Protein Secondary Structure Research Articles

Dy-SheHeRASADe: A representation of the [formula omitted] sheet dynamics through surface descriptors

Molecular dynamics (MD) simulations are important tools for studying the dynamic motions of macromolecules at the atomic level. With the increasing capabilities of high performance computing, MD simulations are becoming more widely used. This allows molecular modelers to simulate the molecular behavior of large molecular architectures for much longer trajectories. Appropriate visualization of MD trajectories is becoming essential to provide an immediate and intuitive understanding of a molecule’s dynamics and function. In this study, we implement a novel 3D graphical representation, Dynamical Sheets Helper for RepresentAtion of SurfAce Descriptors (Dy-SheHeRASADe), to visualize the β sheet secondary structures of proteins in the context of molecular dynamics. Dy-SheHeRASADe is developed in UnityMol, an open source molecular viewer and prototyping platform. We considered β sheet fluctuations and hydrogen bond formation during molecular dynamics simulations to characterize the parts of β sheets with large motions or with labile bonds. We propose two visualization modes based on a surface representation of the β sheets calculated according to the positions of the α carbons and the hydrogen bonds between the β strands. The volumetric mode, in which this surface is enclosed in a semi-transparent volume that represents the fluctuation zone of the sheet during dynamics. The heatmap mode, in which the surface is colored according to the amplitude values of the α carbons. In addition, we quantify the β sheet fluctuations by displaying the values of the largest and smallest movements of the β sheets, the surface area of the sheets, and the number of hydrogen bonds.

Effect of primary copper metabolism disturbance on elemental, protein, and lipid composition of the organs in Jackson toxic milk mouse.

Toxic milk (txJ) is an autosomal recessive mutation in the Atp7b gene in the C3H/HeJ strain, observed at The Jackson Laboratory in Maine, USA. TxJ mice exhibit symptoms similar to those of human Wilson's disease (WD). The study aimed to verify organ involvement in a mouse model of WD. TxJ mice and control animals were sacrificed at 2, 4, 8, and 14months of age. Total X-ray Fluorescence Spectroscopy (TXRF) was used to determine the elemental concentration in organs. Tissue chemical composition was measured by Fourier Transform Infrared Spectroscopy (FTIR). Additionally, hybrid mapping of FTIR and microXRF was performed. Elevated concentrations of Cu were observed in the liver, striatum, eye, heart, and duodenum of txJ mice across age groups. In the striatum of the oldest txJ mice, there was lower lipid content and a higher fraction of saturated fats. The secondary structure of striatum proteins was disturbed in txJ mice. In the livers of txJ mice, higher concentrations of saturated fats and disturbances in the secondary structure of proteins were observed. The concentration of neurofilaments was significantly higher in txJ serum. The distribution of Cu deposits in brains was uniform with no prevalence in any anatomic structure in either group, but significant protein structure changes were observed exclusively in the striatum of txJ. In this txJ animal model of WD, pathologic copper accumulation occurs in the duodenum, heart, and eye tissues. Increased copper concentration in the liver and brain results in increased saturated fat content and disturbances in secondary protein structure, leading to hepatic injury and neurodegeneration.

Application of Attenuated Total Reflectance Fourier-Transform Infrared Spectroscopy in Human Sera: Validate the method for contributing effective strategy for the storage and preservation

The serum is one of the biological specimens that have been extensively studied as biomarkers and is recognized as an effective tool for screening and diagnosing a variety of diseases. Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR) is a practical technique utilized in investigating characteristic spectra in infectious diseases cancer, and metabolic status. However, the pre-analytical procedure as storage condition is a crucial phase that directly impacts the accuracy of the result. In this study, we intend to investigate the effects of serum stabilization under both identical and distinct storage conditions on the FTIR spectral patterns, intensity variations, and macromolecule composition. The ten serum samples were stored in 3 different conditions including 4 °C, −20°C, and −80°C for six different time intervals (7, 14, 21, 28, 56, and 84 days). The spectra were obtained by ATR-FTIR spectroscopy. The serum stabilization was studied in two investigations: one focusing on the stability of serum under identical conditions over six different time intervals, and the other examining the stability of serum stored under three distinct conditions. Principal Component Analysis (PCA) and Area Under the Peak (AUP) were used to investigate clusters in different sets of data across five spectral ranges. The macromolecule composition was identified in conjunction with the intensity measurements. The results showed that the same conditions remained stable across six different time intervals, as indicated by the consistent PCA results. In contrast, the stabilization of serum under different temperature condition showed different major intensities across the five selected positive bands, including 1781 cm−1, 1740 cm−1 1727 cm−1 corresponding to lipid region (1800–1700 cm−1), and Amide region (1700 −1500 cm−1) at 1646 cm−1, and 1632 cm−1, when the serum was stored over 28 days. This might involve lipid peroxidation-induced changes in the secondary structure of proteins. Our findings indicated that serum should be stored at −80°C to ensure stabilization and achieve the highest intensity. Additionally, preserving serum under consistent conditions was crucial to minimize variability and prevent external factors from affecting the results.

Soft Ca2+-induced pea protein gels through mild heating: Controlling elasticity and fracturing behavior

With the rising demand for plant-based protein, understanding the formation of pea protein gels induced by calcium is important for manufacturing of food products with appealing textural properties. Moreover, the moderate temperature processing is becoming of greater and greater interest, based on conditions used for food fermentation. The objective of this study is to understand the structural and rheology behaviour of calcium-induced pea protein aggregates at moderate plateau temperatures i.e. in the range 30–45 °C with holding times from 0 to 60,000s. Based on the combination of confocal fluorescence microscopy (CLSM) imaging, rheology and IR spectroscopy, our results show that despite the relatively low temperature range, thermal agitation not only allows for partial protein particle dissolution, but also induces interactions leading to soft gel formation. Within a shorter holding time (0–600s) range, higher Gʹ/Gʹ0 (t) were observed at 40 °C and 45 °C, the end elastic modulus reaching for any parameters tested at least 1000 Pa. As the holding time was extended to 60,000s, the effect of temperature became less pronounced, i.e., all gels reached similar high values of Gʹ even for the low temperature of 30 °C, which is nearly 3–4 times higher than that formed at 600s holding time (at the temperature plateau). IR spectroscopy measurements showed that the protein secondary structure remained stable within the holding time ranging from 0s to 6,000s, while significant but moderate changes were monitored when extending the holding time to 60,000s, which correlated with a more progressive yielding observed in rheology, pointing to the formation of apparently more fragile physical gels. The combination of the techniques shows that the gel formation and strengthening mainly originated from rearrangements at the colloidal level leading to a denser network, while molecular rearrangements only intervened at the longest holding times (i.e, 60,000s).

Flour Treatments Affect Gluten Protein Extractability, Secondary Structure, and Antibody Reactivity

Commercial Brazilian wheat flour was subjected to extrusion, oven, and microwave treatments. The solubility, monomeric and polymeric proteins, and the glutenin and gliadin profiles of the gluten were analyzed. In addition, in vitro digestibility and response against potential celiac disease immune-stimulatory epitopes were investigated. All treatments resulted in low solubility of the polymeric and monomeric proteins. The amounts of insoluble proteins increased from 5.6% in control flour to approximately 10% for all (treatments), whereas soluble proteins decreased from 6.5% to less than 0.5% post treatment. In addition, the treatments affected glutenin and gliadin profiles. The amount of α/β-gliadin extracted decreased after all treatments, while that of γ-gliadin was unaffected. Finally, the potential celiac disease immune stimulatory epitopes decreased in oven and microwave treatment using the G12 ELISA, but no change was observed using the R5 antibody. However, the alteration of the gluten structure and complexity was not sufficient to render a product safe for consumption for individuals with celiac disease; the number of potential celiac disease immune-stimulatory epitopes remained high.

310-Helix stabilization and screw sense control via stereochemically configured 4-atom hydrocarbon staples

The 310-helix is a crucial secondary structure in proteins, playing an essential role in various protein–protein interactions, yet stabilizing it in biologically relevant peptides remains challenging. In this study, we investigated the potential of 4-atom hydrocarbon staples to stabilize 310-helices in peptides. Using ring-closing metathesis, we demonstrated that the staple’s configuration is critical for both the stabilization and screw sense control of 310-helices. Circular dichroism spectroscopy revealed that the Ri,i+3S(4) staple—a 4-atom cross-link with (R)-configuration at the i position, (S)-configuration at the i + 3 position, and flanked by methyl groups—strongly induces right-handed 310-helices, especially in sequences with proteinogenic l-amino acids. Furthermore, multiple staples effectively stabilized longer peptides, underscoring the versatility of this approach for applications in peptide therapeutics and biomolecular engineering.

Preparation, characterization, stability and application of the H-type aggregates lutein/whey protein/chitosan nanoparticles

Natural lutein is liposoluble and has powerful antioxidant activity, which can be self-aggregated to form H-type aggregates in organic-water systems. However，its application is limited by poor solubility and high instability. Here, whey proteins/chitosan-coated H-type aggregates lutein nanoparticles (NPs) were fabricated via a bottom-up layer-by-layer self-assembly technique. The optimal conditions for the preparation of the NPs (173.3 nm) were determined by the Dynamic Light Scattering and UV–vis spectroscopy. Briefly, three proteins, WPI and WPC and BSA were used to fabricate polysaccharide-protein nanocarriers to encapsulate the lutein. These spectroscopy studies indicated that chitosan and BSA formed hydrophobic microdomain by the intermolecular electrostatic attraction force with remarkable changes of secondary structure in protein. The morphology revealed that the NPs were nearly spherical. The EE of the NPs was >90 %, with a LC of up to 28.32 %. Lutein in NPs can be stabilized as H-type aggregates at different temperatures and pH-values. Additionally, the cytotoxicity test of the NPs on L929 and Caco-2 cells showed that NPs had low cytotoxicity in a limited concentration range. Results indicated that whey protein/chitosan-coated lutein nanoparticles significantly improved water dispersion and stability of lutein and its aggregates, thus broadening their application in nutrient delivery system.

Effect of different thermal processing methods and thermal core temperatures on the protein structure and in vitro digestive characteristics of beef

This study aimed to investigate the effect of different thermal processing treatments on the protein digestion characteristics of beef. The beef samples were subjected to different cooking methods, namely steaming, boiling, and roasting, and different core temperatures (75 °C, 80 °C, 85 °C, and 90 °C), and were subjected to in vitro gastrointestinal digestion simulation. All the thermal processing treatments increased the protein digestibility; the samples that were steamed at 85 °C (S85), boiled at 80 °C (B80), and roasted at 80 °C (R80) showed the biggest gains. The S85 released more peptide species after gastrointestinal digestion, according to peptididomic studies. These differences were closely related to protein structure. Thermal processing treatments resulted in a higher degree of proteolysis and looser protein conformation, as evidenced by decreased intrinsic fluorescence and electrophoretic band intensity, increased surface hydrophobicity, and the change in protein secondary structure from α-helix to β-sheet and random coil. Based on the results, S85 was identified as the optimal thermal processing treatment for enhancing the digestibility of beef protein. The results provide valuable insights into the nutritional qualities and digestion of heat-processed beef protein.

Improving gel properties of low-salt silver carp surimi through single-mode microwave-assisted processing

Surimi, a product derived from low-value fish, is widely used to produce high-value items such as imitation crabsticks and fish balls. However, surimi from freshwater fish like silver carp generally exhibits inferior gel properties compared to marine fish. This study investigated the effects of 915 MHz single-mode microwave-assisted processing on the gel properties of low-salt silver carp surimi. Traditional water bath processing served as the control for comparison. Gel strength, texture, water-holding capacity (WHC), whiteness, protein secondary structure, and microstructure, along with thermal processing efficiency for microbial inactivation were evaluated. The results demonstrated that single-mode microwave processing significantly improved gel properties compared to water bath processing. Compared with the optimal water bath treatment, the gel strength of microwave processed samples increased significantly from 479.32 g·cm to 821.74 g·cm, while WHC increased from 0.77 to 0.87. The microwave processed surimi exhibited a more uniform microstructure. Because it enhanced the dissolution and cross-linking of myofibrillar proteins, leading to superior gel formation characterized by a lower α-helix content (10.31%) and higher β-sheet content (61.70%). Furthermore, microwave processing achieved faster heating rates, reducing the time spent in the critical gel deterioration temperature range, thereby improving overall gel quality. Single-mode microwave-assisted gelation also provided better thermal processing uniformity and efficiency, achieving pasteurization standards. The study highlights the potential of 915 MHz single-mode microwave processing to produce high-quality, low-salt surimi products, meeting contemporary health and convenience demands. These findings offer valuable insights for the industrial application of single-mode microwave technology in surimi production, promoting the development of innovative processing techniques to enhance the quality of surimi-based food products.

Sodium dodecyl sulfate rearranges the conformation of transferrin and attenuates its iron-binding capacity

Sodium dodecyl sulfate (SDS), an anionic surfactant used in many cleaning and hygiene products, is known for its dermal and respiratory toxicity. However, how this surfactant influences the iron dynamics within the body and the mechanism is unknown. We explored the interaction between SDS and human transferrin (HTF), focusing on the effects on iron-binding capacity and structural changes. Results revealed that SDS exposure led to a significant release of iron from HTF in a dose-dependent manner, changing its structure and reducing the iron-binding ability. Spectroscopic analyses showed that the protein secondary structure and skeleton, as well as the micro-environment of aromatic amino acids of HTF, were destroyed after SDS binding. Isothermal titration calorimetry (ITC) results (ΔG, ΔS, and ΔH were −40.1 kcal·mol−1, 0.16 kcal·mol−1·K-1, and 10.1 kcal·mol−1, respectively) indicated a spontaneous and hydrophobic interaction with one strong binding site. Molecular docking identified the preferred binding sites, emphasizing hydrophobic forces (with the hydrophobic tail) and hydrogen bonds (with the hydrophilic head) as the primary driving forces, which aligns with the ITC results. Overall, this comprehensive analysis sheds light on the intricate interplay between SDS and HTF, providing insights into potential health risks associated with SDS exposure.

Reduction of soybean globulin antigen by soybean protein isolate/γ-aminobutyric acid complexes: Effect of the different concentrations of γ-aminobutyric acid on the protein modification, antigen levels, and foaming properties

Soybean flour has received increasing attention because of its unique nutritional properties. However, potential allergies to soy protein limit its application. This study aims to investigate the impact of various concentrations of γ-aminobutyric acid (GABA) on the secondary structure, foaming properties, and antigenicity of soybean protein obtained from soybean flour under thermal sterilisation. GABA increased the content of α-helix, reduced β-turn and random coil in soybean protein. The results indicated that after heating treatment, the concentration of GABA significantly affects the spatial conformation of soybean protein isolates (SPI). When the concentration of GABA was 0.40% (w/v), the particle size, zeta potential, and surface hydrophobicity of the SPI were the lowest, whereas the disulfide bond content was the highest. Multi-spectral technologies indicated that adding 0.40% GABA could assemble the system in a relatively stable manner. Moreover, the rigid structure of the protein was destroyed. This structural change significantly reduced the foaming and allergy of the protein. Adding 0.40% GABA could reduce the β-conglycinin antigen concentration from 24.26 mg/mL to 4.43 mg/mL. This study provides new insights into the production of new low-allergenic soybean flour. Additionally, it offers an assurance for the safe consumption of soybeans by individuals with allergies.

Mechanism of Toona sinensis seed polyphenols inhibiting oxidation and modifying physicochemical and gel properties of pork myofibrillar protein under oxidation system

This research aimed to elucidate how Toona sinensis seed polyphenols (TSSs) inhibited pork myofibrillar protein (MP) oxidation and modified physicochemical and gel properties in the Fenton oxidation system. Our result displayed that TSSs had a lower carbonyl (from 1.38 to 0.59 nmol/mg) and dityrosine contents (from 47.22 to 25.07), and higher free amino content (from 386.99 to 485.00 nmol/mg), followed by ellagic acid (EA) and quercetin-3-O-rhamnoside (QC). Meanwhile, the incorporation of phenolic compounds changed secondary and tertiary structure of proteins and then increased solubility and absolute value of zeta potential, as well as decreased turbidity and average particle size. Molecular docking indicated that MP interacted with EA primarily via hydrogen bonds and hydrophobic interaction, and with QC mostly through hydrogen bonds and electrostatic interaction. Otherwise, the incorporation of EA promoted MP gel to form a honeycomb-like microstructure after oxidation. Therefore, TSSs, EA, and QC could significantly inhibit MP oxidation as well as modify its physicochemical properties, but only EA enhanced its gel properties after oxidation. The results could be useful to improve the comprehensive utilization of plant by-products and provide theoretical references for the role of TSSs in the improvement of meat products.

Influence of low voltage programmed thawing on the quality of frozen pork and its myofibrillar protein

This study explored the effects of low voltage programmed thawing (LVPT) on thawing period, water status, current density as well as physicochemical properties of porcine longissimus dorsi muscle, considering air thawing (AT), water immersion thawing (WT) and cold storage thawing (CST) for the comparison, additionally making fresh meat (FM) as the control. The thawing process used current limiting to gradually reduce the maximum output current to 500, 200 and 100 mA, respectively, by applying a safe voltage of 35 V in a home defrosting apparatus. Using two pairs of foil plate, the thawing (LVPT-2) with dual current loop accelerated the melting of ice crystals than the process with one pair of polar plate (LVPT-1) with one current loop. From −18 °C to −1 °C, the thawing period of LVPT-2 was reduced by 14.54 %, 11.72 %, and 15.95 % compared with that of LVPT-1 for samples within the thickness of 2, 3 and 4 cm, respectively. During the process, the intensity and density of the current loaded on the frozen meat gradually increased. LVPT-1 retained water and reduced its migration inside the meat, and protein solubility was better maintained. As the thickness increased, the effect of LVPT-2 on the moisture distribution and protein solubility of the sample decreased. LVPT-1 treatment resulted in less fat oxidation as well as stable secondary and tertiary structures of myofibrillar proteins compared to other treatments. At low voltage, the ability of LVPT −2 to maintain meat quality was reduced due to the increase in current density. In addition, LVPT-1 reduced muscle damage because of rapid melting of ice crystals. In contrast, LVPT-2 was conductive the formation of hot spots due to dual current loop passed through the pork in final phase of thawing, which would adversely influence the quality of thawed meat. Finally, LVPT could improve the rate of thawing, water binding capacity and meat quality, especially, there was no overheating effect on the meat because of current limiting.

In silico analysis and structural vaccinology prediction of Toxoplasma gondii ROP41 gene via immunoinformatics methods as a vaccine candidate

IntroductionToxoplasma gondii (T. gondii) infects all warm-blooded animals, including humans. Currently, no effective treatments exist to prevent the generation of chronic tissue cysts in infected hosts. Therefore, developing a vaccine to protect to deal with toxoplasmosis is a promising strategy, as a single immunization could provide lifelong protective immunity. Rhoptry proteins (ROPs) play a vital role for the parasite's survival within host cells and perform critical functions during different phases of parasite invasion. Little is known about ROP41 gene. Nevertheless, Understanding the characteristics of ROP41 will enhance diagnostic and vaccine research. Materials and MethodsThe current article provides a comprehensive analysis of the essential components of the ROP41 protein, including its transmembrane domain, physico-chemical properties, subcellular location, tertiary and secondary structures, and potential T- and B-cell epitopes. These features were determined by many bioinformatics approaches to identify possible epitopes for developing a highly effective vaccine. ResultsROP41 protein showed 36 possible post-translational modification regions. The ROP41 protein secondary structure contains 17.35 % extended strand, 33.47 % alpha-helix, and 49.18 % random coil. Also, ROP41 showed many possible B- and T-cell epitopes. According to the Ramachandran plot, 90.78 % of amino acid residues had been placed in favored, 3.28 % in outlier, and 5.94 % in allowed areas. Also, the allergenicity and antigenicity evaluation indicated that ROP41 is non-allergenic and immunogenic. ConclusionThe current study offered critical basic and conceptual information on ROP41 to increase a successful vaccine in opposition to continual and acute toxoplasmosis for in addition in vivo assessments. Further research is necessary for the development of vaccines utilizing ROP41 alone or combined with various antigens.

Ferritin adsorption onto chrysotile asbestos fibers influences the protein secondary structure

Asbestos fiber exposure triggers chronic inflammation and cancer. Asbestos fibers can adsorb different types of proteins. The mechanism of this adsorption, not yet completely understood, has been studied in detail mainly with serum albumin and was shown to induce structural changes in the bound protein. The findings of these works regarded mainly the changes of the protein structure, independently of any relation with asbestos-related diseases. For the first time, we have focused our attention to the consequences of the interaction between asbestos fibers and ferritin, a protein involved in iron metabolism, which is strongly modified in asbestos-related diseases. Even if it is known that ferritin can be adsorbed by asbestos fibers, the results of this interaction for the ferritin secondary structure has not previously been studied. One consequence of asbestos-ferritin interaction, is the formation of the so-called ferruginous/asbestos bodies (ABs). In the AB-coating material, the secondary structure of ferritin is modified, and at present, it is unclear whether or not this modification is a direct consequence of the asbestos interaction. In the present study, chrysotile asbestos, more than other asbestos fiber types tested, was found to rapidly bind holo-ferritin, and the presence of iron seemed to play a key role in this process, since iron-free apo-ferritin was adsorbed at a lower level, and iron-saturated chrysotile lost its ferritin-adsorbing capacity. To directly study the details of ferritin adsorption on asbestos fibers, High Resolution Transmission Electron Microscopy (HR-TEM) was employed together with FTIR microspectroscopy and Infrared nanoscopy, which to the best of our knowledge, have not previously been used for this purpose. Chrysotile-bound apo-ferritin underwent a significant change in secondary structure, showing a shift from a prevalent α-helix to a β-sheet conformation. Conversely, the adsorbed holo-ferritin structure appeared to be only weakly modified. These findings add a new potential mechanism to the toxic activities of asbestos: the fibers can modify the structure, and very likely, the function of adsorbed proteins. This, in relation to ferritin, could be a key mechanism in cell iron homeostasis alteration, typically reported in asbestos-related diseases.

Study on the effects of pre-slaughter transport stress on water holding capacity of pork: Insights from oxidation, structure, function, and degradation properties of protein

This work systematically investigated the effects of pre-slaughter transport stress on pork water holding capacity (WHC) during aging from the perspectives of oxidation, structure, function, and degradation properties of protein. Pigs were randomly divided into three-hour transport (Transport-induced stress, T group) and three-hour transport followed by three-hour resting (Control, TR group). Results demonstrated that T treatment markedly declined pork WHC. Compared with TR group, T group presented increased oxidation levels. Meanwhile, T treatment exacerbated the shift of protein secondary structure from α-helix to random coil and protein unfolding levels. The decreased solubility, thermal stability, and degraded levels of proteins were also observed in T group. Additionally, muscle contractions of T group were more severe than TR group. This study supported that pre-slaughter transport stress altered physicochemical properties and structures of postmortem muscle proteins, which reduced pork WHC via impairing the interactions between protein and water molecules and changing the muscle fiber structure.

Arbuscular mycorrhizal fungi affected soft wheat quality properties and nutritional index by regulating the composition and secondary structure of protein

Arbuscular mycorrhizal fungi (AMF) inoculation has important regulatory influence on plant growth and nitrogen uptake, which are intimately associated with soft wheat yield and quality. The study aimed to investigate the impact of AMF inoculation on soft wheat grain yield, protein compositions, protein quality, secondary structure of gluten, dough properties and biscuits baking quality. In this study, AMF inoculation significantly increased grain yield. AMF inoculation decreased grain protein content by 5.1%, glutenin content by 8.5%, GMP by 14.3%, and HMW-GS by 8.8% compared with CK. Conversely, AMF inoculation increased the ratio of gliadin/glutenin. Further analysis showed AMF treatment had a looser gluten network than CK, significantly reduced β-sheet and β-turn content, while α-helix content increased. The nutritional index of grain protein was slightly reduced under AMF inoculation, yet the biological value was improved. Reduced wet gluten content, gluten performance index and dough development time under AMF treatment through regulation of soft wheat protein composition and gluten protein structure. Therefore, biscuits in AMF treatment showed reduced thickness, hardness, significantly greater spread ratio and sensory score compared with CK. These indicate that AMF application would be a beneficial agronomic practice to synergistically optimize yield and grain quality in soft wheat.

Mechanism of flavonols for binding protein and inhibiting cell activity: Regulation by B-ring hydroxyl groups and Cu(II) coordination

In this study, we aimed to elucidate the mechanism of flavonol-Cu(II) coordination binding to human serum albumin (HSA) and its effect on cellular activity, focusing on the regulation by the number of B-ring hydroxyl groups and Cu(II) coordination. The number of B-ring hydroxyl groups was positively associated with fluorescence quenching ability, secondary structure modification, and protein affinity. The coordination of Cu(II) altered the binding capacity, interaction, binding site, and binding kinetics between flavonols and proteins, as well as the secondary structure, fluorescence lifetime, and microscopic state of proteins. The number of B-ring hydroxyl groups was positively correlated with the ability of flavonols to inhibit HepG2 cell activity, and this correlation was not affected by Cu(II) coordination. However, Cu(II) binding weakened the ability of flavonols to inhibit HepG2 cell activity. This study contributes to a comprehensive understanding of how the number of hydroxyl groups in the B-ring of flavonols and the presence of copper ions affect their transport in the blood, providing new insights into the bioavailability of flavonols.

Rapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1D 13C Nuclear Magnetic Resonance Spectrum.

The function of a protein is predicated upon its three-dimensional fold. Representing its complex structure as a series of repeating secondary structural elements is one of the most useful ways by which we study, characterize, and visualize a protein. Consequently, experimental methods that quantify the secondary structure content allow us to connect a protein's structure to its function. Here, we introduce an automated gradient descent-based method we refer to as secondary-structure distribution by NMR that allows for rapid quantification of the protein secondary structure composition of a protein from a single, 1D 13C NMR spectrum without chemical shift assignments. The analysis of nearly 900 proteins with known structure and chemical shifts demonstrates the capabilities of our approach. We show that these results rival alternative techniques such as FT-IR and circular dichroism that are commonly used to estimate secondary structure compositions. The resulting method requires only the primary sequence of the protein and its referenced 13C NMR spectrum. Each residue is modeled in an ensemble of secondary structures with percentage contributions from random coil, α-helix, and β-sheet secondary structures obtained by minimizing the difference between a simulated and experimental 1D 13C NMR spectrum. The capabilities of the method are demonstrated as applied to samples at natural abundance or enriched in 13C, acquired by either solution or solid-state NMR, and even on low magnetic field benchtop NMR spectrometers. This approach allows for rapid characterization of protein secondary structure across traditionally challenging to characterize states including liquid-liquid phase-separated, membrane-bound, or aggregated states.

CHANGES IN SECONDARY STRUCTURE OF PROTEIN IN SKELETAL MUSCLE DUE TO HIGH-CARBOHYDRATE OR HIGH-FAT DIETS

Objective: Obesity, which arises from changes in lifestyle and feeding habits, is a threat to human health. One essential contributor to the increase in obesity rates is the popularity of high-calorie diets. This study aims to investigate high-fat (HFD) and high-carbohydrate (HCD) diet-induced molecular changes in protein secondary structure in longissimus dorsi skeletal muscle tissues of female inbred C57BL/6J mice by utilizing Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy. Materials and Methods: Mice were fed a control diet, HCD, or HFD for 24 weeks. Their skeletal muscle tissues were collected, and their spectra were recorded using a Bruker Invenio S ATR-FTIR spectrometer in the 4000-400 cm-1 region. Results: The protein secondary structure profiles of the HCD group demonstrated a significant rise in antiparallel β-sheet and β-turn and a decline in parallel β-sheets together with the insignificant increase in aggregated β-sheets and a decrease in α-helix. The impact of an HFD on protein conformation is less pronounced than HCD. The HFD diet led to an increase in antiparallel β-sheets and a decrease in parallel β-sheets. Although it was not significant, an increase was observed in β-turn and α-helix. Conclusion: These results propose the appearance of protein aggregation and/or formation of protein-protein intermolecular interaction in skeletal muscle tissues of female inbred C57BL/6J mice. Collectively, these data suggest that both high-calorie diets impair secondary structures of protein in skeletal muscle that may affect its metabolic function.