Secondary Structure Conformation Research Articles

Effect of Cu2+ on the binding of catechins to zein through multi-spectral and in silico analyses

This study aimed to elucidate how Cu2+ influences the interaction between catechins and zein using multi-spectral and molecular modeling techniques. As a result, UV–vis spectra revealed characteristic changes, indicating chelation between catechins and Cu2+ at a 1:1 M ratio. Fluorescence spectra further confirmed interaction through a static quenching mechanism between catechins/catechin-Cu2+ complexes and zein. Catechins induced changes in the microenvironment and hydrophobicity surrounding the binding site of zein, whereas Cu2+ had minimal impact on these aspects. CD spectra underscored catechins' role in altering zein's secondary structure conformation, alongside Cu2+. Various types of interactions (hydrophobic, hydrogen bonding, electrostatic, and van der Waals) contributed to the binding of catechins/catechin-Cu2+ complexes with zein. Molecular modeling elucidated key residues and binding conformations, highlighting the significance of hydrophobic interactions and hydrogen bonding in their association. These findings not only deepen our understanding of catechin-Cu2+-zein interactions but also underscore their potential applications in the food industry.

Adaptability to the environment of protease by secondary structure changes and application to enzyme-selective hydrolysis

The reactions involving enzymes are significantly influenced by various environmental factors. Clarity of how the activity and structure of proteases impact their function is crucial for more efficient application of enzymes as a tool. The impact of temperature, pH, and ionic strength on changes in protease activity, secondary structure, and protein conformation during enzymatic hydrolysis were investigated in this study. The enzymatic activity and secondary structure of acid-base protease were found to undergo significant modifications under different physical conditions, as demonstrated by UV spectrophotometry and FTIR spectroscopy analysis. Specifically, variations in α-helix and β-fold content were observed to correlate with changes in enzyme activity. Molecular simulation analysis revealed that physical conditions have varying effects on the protease, particularly influencing enzyme activity and secondary structure. Evaluation of the proteases indicated alterations in both enzyme activity and structure. This treatment selectively hydrolyzed β-lactoglobulin and reduced sensitization. These findings offer novel perspectives on the functionalities and regulatory mechanisms of proteases, as well as potential industrial applications.

Intronic RNA secondary structural information captured for the human MYC pre-mRNA

Abstract To address the lack of intronic reads in secondary structure probing data for the human MYC pre-mRNA, we developed a method that combines spliceosomal inhibition with RNA probing and sequencing. Here, the SIRP-seq method was applied to study the secondary structure of human MYC RNAs by chemically probing HeLa cells with dimethyl sulfate in the presence of the small molecule spliceosome inhibitor pladienolide B. Pladienolide B binds to the SF3B complex of the spliceosome to inhibit intron removal during splicing, resulting in retained intronic sequences. This method was used to increase the read coverage over intronic regions of MYC. The purpose for increasing coverage across introns was to generate complete reactivity profiles for intronic sequences via the DMS-MaPseq approach. Notably, depth was sufficient for analysis by the program DRACO, which was able to deduce distinct reactivity profiles and predict multiple secondary structural conformations as well as their suggested stoichiometric abundances. The results presented here provide a new method for intronic RNA secondary structural analyses, as well as specific structural insights relevant to MYC RNA splicing regulation and therapeutic targeting.

Exploring the therapeutic potential of rutin through investigating its inhibitory mechanism on lactate dehydrogenase: Multi-spectral methods and computer simulation

Lactate dehydrogenase (LDH), a crucial enzyme in anaerobic glycolysis, plays a pivotal role in the energy metabolism of tumor cells, positioning it as a promising target for tumor treatment. Rutin, a plant-based flavonoid, offers benefits like antioxidant, antiapoptotic, and antineoplastic effects. This study employed diverse experiments to investigate the inhibitory mechanism of rutin on LDH through a binding perspective. The outcomes revealed that rutin underwent spontaneous binding within the coenzyme binding site of LDH, leading to the formation of a stable binary complex driven by hydrophobic forces, with hydrogen bonds also contributing significantly to sustaining the stability of the LDH-rutin complex. The binding constant (Ka) for the LDH-rutin system was 2.692 ± 0.015 × 104 M−1 at 298 K. Furthermore, rutin induced the alterations in the secondary structure conformation of LDH, characterized by a decrease in α-helix and an increase in antiparallel and parallel β-sheet, and β-turn. Rutin augmented the stability of coenzyme binding to LDH, which could potentially hinder the conversion process among coenzymes. Specifically, Arg98 in the active site loop of LDH provided essential binding energy contribution in the binding process. These outcomes might explain the dose-dependent inhibition of the catalytic activity of LDH by rutin. Interestingly, both the food additives ascorbic acid and tetrahydrocurcumin could reduce the binding stability of LDH and rutin. Meanwhile, these food additives did not produce positive synergism or antagonism on the rutin binding to LDH. Overall, this research could offer a unique insight into the therapeutic potential and medicinal worth of rutin.

NMR characterization and ligand binding site of the stem-loop 2 motif from the Delta variant of SARS-CoV-2.

The stem-loop 2 motif (s2m) in SARS-CoV-2 (SCoV-2) is located in the 3'-UTR. Although s2m has been reported to display characteristics of a mobile genomic element that might lead to an evolutionary advantage, its function has remained unknown. The secondary structure of the original SCoV-2 RNA sequence (Wuhan-Hu-1) was determined by NMR in late 2020, delineating the base-pairing pattern and revealing substantial differences in secondary structure compared to SARS-CoV-1 (SCoV-1). The existence of a single G29742-A29756 mismatch in the upper stem of s2m leads to its destabilization and impedes a complete NMR analysis. With Delta, a variant of concern has evolved with one mutation compared to the original sequence that replaces G29742 by U29742. We show here that this mutation results in a more defined structure at ambient temperature accompanied by a rise in melting temperature. Consequently, we were able to identify >90% of the relevant NMR resonances using a combination of selective RNA labeling and filtered 2D NOESY as well as 4D NMR experiments. We present a comprehensive NMR analysis of the secondary structure, (sub)nanosecond dynamics, and ribose conformation of s2m Delta based on heteronuclear 13C NOE and T 1 measurements and ribose carbon chemical shift-derived canonical coordinates. We further show that the G29742U mutation in Delta has no influence on the druggability of s2m compared to the Wuhan-Hu-1 sequence. With the assignment at hand, we identify the flexible regions of s2m as the primary site for small molecule binding.

DERNA Enables Pareto Optimal RNA Design.

The design of an RNA sequence that encodes an input target protein sequence is a crucial aspect of messenger RNA (mRNA) vaccine development. There are an exponential number of possible RNA sequences for a single target protein due to codon degeneracy. These potential RNA sequences can assume various secondary structure conformations, each with distinct minimum free energy (MFE), impacting thermodynamic stability and mRNA half-life. Furthermore, the presence of species-specific codon usage bias, quantified by the codon adaptation index (CAI), plays a vital role in translation efficiency. While earlier studies focused on optimizing either MFE or CAI, recent research has underscored the advantages of simultaneously optimizing both objectives. However, optimizing one objective comes at the expense of the other. In this work, we present the Pareto Optimal RNA Design problem, aiming to identify the set of Pareto optimal solutions for which no alternative solutions exist that exhibit better MFE and CAI values. Our algorithm DEsign RNA (DERNA) uses the weighted sum method to enumerate the Pareto front by optimizing convex combinations of both objectives. We use dynamic programming to solve each convex combination in time and space. Compared with a CDSfold, previous approach that only optimizes MFE, we show on a benchmark data set that DERNA obtains solutions with identical MFE but superior CAI. Moreover, we show that DERNA matches the performance in terms of solution quality of LinearDesign, a recent approach that similarly seeks to balance MFE and CAI. We conclude by demonstrating our method's potential for mRNA vaccine design for the SARS-CoV-2 spike protein.

Pyruvate kinase deficiency and PKLR gene mutations: Insights from molecular dynamics simulation analysis

Pyruvate kinase deficiency is a rare hereditary erythrocyte enzyme disease caused by mutations in the pyruvate kinase liver and red blood cell gene. The clinical presentations of pyruvate kinase deficiency are significantly heterogeneous, ranging from just mild anemia to hemolytic crisis or even death. The proband in our study was a 2-year-old girl for severe skin and scleral icterus with progressive aggravation. We collected the family's data for further analysis. Whole exome genome sequencing of the pedigree revealed a novel compound heterozygous mutation, c.1097del (p.P366Lfs*12) and c.1493G > A (p.R498H), in the pyruvate kinase liver and red blood cell gene. Furthermore, molecular dynamics simulations were employed to uncover differences between the wild type and mutant pyruvate kinase liver and red blood cell proteins, focusing on structural stability, protein flexibility, secondary structure, and overall conformation. The combined bioinformatic tools were also utilised to assess the effects of the missense mutation on protein function. Thereafter, wild type and mutant plasmids were constructed and transfected into 293T cells, and Western blot assay was conducted to validate the impact of the mutations on the expression of pyruvate kinase liver and red blood cell protein. The data presented in our study enriches the genotype database and provides evidence for genetic counseling and molecular diagnosis of pyruvate kinase deficiency.

Rational design of small-sized peptidomimetic inhibitors disrupting protein-protein interaction.

Protein-protein interactions are fundamental to nearly all biological processes. Due to their structural flexibility, peptides have emerged as promising candidates for developing inhibitors targeting large and planar PPI interfaces. However, their limited drug-like properties pose challenges. Hence, rational modifications based on peptide structures are anticipated to expedite the innovation of peptide-based therapeutics. This review comprehensively examines the design strategies for developing small-sized peptidomimetic inhibitors targeting PPI interfaces, which predominantly encompass two primary categories: peptidomimetics with abbreviated sequences and low molecular weights and peptidomimetics mimicking secondary structural conformations. We have also meticulously detailed several instances of designing and optimizing small-sized peptidomimetics targeting PPIs, including MLL1-WDR5, PD-1/PD-L1, and Bak/Bcl-xL, among others, to elucidate the potential application prospects of these design strategies. Hopefully, this review will provide valuable insights and inspiration for the future development of PPI small-sized peptidomimetic inhibitors in pharmaceutical research endeavors.

Optimization of active pectin coating formulation and its effect on surface morphology and shelf-life of white button mushroom (Agaricus bisporus)

The present work aimed to optimize an active pectin-based coating to preserve microbial and enzymatic stability and maintain the quality parameters of white button mushrooms (WBM), thus increasing their shelf stability. d-optimal mixture design was implemented to study the effect of pectin (X1), ascorbic acid (X2), and ethylene-diamine-tetra acetic acid (EDTA) (X3) on polyphenol oxidase (PPO) inhibition, browning index, and total phenolic content. The optimal coating was a mixture of 2.55% w/v pectin, 0.67% w/v ascorbic acid, and 0.78% w/v EDTA. Further, the optimally coated WBM was stored for 6 days at 20 ± 1 °C. The coating on WBM significantly prevented the growth of natural microflora in the sample. Similarly, a maximum of 84% PPO inhibition was achieved at the end of the storage period. A minimum browning index (BI) of 66 was observed after six days of storage, significantly lower than that of the uncoated sample with a BI of 72.72 ± 0.90. Maximum phenolic content of 10.23 mgGAE/g WBM (dry basis) was preserved till day 6, while the antioxidant capacity was 7.16 ± 0.20 mg GAEAOC/g WBM (dry basis). Based on microbial safety and overall quality parameters, the optimal pectin-based ascorbic acid and EDTA-enriched coating led to a shelf-life of 4 days against 2 days for uncoated mushrooms at 20 °C. The optimized coating of mushrooms resulted in competitive inhibition of PPO. Fourier transform infrared (FTIR) spectroscopy revealed that EDTA and optimized coating modulated the secondary structure conformation in the amide I region. Microstructural analysis of the mushroom cap surface through scanning electron microscopy (SEM) showed that the optimized coating formed a homogeneous protective barrier on the mushroom surface, leading to the closure of intercellular spaces on the surface. The optimized coating can help mitigate postharvest losses due to the high perishability of white button mushrooms and provides a valuable solution for the industry to enhance product quality and safety.

Interactions of Turmeric- and Curcumin-Functionalized Gold Nanoparticles with Human Serum Albumin: Exploration of Protein Corona Formation, Binding, Thermodynamics, and Antifibrillation Studies.

In order to better understand the bioavailability and biocompatibility of polyphenol-assisted surface-modified bioengineered nanoparticles in nanomedicine applications, here, we address a series of photophysical experiments to quantify the binding affinity of serum albumin toward polyphenol-capped gold nanoparticles. For this, two different gold nanoparticles (AuNPs) were synthesized via the green synthesis approach, where curcumin and turmeric extract act as reducing as well as capping agents. The size, surface charge, and surface plasmon bands of the AuNPs were highly affected by the adsorption of human serum albumin (HSA) during protein corona formation, which was investigated using dynamic light scattering (DLS), ξ-potential, ultraviolet-visible (UV-vis) spectroscopy, and transmission electron microscopy (TEM) measurements. Fluorescence-based methods, absorbance, and SERS experiments were carried out to evaluate the binding aspects of AuNPs with HSA. We found that the AuNPs show moderate binding affinity toward HSA (Kb ∼ 104 M-1), irrespective of the capping agents on the surface. Hydrophobic association, along with some contribution of electrostatic interaction, played a key role in the binding process. The binding interaction was more toward the subdomain IIA region of HSA, as indicated by the competitive displacement studies using site-specific binders (warfarin and flufenamic acid). Because of the large surface curvature of small-sized AuNPs, the secondary structural conformations of HSA were slightly altered, as revealed by circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, and surface-enhanced Raman scattering (SERS) measurements. Additionally, the findings of the binding interactions were re-evaluated using molecular dynamics (MD) simulation studies by determining the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and changes in the binding energy of HSA upon complexation with AuNPs. To determine the tentative evidence for pharmacokinetic administration, these biocompatible AuNPs were applied to inhibit the amyloid fibril formation of HSA and monitored by using the thioflavin T (ThT) assay, ANS fluorescence assay, fluorescence microscopic imaging, and FESEM. AuNPs were found to show better resistance toward fibrillation of the adsorbed protein.

Deciphering the interaction mechanism and binding mode between chickpea protein isolate and flavonoids based on experimental studies and molecular simulation.

Chickpea protein isolate (CPI) is a promising novel plant protein, and protein-flavonoid system has also been applied in various food products. However, the interaction mechanism between CPI and flavonoids remains to be elucidated. In this paper, the affinity behavior between flavonoids and CPI was explained by constructing the three-dimensional quantitative structure-activity relationship (R2=0.988, Q2=0.777). Subsequently, four representative flavonoids were selected for further study. Multi-spectroscopy analysis showed that the sequence of affinity for CPI was puerarin>apigenin>naringenin>epigallocatechin gallate. Meanwhile, flavonoids altered the secondary structure and spatial conformation of CPI, leading to the static quenching of CPI. Additionally, thermodynamic analysis indicated that hydrogen bonding and van der Waals forces were the main driving forces for complex binding. Molecular docking and molecular dynamics simulations further explored the binding sites and conformations of complexes. This study provides theoretical guidance for in-depth research on the interaction patterns between biomacromolecules and small molecules in food matrices.

Functional development of porcine spleen as a by-product of pig slaughterhouse: Preparation, identification and bioactive activities of a novel peptide

Porcine spleen, by-product of pig slaughterhouses, was often threw away due to underutilization, resulting in the neglect of the development of high-quality active materials. In this study, water-soluble porcine spleen peptide (w-PSP) was prepared by enzymatic hydrolysis. It was a mixed peptide with a molecular weight of less than 3000 Da and contained 7097 short peptides consisting of 5–15 amino acids residues. The w-PSP contained 65.33% hydrophilic amino acids. β-sheet was the main secondary structure conformation in w-PSP. The activity verification experiments confirmed that w-PSP presented no antitumor activity in vitro and in vivo. But it exhibited conspicuous antioxidant properties. The maximum scavenging rates of w-PSP to 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals were 78.19% and 75.53%, respectively. Anti-superoxide anion (O2-) radical activity and anti-hydroxyl (OH) radical activity of w-PSP reached 94.19 U/L and 396.40 U/mL. Besides, the activities of glutathione peroxidase (GSH-PX) in liver, spleen, kidney and serum of w-PSP treated mice were significantly increased to 266.82 mgGSH/gprot, 226.37 mgGSH/gprot, 239.03 mgGSH/gprot and 1376.38 mgGSH/L. The activities of superoxide dismutase (SOD) in liver, spleen, kidney and serum of w-PSP treated mice were increased to 1614.66 U/mgprot, 1614.51 U/mgprot, 677.11 U/mgprot and 156.91 U/mL. The malondialdehyde (MDA) contents in w-PSP treatment groups were obviously decreased. De novo sequencing and bioinformatics prediction were used to identify and analyze peptides in w-PSP. Good molecular docking results suggested the antioxidant mechanism of w-PSP might be related to the Keap1-Nrf2 signaling pathway.

Genetic detection of two novel LRP5 pathogenic variants in patients with familial exudative vitreoretinopathy

BackgroundFamilial exudative vitreoretinopathy (FEVR) is a genetic eye disorder that leads to abnormal development of retinal blood vessels, resulting in vision impairment. This study aims to identify pathogenic variants by targeted exome sequencing in 9 independent pedigrees with FEVR and characterize the novel pathogenic variants by molecular dynamics simulation.MethodsClinical data were collected from 9 families with FEVR. The causative genes were screened by targeted next-generation sequencing (TGS) and verified by Sanger sequencing. In silico analyses (SIFT, Polyphen2, Revel, MutationTaster, and GERP + +) were carried out to evaluate the pathogenicity of the variants. Molecular dynamics was simulated to predict protein conformation and flexibility transformation alterations on pathogenesis. Furthermore, molecular docking techniques were employed to explore the interactions and binding properties between LRP5 and DKK1 proteins relevant to the disease.ResultsA 44% overall detection rate was achieved with four variants including c.4289delC: p.Pro1431Argfs*8, c.2073G > T: p.Trp691Cys, c.1801G > A: p.Gly601Arg in LRP5 and c.633 T > A: p.Tyr211* in TSPAN12 in 4 unrelated probands. Based on in silico analysis and ACMG standard, two of them, c.4289delC: p.Pro1431Argfs*8 and c.2073G > T: p.Trp691Cys of LRP5 were identified as novel pathogenic variants. Based on computational predictions using molecular dynamics simulations and molecular docking, there are indications that these two variants might lead to alterations in the secondary structure and spatial conformation of the protein, potentially impacting its rigidity and flexibility. Furthermore, these pathogenic variants are speculated to potentially influence hydrogen bonding interactions and could result in an increased binding affinity with the DKK1 protein.ConclusionsTwo novel genetic variants of the LRP5 gene were identified, expanding the range of mutations associated with FEVR. Through molecular dynamics simulations and molecular docking, the potential impact of these variants on protein structure and their interactions with the DKK1 protein has been explored. These findings provide further support for the involvement of these variants in the pathogenesis of the disease.

Exploring the effect of a series of flavonoids on tyrosinase using integrated enzyme kinetics, multispectroscopic, and molecular modelling analyses

The control of food browning can be achieved by inhibiting tyrosinase (TY) activity, but current studies on the interaction of flavonoids as potent inhibitors with TY are inadequate. Herein, the effect of a library of flavonoids on TY was investigated using enzyme kinetics, multispectroscopic methods, and molecular modelling. Some flavonoids including 4, 8, 10, 17, 18, 28, 30, 33, and 34 exhibited potent TY inhibitory activity, with compound 10 demonstrating reversible inhibition in a mixed-competitive manner. Ultraviolet-visible spectral changes confirmed the formation of flavonoid-TY complexes. Fluorescence quenching analysis suggested effective intrinsic fluorescence quenching by flavonoids through static quenching with the ground-state complex formation. Synchronous fluorescence spectra showed the microenvironment change around the fluorophores induced by flavonoids. ANS-binding fluorescence assay indicated TY's surface hydrophobicity change by flavonoids and highlighted the change in secondary structure conformation, which was further confirmed by Fourier-transform infrared spectra. Molecular modelling results helped visualize the preferred binding conformation at the active site of TY, and demonstrated the important role of hydrophobic interaction and hydrogen bonding in stabilizing the flavonoid-TY complexes. These findings prove that diverse flavonoid structures distinctly impact their binding behavior on TY and contribute to understanding flavonoids' potential as TY inhibitors in controlling food browning.

Effects of carboxymethyl chitosan on the gelling properties, microstructure, and molecular forces of Pleurotus eryngii protein gels

Protein-polysaccharide interactions play a crucial role in development of plant-based food products. This study aimed to investigate the effects of different carboxymethyl chitosan (CMCS) concentrations (0–5.0%) on the gelation, structural properties, molecular interactions, and microstructure of the Pleurotus eryngii protein (PEP) gels. The results showed that the addition of CMCS could improve the rheological, textural properties and water holding capacity of the PEP/CMCS composite gels. Fluorescence spectra, fourier transform infrared spectrum and chemical interaction forces analysis suggested that the formation of the CMCS/PEP complex occurred by static quenching mechanism. The addition of CMCS changed the secondary structure and molecular conformation of the protein, also significantly enhanced the hydrophobic interaction and disulfide bonds of PEP molecules, thus increased the gel properties of PEP. Scanning electron microscopy revealed a denser and uniform network structure with small pores in the CMCS/PEP composite gels. Overall, these results provided an important basis for CMCS to improve the heat-induced gel properties of PEP, and also provided information on the potential use of composite gel as meat analogs in the food processing industry.

Deciphering the binding site and mechanism of new methylene blue with serum albumins: A multispectroscopic and computational investigation

Herein, the interaction mechanism of new methylene blue (NMB) with human serum albumin (HSA) and bovine serum albumin (BSA) was carefully investigated both experimentally and conceptually, employing experimental and insilico analysis. The steady-state emission spectral studies showed that the emission intensity of HSA and BSA was quenched significantly by NMB. The findings of the Stern–Volmer and double logarithmic plot revealed that the observed emission quenching process was through a static quenching mechanism and the measured binding constant values (Kb) for HSA–NMB and BSA–NMB are 2.766 and 1.187 × 105 dm3 mol−1 respectively. The time-resolved fluorescence lifetime measurement and UV–vis absorption investigation further verify the complex formation between NMB and HSA/BSA. The assessment of thermodynamic parameters disclosed the binding process was spontaneous driven by hydrogen bonds (H-bond) and van der Waals interactions, which contributed a significant role in the complexation. Moreover, the secondary structural conformation and microenvironment of HSA/BSA were modified in the presence of NMB, as evidenced by circular dichroism and synchronous fluorescence data. Molecular docking study predicted a plausible binding mode of NMB inside the binding pocket of HSA and BSA. These results demonstrated that the stabilized NMB is found at the Subdomain IIA (site I) of both the proteins and the results were correlated well with the competitive binding assay. Additionally, the principal components analysis revealed less variation of docked poses for HSA, while, more dispersed docked poses were observed for the BSA model. This also highlights the effects of docking towards a modeled protein (BSA). Molecular dynamic (MD) simulation based binding free energy (ΔGmmgbsa) estimation obtained at 298, 303, 308 and 313 K, were in good agreement with our experimental (ΔGbind) values.

Impacts of Industrial Modification on the Structure and Gel Features of Soy Protein Isolate and its Composite Gel with Myofibrillar Protein.

Native soy protein isolate (N-SPI) has a low denaturation point and low solubility, limiting its industrial application. The influence of different industrial modification methods (heat (H), alkaline (A), glycosylation (G), and oxidation (O)) on the structure of SPI, the properties of the gel, and the gel properties of soy protein isolate (SPI) in myofibril protein (MP) was evaluated. The study found that four industrial modifications did not influence the subunit composition of SPI. However, the four industrial modifications altered SPI's secondary structure and disulfide bond conformation content. A-SPI exhibits the highest surface hydrophobicity and I850/830 ratio but the lowest thermal stability. G-SPI exhibits the highest disulfide bond content and the best gel properties. Compared with MP gel, the addition of H-SPI, A-SPI, G-SPI, and O-SPI components significantly improved the properties of the gel. Additionally, MP-ASPI gel exhibits the best properties and microstructure. Overall, the four industrial modification effects may impact SPI's structure and gel properties in different ways. A-SPI could be a potential functionality-enhanced soy protein ingredient in comminuted meat products. The present study results will provide a theoretical basis for the industrialized production of SPI.

Non-Perturbative Identification and Subtyping of Amyloidosis in Human Kidney Tissue with Raman Spectroscopy and Machine Learning.

Amyloids are proteins with characteristic beta-sheet secondary structures that display fibrillary ultrastructural configurations. They can result in pathologic lesions when deposited in human organs. Various types of amyloid protein can be routinely identified in human tissue specimens by special stains, immunolabeling, and electron microscopy, and, for certain forms of amyloidosis, mass spectrometry is required. In this study, we applied Raman spectroscopy to identify immunoglobulin light chain and amyloid A amyloidosis in human renal tissue biopsies and compared the results with a normal kidney biopsy as a control case. Raman spectra of amyloid fibrils within unstained, frozen, human kidney tissue demonstrated changes in conformation of protein secondary structures. By using t-distributed stochastic neighbor embedding (t-SNE) and density-based spatial clustering of applications with noise (DBSCAN), Raman spectroscopic data were accurately classified with respect to each amyloid type and deposition site. To the best of our knowledge, this is the first time Raman spectroscopy has been used for amyloid characterization of ex vivo human kidney tissue samples. Our approach, using Raman spectroscopy with machine learning algorithms, shows the potential for the identification of amyloid in pathologic lesions.

Study of the Molecular Structure of Proteins in Eggs under Different Storage Conditions

The aim of this study is to reveal the relationship between changes in the physical and chemical characterization of eggs during storage and to provide a new way to assess egg freshness at the molecular chemical level. In this study, the Fourier transform infrared (FTIR) spectra of egg albumin from 60 fresh eggs (ISA Brown layer) stored for 1, 10, 20, 30, and 40 days at 4°C and 10°C were measured ( n = 6 ), and the amide I band of the egg albumin spectra was quantified by Fourier deconvolution and curve fitting to obtain the composition of the protein molecular structure. The results showed that different storage temperatures and storage times led to protein denaturation, resulting in changes in the conformation of the protein secondary structure. With increasing storage temperature and storage time, the content of the ordered structures β-sheet and α-helix in the egg protein secondary structure decreased significantly ( p < 0.05 ), and the content of the disordered structure β-turn and random coil increased significantly ( p < 0.05 ). Based on the pattern of protein secondary structure changes during storage, it was found that fresh eggs were better stored at 4°C for up to 15 days. Spearman’s correlation analysis of egg protein height, Haugh unit, egg weight, and protein secondary structure in eggs stored at 4°C showed a significant positive correlation between β-sheet and α-helix and egg weight, protein height, and Haugh unit. And a significant negative correlation between random coil and egg weight, protein height, and Haugh unit. Therefore, a curve fitting method based on Fourier transform infrared spectroscopy of deconvoluted spectra is an effective method for evaluating egg quality and freshness.

Mayonnaise-like high internal phase Pickering emulsions stabilized by co-assembled phosphorylated perilla protein isolate and chitosan for extrusion 3D printing application

In this study, the feasibility of the mayonnaise-like high internal phase Pickering emulsions (HIPPEs) prepared by phosphorylated perilla protein isolate-chitosan composite nanoparticles (LZPI-CS CNPs) as three-dimensional (3D) printing inks and lipid-soluble β-carotene delivery vehicles was explored. The spherical LZPI-CS CNPs (232–336 nm in particle size) were formed by hydrogen bonds and electrostatic interaction, which exhibited improved wettability and superior capacity to reduce interfacial tension and enhance the viscoelasticity of the interfacial film even at low chitosan (CS) concentration. The rigid and dense interfacial architecture formed by LZPI-CS CNPs provided steric barrier and strong electrostatic repulsion, preventing droplets from coalescence during long-term storage, centrifugation and heat treatment. The incorporation of CS also obviously reduced the adsorption percentage of phosphorylated perilla protein isolate (LZPI) at the oil-water interface (from 87.27% to 83.15%), and caused the changes of its secondary structure and tertiary conformation. More interestingly, increasing the CS concentration (0.1–0.6 wt%) in LZPI-CS CNPs led to a progressive strengthening of viscosity, viscoelasticity and thixotropy-recovery capacity of HIPPEs, allowing their controllable injectability and printability during 3D printing. The HIPPEs prepared by LZPI-CS CNPs containing 0.6 wt% CS exhibited the most favorable shape fidelity, printing resolution and clear outline. Additionally, the stability of β-carotene against different environmental stresses was also significantly enhanced after encapsulation with HIPPEs. These findings demonstrated that the complexation of LZPI and CS could provide an effective strategy to construct mayonnaise-like HIPPEs as 3D printing inks and delivery vehicles of hydrophobic bioactive components. • The interfacial properties of LZPI could be adjusted by the concentration of CS. • HIPPEs stabilized by LZPI-CS CNPs exhibited superior stability. • The addition of CS improved the viscosity and stiffness of HIPPEs. • 3D printing cylinder based on HIPPEs containing 0.6 wt% CS showed high resolution and clear outline. • The stability of β-carotene was enhanced after HIPPEs encapsulation.