and have potential applications including information storage, energy transduction, ultralow-power nanoelectronics1,2 and biomedical devices3. These functions would benefit from nanoscale control of ferroelectric structure, the ability to switch polarization with lower applied fields (low coercive field) and biocompatibility. Soft ferroelectrics based on poly(vinylidene fluoride) (PVDF)4-6 have a thermodynamically unstable ferroelectric phase in the homopolymer, complex semi-crystalline structures, and high coercive fields. Here we report on ferroelectric materials formed by water-soluble molecules containing only six VDF repeating units covalently conjugated to a tetrapeptide, with the propensity to assemble into the β-sheet structures that are ubiquitous in proteins. This led to the discovery of ribbon-shaped ferroelectric supramolecular assemblies that are thermodynamically stable with their long axes parallel to both the preferred hydrogen-bonding direction of β-sheets and the bistable polar axes of VDF hexamers. Relative to a commonly used ferroelectric copolymer, the biomolecular assemblies exhibit a coercive field that is two orders of magnitude lower, as the result of supramolecular dynamics, and a similar level of remnant polarization, despite having a peptide content of 49 wt%. Furthermore, the Curie temperature of the assemblies is about 40 °C higher than that of a copolymer containing a similar amount of VDF. This supramolecular system was created using a biologically inspired strategy that is attractive in terms of sustainability and that could lead to new functions for soft ferroelectrics.