Globular Proteins Research Articles

The Functionality of IbpA from Acholeplasma laidlawii Is Governed by Dynamic Rearrangement of Its Globular-Fibrillar Quaternary Structure.

Small heat shock proteins (sHSPs) represent a first line of stress defense in many bacteria. The primary function of these molecular chaperones involves preventing irreversible protein denaturation and aggregation. In Escherichia coli, fibrillar EcIbpA binds unfolded proteins and keeps them in a folding-competent state. Further, its structural homologue EcIbpB induces the transition of EcIbpA to globules, thereby facilitating the substrate transfer to the HSP70-HSP100 system for refolding. The phytopathogenic Acholeplasma laidlawii possesses only a single sHSP, AlIbpA. Here, we demonstrate non-trivial features of the function and regulation of the chaperone-like activity of AlIbpA according to its interaction with other components of the mycoplasma multi-chaperone network. Our results show that the efficiency of the A. laidlawii multi-chaperone system is driven with the ability of AlIbpA to form both globular and fibrillar structures, thus combining functions of both IbpA and IbpB when transferring the substrate proteins to the HSP70-HSP100 system. In contrast to EcIbpA and EcIbpB, AlIbpA appears as an sHSP, in which the competition between the N- and C-terminal domains regulates the shift of the protein quaternary structure between a fibrillar and globular form, thus representing a molecular mechanism of its functional regulation. While the C-terminus of AlIbpA is responsible for fibrils formation and substrate capture, the N-terminus seems to have a similar function to EcIbpB through facilitating further substrate protein disaggregation using HSP70. Moreover, our results indicate that prior to the final disaggregation process, AlIbpA can directly transfer the substrate to HSP100, thereby representing an alternative mechanism in the HSP interaction network.

Oligomeric and Fibrillar α-Synuclein Display Persistent Dynamics and Compressibility under Controlled Confinement.

The roles of α-synuclein in neurotransmitter release in brain neurons and in the Parkinson's disease condition have challenged comprehensive description. To gain insight into molecular mechanistic properties that actuate α-synuclein function and dysfunction, the coupled protein and solvent dynamics of oligomer and fibril forms of human α-synuclein are examined in a low-temperature system that allows control of confinement and localization of a motionally sensitive electron paramagnetic resonance spin probe in the coupled solvent-protein regions. The rotational mobility of the spin probe resolves two distinct α-synuclein-associated solvent components for oligomers and fibrils, as for globular proteins, but with dramatically higher fluidities at each temperature, that are comparable to low-confinement, aqueous-cryosolvent mesophases. In contrast to the temperature-independent volumes of the solvent phases that surround globular and condensate-forming proteins, the higher-fluidity mesophase volume of α-synuclein oligomers and fibrils decreases with decreasing temperature, signaling a compression of this phase. This unique property and thermal hysteresis in the mobilities and component weights, together with previous high-resolution structural characterizations, suggest a model in which the dynamically disordered C-terminal domain of α-synuclein creates a compressible phase that maintains high fluidity under confinement. Robust dynamics and compressibility are fundamental molecular mechanical properties of α-synuclein oligomers and fibrils, which may contribute to dysfunction and inform about function.

Dermoscopic Diagnosis of a Non-Pigmented Skin Tumor: Eccrine Poroma

Dear Editor, Eccrine poroma stands as a benign adnexal neoplasm that originates from the acrosyringium. It typically emerges as solitary, flesh-colored, or erythematous papules, plaques, or nodules, primarily appearing in areas with sweat glands. As well as pigmented lesions, dermoscopy has proven to enhance the clinical diagnosis of numerous non-pigmented skin tumors, including eccrine poroma. Herein we present a case of eccrine poroma located on the dorsal aspect of the left foot, with characteristic dermoscopic features. A 60-year-old woman was admitted with an asymptomatic lesion on the dorsum of her left foot, which had manifested approximately four years before. Clinically, the lesion presented as a well-circumscribed, violaceous, 0.9x0.9 cm papule (Figure 1a). Dermoscopic examination revealed flower-like and leaf-like vascular patterns, white interlacing areas, glomerular vessels, and milky red globules (Figures 1c-d). The lesion was excised and histopathologic findings were consistent with eccrine poroma (Figure 1b). Eccrine poroma (EP) is an adnexal tumor originating in the intraepidermal part of the eccrine sweat gland duct. Dermoscopy and histopathology help to differentiate EP from pyogenic granuloma, seborrheic keratosis, verruca vulgaris, basal cell carcinoma, squamous cell carcinoma, and amelanotic melanoma. Well-defined dermoscopic features in EP are: White interlacing areas around vessels, milky-red globules, flower-like and leaf-like vascular patterns, glomerular vessels, hairpin vessels, yellow structureless areas, poorly visualized vessels, and well-circumscribed globular or lacuna-like structures separated by white to pink mesh bands [1-3]. Histologically, EP manifests as a well-contained tumor constituted of proliferative cuboidal or poroid cells, often extending from the basal epidermis into the dermal layer. Shave, electrosurgical destruction or simple excision may be the treatment of lesions, depending on the depth of the lesion. Kind Regards

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Subcritical water‐treated soy protein‐gum Arabic core‐shell nanoparticles as phytosterol carriers

SummarySoy protein‐gum Arabic (GA) core‐shell nanoparticles were fabricated as carriers for hydrophobic phytosterol (PS) using an anti‐solvent precipitation (pH 7.0) and then coating GA on the surface of protein‐based PS nanoparticles at pH 4.5. PS nanoparticles stabilised by heat‐treated soy protein isolate (SPI), especially subcritical water‐treated SPI (SW, 120 °C), exhibited higher encapsulation efficiency (EE), loading amount (LA) and colloidal stability than native SPI‐stabilised PS nanoparticles. The highly flexible conformation and more exposed hydrophobic clusters of SW‐treated SPI could result in a quick encapsulation of more PS into the interior of protein molecules during anti‐solvent precipitation. However, for native SPI with rigid globular structure, the loading of PS mainly occurred on the surface hydrophobic sites of protein molecules. After introducing GA (≥5 mg mL−1) to PS nanoparticles fabricated by SW‐treated SPI, submicron‐sized (Dh 250.71~341.76 nm) core‐shell nanoparticles with high acid solubility and thermal stability were formed. The coating of GA decelerated the digestion of SW‐treated SPI, and improved the EE, LA and in vitro bioaccessibility of PS under acidic environment. These results reveal the protein structure dependence of PS encapsulation and provide a simple approach to fabricate biopolymer‐based nanoparticle delivery system for hydrophobic bioactives in acidified functional drinks.

Phosphorylated pullulan promotes calcification during bone regeneration in the bone defects of rat tibiae.

The current study aimed to evaluate bone tissue regeneration using a combination of β-tricalcium phosphate (βTCP) and phosphorylated pullulan (PPL, a phosphate-rich polysaccharide polymer consisting of maltotriose units). Round defects of 2mm diameter were created in the arterial center of rat tibiae, which were further treated with vehicle (control group), βTCP (βTCP group), or βTCP + PPL (βTCP + PPL group) grafts. The control specimens without bone grafts exhibited rapid bone formation after 1week; however, the regenerated bone was not resorbed until 4weeks. In contrast, βTCP-grafted specimens exhibited fewer but thicker trabeculae, whereas the βTCP + PPL group displayed many fine trabeculae at 4weeks. In the βTCP + PPL group, new bone was associated with the βTCP granules and PPL. Similarly, PHOSPHO1-positive osteoblasts were localized on the βTCP granules as well as the PPL. On the other hand, TRAP-reactive osteoclasts predominantly localized on newly-formed bone and βTCP granules rather than on the PPL. No significant differences were observed in the expression of Alp, Integrin αv, Osteopontin, Osteocalcin, and Dmp-1 in PPL-treated MC3T3-E1 osteoblastic cells, suggesting that PPL did not facilitate osteoblastic differentiation. However, von Kossa staining identified abundant needle-like calcified structures extending inside the PPL. Furthermore, transmission electron microscopy (TEM) revealed many globular structures identical to calcified nodules. In addition, calcified collagen fibrils were observed in the superficial layer of the PPL. Thus, PPL may serve as a scaffold for osteoblastic bone formation and promotes calcification on its surface. In conclusion, we speculated that βTCP and PPL might promote bone regeneration and could be integrated into promising osteoconductive materials.

Air-water interface properties and foam stabilization by mildly extracted lentil protein

Lentil proteins have shown potential as substitutes for animal proteins in foam-based food products, although the mechanisms by which the proteins stabilize the air-water interface are largely unexplored. Here, we systematically studied the air-water interfacial behavior (including adsorption kinetics, and interfacial dilatational and shear rheology), interfacial structures and foaming properties of mildly extracted lentil protein isolate (LPI). We compared these properties of LPI with two animal-based proteins commonly used in food industry, i.e., dairy-derived whey protein isolate (WPI) and egg-derived egg white protein isolate (EPI). The mildly extracted LPI had high protein content (85.2%), high protein solubility (91%) and high nativity, with a globulin-to-albumin ratio of 81:19. LPI adsorbed fast at the air-water interface, showing a foam overrun of 285% that is comparable with WPI and EPI. Although LPI formed interfaces with lower stiffness than EPI, it showed comparable foam half-life time (115 min) with EPI, due to the higher thickness of the interface formed by LPI, which is dominated by lentil globular protein particles with a size around 11 nm. The lentil globular proteins appear to have weaker in-plane interactions than smaller WPI molecules at the air-water interface, resulting in a pronouncedly lower interfacial stiffness and foam half-life time of LPI compared to WPI (295 min). However, the LPI-formed interface is more stretchable than the WPI-formed interface and shows less disruption in both large dilatational and shear deformations. Thus, LPI might have comparable or better performance than WPI in stabilizing foam under processing conditions. Overall, lentil proteins have good foaming properties and could be applied as an animal-based protein replacer in producing foam-based food products.

Microscopy and modelling investigations on the morphology of the biofilm exopolysaccharide produced by Burkholderia multivorans strain C1576

Bacteria form very often biofilms where they embed in a self-synthesized matrix exhibiting a gel-like appearance. Matrices offer several advantages, including defence against external threats and the easiness of intercellular communication. In infections, biofilm formation enhances bacteria resistance against antimicrobials, causing serious clinical problems for patients' treatments. Biofilm matrices are composed of proteins, extracellular DNA, and polysaccharides, the latter being the major responsible for matrix architecture. The repeating unit of the biofilm polysaccharide synthesized by Burkholderia multivorans strain C1576 contains two mannoses and two sequentially linked rhamnoses, one of them 50 % methylated on C-3. Rhamnose, a 6-deoxysugar, has lower polarity than other common monosaccharides and its methylation further reduces polarity. This suggests a possible role of this polysaccharide in the biofilm matrix; in fact, computer modelling and atomic force microscopy studies evidenced intra- and inter-molecular non-polar interactions both within polysaccharides and with aliphatic molecules. In this paper, the polysaccharide three-dimensional morphology was investigated using atomic force microscopy in both solid and solution states. Independent evidence of the polymer conformation was obtained by transmission electron microscopy which confirmed the formation of globular compact structures. Finally, data from computer dynamic simulations were used to model the three-dimensional structure.

OR14-01 Contact Between Thyroglobulin Opposite Domains Assists Its Upstream Regions In Intracellular Trafficking For Thyroid Hormonogenesis

Abstract Disclosure: C.E. Citterio: None. K. Kim: None. B. Rajesh: None. K. Pena: None. O.B. Clarke: None. P. Arvan: None. Thyroglobulin (Tg), must be released into the lumen of thyroid follicles to facilitate thyroid hormone synthesis. The Tg primary sequence (∼2,760 amino acids) includes regions I, II, III, as well as ∼570 residues of cholinesterase-like (ChEL) domain (which bears 47% similarity to acetylcholinesterase), folded as a globular protein with multiple contacts between different Tg regions. The ChEL domain is reported to function as an intramolecular chaperone assisting Tg region I. This function cannot be replaced by acetylcholinesterase or neuroligins, indicating a unique function of Tg ChEL. However, the specific amino acids of ChEL neighboring upstream Tg regions have only recently been identified, and the key functional residues for Tg folding remain unknown. Here, we’ve combined structural analyses with functional characterization of recombinant Tg expressed in cell culture. We’ve identified hTg-ChEL K2223 and W2222 as amino acids that exhibit the closest physical proximity with Tg region I. By cryo-EM of Tg (both human and bovine), Tg-K2223 and Tg-W2222 reside only ∼4.5Å from Tg-W1089 and Tg-P1098, respectively, both of which are located in the Tg 1-9 repeat within region I. We’ve employed site-directed mutagenesis to determine the impact of these contacts by studying both full length Tg as well as Tg expressed in a two-component system in cultured cells. We find that secretory ChEL-K2223E and ChEL-W2222A behave much like WT secretory ChEL; both mutants are reasonably well expressed and secreted efficiently. However, when secretory ChEL was co-expressed with Tg region I-II-III lacking its own ChEL domain, region I-II-III secretion could be rescued in the presence of WT secretory ChEL, but not by co-expression of either ChEL-K2223E or ChEL-W2222A. In context of a single contiguous full length Tg, both expression and secretion of Tg-K2223E and Tg-W2222A were significantly diminished. These results highlight two residues (K2223 and W2222) that are not needed for the independent folding (or endoplasmic reticulum export) of the Tg ChEL domain, but are key residues for contacting Tg region I, thereby offering the overall Tg structure a great increase in conformational stability, which is needed to satisfy endoplasmic reticulum quality control requirements for intracellular protein trafficking. These findings point to the possibility that mutations altering regional contacts within the Tg structure could contribute to the molecular pathogenesis of congenital hypothyroidism. Presentation: Friday, June 16, 2023

Formulation, Characterization, and Evaluation of β-Cyclodextrin Functionalized Hypericin Loaded Nanocarriers.

St. John's wort in western Europe has been extensively utilized for the treatment of mild to moderate depression. Hypericin, a red pigment, is found to be responsible for its antidepressant activity. The aim of the current study was to prepare a nanoemulsion (O/W) of hypericin designed for immediate delivery of the drug to the brain for the treatment of depression. The nanoemulsion was prepared by means of a homogenization technique, and that was followed by its physicochemical evaluation. Tween-80, Span-80, β-cyclodextrin, ethanol, and eucalyptus oil were utilized for the manufacturing of the nanoemulsion. Morphological studies have revealed globular structures of nanosize that were confirmed by the zeta analysis. The consistency of particles was revealed by the low polydispersity values. pH values of all formulations lay within the range of nasal pH. The viscosity of the prepared formulations was affected by the increase in concentrations of β-cyclodextrin. After passing from the centrifugation and freeze-thaw studies, the prepared formulations showed good stability. Formulation F2 having a composition of oil phase (0.125 mL), aqueous phase (1.25 mL), and β-cyclodextrin (8%) showed the best results out of all the formulations, and F2 had a pH of 5.7, 5.35 cP viscosity, 1.332 refractive index, 148.8 globule size, and -10.8 zeta potential. The mean percentage drug release and in vitro and ex vivo percentage drug permeations were observed to be 71.75, 76, and 75.07%, respectively. Meanwhile, formulation F2 showed the maximum drug release and permeation. In vivo behavior studies including the open field test, elevated plus maze test, and tail suspension test were conducted to see the antidepressant effect of hypericin along with comparison with a commercially available treatment. In conclusion, the prepared formulation shows good efficacy as an antidepressant and can be considered as a natural alternative over synthetic drugs.

Dynamic Surface Properties of α-Lactalbumin Fibril Dispersions.

The dynamic surface properties of aqueous dispersions of α-lactalbumin (ALA) amyloid fibrils differ noticeably from the properties of the fibril dispersions of other globular proteins. As a result, the protocol of the application of ALA fibrils to form stable foams and emulsions has to be deviate from that of other protein fibrils. Unlike the fibrils of β-lactoglobulin and lysozyme, ALA fibrils can be easily purified from hydrolyzed peptides and native protein molecules. The application of the oscillating barrier method shows that the dynamic surface elasticity of ALA fibril dispersions exceeds the surface elasticity of native protein solutions at pH 2. ALA fibrils proved to be stable at this pH, but the stability breaks at higher pH levels when the fibrils start to release small peptides of high surface activity. As a result, the dynamic surface properties of ALA coincide with those of native protein solutions. The ionic strength strongly influences the adsorption kinetics of both fibril dispersions and native protein solutions but have almost no impact on the structure of the adsorption layers.

The role of hydrophobic interactions in the molten globule state of globular protein modulated by surfactants.

In order to highlight the role of hydrophobic interactions in the molten globule (MG) state of globular protein modulated by surfactants, the interactions of bovine α-lactalbumin (α-LA) with alkyl trimethylammonium bromides (CnTAB, n=10, 12, 14, and 16) have been studied by experimental and theoretical techniques. Isothermal titration calorimetry (ITC) showed that the enthalpy changes (ΔH) and area of the enthalpogram increased with increasing the chain length of CnTAB. The result of fluorescence, circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) spectrum suggested that C10TAB and C12TAB unfolded α-LA partially, C14TAB reconstructed protein with a native-like secondary structure content, and C16TAB induced an MG state α-LA. The SAXS results confirmed that the tertiary structure of α-LA was disrupted by C16TAB forming an MG state complex with a micelle-like structure even at the surfactants concentrations below CMC. As indicated by MD results, the β-domain and unstructured region(s) were involved in the MG state α-LA modulated by CnTAB. This work not only provides molecular insights into the role of hydrophobic interactions in the MG state of a globular protein but also helps understand the mechanism of preparing α-LA based biomacromolecule modulated by hydrophobic interactions.

Experimental investigation of sustainable Corrosion Inhibitor Albumin on low-carbon steel in 1N HCl and 1N H2SO4

Sustainable corrosion inhibitors are being developed as many of them are ecologically friendly, biodegradable, and devoid of heavy metals and other potentially dangerous compounds. Albumin, a member of the globular protein family obtained from egg white, has found its application in a variety of various applications due to its intrinsic pharmacological qualities (anti-bacterial, immunomodulating, and anti-cancer angiotensin-converting enzyme inhibition). Herein, Albumin extract containing atoms with lone pairs of electrons such as Nitrogen (N), Oxygen (O) and having an aromatic ring (unsaturation) has been investigated as an eco-friendly inhibitor for low-carbon steel. The present work studied the inhibition action of Albumin extract for low-carbon steel in 1N acidic chloride and sulfate media using gravimetric, and electrochemical methods, viz potentiodynamic polarization (PDP) and AC impedance studies (EIS). The results obtained from PDP and EIS analysis revealed that the inhibitor exhibited anodic inhibition in 1N HCl (92.72%) and mixed-type but predominantly cathodic inhibition in 1N H2SO4 (79.23%). The studied green corrosion inhibitor followed Langmuir monolayer adsorption and the formation of a protective film on a low-carbon steel surface was confirmed with AFM and FT-IR results. Thus, Albumin extract exhibited excellent corrosion resistance on low-carbon steel.

A Rare Case of Incontinentia Pigmenti in a Male Child with Dermoscopic and Histopathological Correlation

Abstract Incontinentia pigmenti (IP) is a rare X-linked genodermatosis mostly occurring in females with the condition being fatal in males but certain mechanisms may allow survival of male subjects. We report a rare case of IP in a 19-day-old male patient with no history of similar lesions in the family adding to its rarity. The histopathological correlation of the lesions with dermatoscopy showed yellow oil drop-like globular structures correlating with spongiosis in the vesicular stage and verrucous lesions showed brown blotches in a circular pattern with overlying gray-brown dots correlating with hyperkeratosis and dyskeratosis.

The antimicrobial peptide database is 20 years old: Recent developments and future directions.

In 2023, the Antimicrobial Peptide Database (currently available at https://aps.unmc.edu) is 20-years-old. The timeline for the APD expansion in peptide entries, classification methods, search functions, post-translational modifications, binding targets, and mechanisms of action of antimicrobial peptides (AMPs) has been summarized in our previous Protein Science paper. This article highlights new database additions and findings. To facilitate antimicrobial development to combat drug-resistant pathogens, the APD has been re-annotating the data for antibacterial activity (active, inactive, and uncertain), toxicity (hemolytic and nonhemolytic AMPs), and salt tolerance (salt sensitive and insensitive). Comparison of the respective desired and undesired AMP groups produces new knowledge for peptide design. Our unification of AMPs from the six life kingdoms into "natural AMPs" enabled the first comparison with globular or transmembrane proteins. Due to the dominance of amphipathic helical and disulfide-linked peptides, cysteine, glycine, and lysine in natural AMPs are much more abundant than those in globular proteins. To include peptides predicted by machine learning, a new "predicted" group has been created. Remarkably, the averaged amino acid composition of predicted peptides is located between the lower bound of natural AMPs and the upper bound of synthetic peptides. Synthetic peptides in the current APD, with the highest cationic and hydrophobic amino acid percentages, are mostly designed with varying degrees of optimization. Hence, natural AMPs accumulated in the APD over 20 years have laid the foundation for machine learning prediction. We discuss future directions for peptide discovery. It is anticipated that the APD will continue to play a role in research and education.

Неотерический взгляд на sp2 аморфный углерод

Presented is a concentrated synopsis of facilities of empirical and virtual analytics that, once applied, have provided a fully new vision of sp2 amorphous carbons. This study proved that the solids are multilevel structures, started with the first-level basic structural units (BSUs) and accomplished as macroscopic agglomerates of globular structures, consisting, in its turn, of stacked BSUs. BSUs present necklaced graphene molecules, size, and shape of which are governed by the relevant graphene domains while chemical composition in addition to basic carbon is controlled with heteroatoms of the necklaces. This study shows that BSUs and stacks of BSUs determine the short-range order of the solids and are the main subject of the applied analytics. The synopsis consists of two parts related to empirical and virtual analytics. The former is composed of sections related to structural determination, total and atomic chemical content evaluation and elicitation of the covalent bond composition. The second presents new analytic approaches based on the Digital Twins concept and virtual vibrational spectrometry. The synopsis is configured as an atlas composed of generalized pictures accompanied with necessary explanations to be discussed in detail in the extended references.

Single-Molecule Dendritic MRI Nanoprobes Reveal the Size-Dependent Tumor Entrance.

The tumor entrance of drug delivery systems, including therapeutic proteins and nanomedicine, plays an essential role in affecting the treatment outcome. Nanoparticle size is a critical but contradictory factor in making a trade-off among blood circulation, tumor accumulation, and penetration. Here, this work designs a series of single-molecule gadolinium (Gd)-based magnetic resonance imaging (MRI) nanoprobes with well-defined sizes to precisely explore the size-dependent tumor entrance in vivo. The MRI nanoprobes obtained by divergent synthesis contain a core molecule of macrocyclic Gd(III)-chelate and different layers of dendritic lysine units, mimicking globular protein. This work finds that the r1 relaxivity and MR imaging signals increase with the nanoparticle size. The nanoprobe with a lower limit of critical size threshold ≈8.0nm achieves superior tumor accumulation and penetration. These single-molecule MRI nanoprobes can be served to precisely examine the size-related nanoparticle-biological interactions.

Low-temperature detection of acetone gas using ZnO-TiO2 nanorod on tapered multimode fiber decorated with Au-Pd thin films

This paper presents the influence of titanium dioxide (TiO2) as a catalyst to the zinc oxide (ZnO) nanorods coated on the tapered MMF fiber utilized as a sensing layer for the detection of acetone gas at low temperatures. To enhance the sensitivity of the sensor ZnO-TiO2 nanorods were decorated with Au-Pd film. Hydrothermal method was used to synthesize the ZnO nanorods while TiO2 powder was incorporated by using a simple doping procedure during fabrication. The decoration of the Au-Pd thin films is integrated with the ZnO-TiO2 by using DC sputtering method. The ZnO doped with 15 mM TiO2 shows a strong and significant peak based on XRD analysis which can be indexed to the hexagonal phase of ZnO. A few globular structures of TiO2 were randomly distributed as observed by the SEM image. Four different fiber sensing layers were prepared with respect to 10 mM ZnO precursor; ZnO nanorods (ZN), ZnO nanorods decorated with Au-Pd thin films (ZNAP), ZnO-15 mM TiO2 nanorods (ZTN) and ZnO-15 mM TiO2 nanorods decorated with Au-Pd thin films (ZTNAP). The spectrometry setup was used to measure the response of the sensor toward different concentrations of acetone gas in terms of intensity with respect to its wavelength. Notable output intensity responses were observed for ZTNAP in terms of sensitivity and standard deviation towards various acetone concentrations while the repeatability curve showed a high response of acetone gas at 10,000 ppm. All experiments were performed at the low temperature of 87 °C.

A three-state mechanism for trifluoroethanol denaturation of an intrinsically disordered protein (IDP).

Relating the amino acid composition and sequence to chain folding and binding preferences of intrinsically disordered proteins (IDPs) has emerged as a huge challenge. While globular proteins have respective 3D structures that are unique to their individual functions, IDPs violate this structure-function paradigm because rather than having a well-defined structure an ensemble of rapidly interconverting disordered structures characterize an IDP. This work measures 2,2,2-trifluoroethanol (TFE)-induced equilibrium transitions of an IDP called AtPP16-1 (Arabidopsis thaliana phloem protein type 16-1) by using fluorescence, circular dichroism, infrared, and NMR methods at pH 4, 298 K. Low TFE reversibly removes the tertiary structure to produce an ensemble of obligate intermediate ($\mathrm{I}$) retaining the native-state ($\mathrm{N}$) secondary structure. The intermediate $\mathrm{I}$ is preceded by a non-obligate tryptophan-specific intermediate ${\mathrm{I}}_{\mathrm{w}}$ whose population is detectable for AtPP16-1 specifically. Accumulation of such non-obligate intermediates is discriminated according to the sequence composition of the protein. In all cases, however, a tertiary structure-unfolded general obligate intermediate $\mathrm{I}$ is indispensable. The $\mathrm{I}$ensemble has higher helical propensity conducive to the acquisition of an exceedingly large level of α-helices by a reversible denaturation transition of $\mathrm{I}$ to the denatured state $\mathrm{D}$ as the TFE level is increased. Strikingly, it is the same $\mathrm{N}\rightleftharpoons \mathrm{I}\rightleftharpoons \mathrm{D}$ scheme typifying the TFE transitions of globular proteins. The high-energy state $\mathrm{I}$ characterized by increased helical propensity is called a universal intermediate encountered in both genera of globular and disordered proteins. Neither $\mathrm{I}$ nor $\mathrm{D}$ strictly show molten globule (MG)-like properties, dismissing the belief that TFE promotes MGs.

AQcalc: A web server that identifies weak molecular interactions in protein structures.

Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.