Changes In Secondary Structure Research Articles

Inhibition of albendazole and 2-(2-aminophenyl)-1H-benzimidazole against tyrosinase: mechanism, structure-activity relationship, and anti-browning effect.

Tyrosinase is the key enzyme involved in enzymatic browning of plant-derived foods. Inhibition of tyrosinase activity contributes to the control of food browning. Due to safety regulations or other issues, most identified tyrosinase inhibitors are not suitable for practical use. Therefore, it is necessary to search for novel tyrosinase inhibitors. In this study, the anti-tyrosinase activity and mechanism of albendazole and 2-(2-aminophenyl)-1H-benzimidazole (2-2-A-1HB) were investigated through ultraviolet-visible absorption spectroscopy, fluorescence spectra, molecular docking, and molecular dynamic (MD) simulation. The anti-browning effect of albendazole on fresh-cut apples was then elucidated. Albendazole and 2-2-A-1HB were both efficient tyrosinase inhibitors with IC50 of 51 ± 1.5 and 128 ± 1.3 μmol L-1 , respectively. Albendazole suppressed tyrosinase non-competitively and formed tyrosinase-albendazole complex statically. Hydrogen bond and hydrophobic interaction were major driving forces in stabilizing the tyrosinase-albendazole complex. While 2-2-A-1HB inhibited the enzyme competitively and quenched its intrinsic fluorescence through a static mechanism, it generated strong binding affinity with tyrosinase through hydrophobic interaction. MD simulations further validated that albendazole/2-2-A-1HB could form stable complexes with tyrosinase and loosened its basic framework structure, leading to a change in secondary structure and conformation. In addition, albendazole could delay the browning of fresh-cut apples by inhibiting the activity of polyphenol oxidase, peroxidase and phenylalanine ammonia-lyase, and reducing the oxidation of phenolic compounds. This research might provide a deep view of tyrosinase inhibition by benzimidazole derivatives and a theoretical basis for developing albendazole as a potential fresh-keeping agent. © 2023 Society of Chemical Industry.

The pH-responsive precipitation–redissolution of the CspB fusion protein, CspB50TEV-Teriparatide, triggered by changes in secondary structure

Cell surface protein B (CspB) fusion proteins can undergo reversible pH-responsive precipitation–redissolution. A pH-responsive precipitation–redissolution of CspB tag purification (pPRCP) method was established for protein purification using this property. However, the mechanism of the pH-responsive precipitation of CspB fusion proteins is unknown, which has made it difficult to set process parameters for pPRCP. In this study, we investigated the mechanism of the pH-responsive precipitation of CspB fusion proteins using CspB50TEV-Teriparatide (CspB-teri) as a model. As expected, CspB-Teri was reversibly precipitated at acidic pH. By contrast, CspB-Teri was not precipitated under unfolding conditions induced by trifluoroethanol, urea, or guanidine hydrochloride, even at acidic pH. The conformation of CspB-Teri changed to a β-sheet-rich structure as the pH decreased, followed by the formation of intermolecular interactions, which caused precipitation. The particle size of the CspB-Teri precipitate increased in a protein concentration-dependent manner. These results indicated that the pH-responsive precipitation of CspB-Teri is triggered by the formation of a β-sheet structure in response to decreasing pH, and the growth of the precipitate particles occurred through intermolecular interactions.

Analysis of riboflavin/ultraviolet a corneal cross-linking by molecular spectroscopy

Corneal cross-linking (CXL) with riboflavin and ultraviolet A light is a therapeutic procedure to restore the mechanical stability of corneal tissue. The treatment method is applied to pathological tissue, such as keratoconus and induces the formation of new cross-links. At present, the molecular mechanisms of induced cross-linking are still not known exactly. In this study, we investigated molecular alterations within porcine cornea tissue after treatment with riboflavin and ultraviolet A light by surface enhanced Raman spectroscopy (SERS). For that purpose, after CXL treatment a thin silver layer was vapor-deposited onto cornea flaps. To explore molecular alterations induced by the photochemical process hierarchical cluster analysis (HCA) was used. The detailed analysis of SERS spectra reveals that there is no general change in collagen secondary structure while modifications on amino acid side chains are the most dominant outcome. The formation of secondary and aromatic amine groups as well as methylene and carbonyl groups were observed. Even though successful cross-linking could not be registered in all treated samples, Raman signals of newly formed chemical groups are already present in riboflavin only treated corneas.

Effect of pH on the secondary structure and thermostability of beetle luciferases: structural origin of pH-insensitivity.

Beetle luciferases were classified into three functional groups: (1) pH-sensitive yellow-green-emitting (fireflies) which change the bioluminescence color to red at acidic pH, high temperatures and presence of heavy metals; (2) the pH-insensitive green-yellow-emitting (click beetles, railroad worms and firefly isozymes) which are not affected by these factors, and (3) pH-insensitive red-emitting. Although the pH-sensing site in firefly luciferases was recently identified, it is unclear why some luciferases are pH-insensitive despite the presence of someconserved pH-sensing residues. Through circular dichroism, we compared the secondary structural changes and unfolding temperature of luciferases of representatives ofthese three groups: (1) pH-sensitive green-yellow-emitting Macrolampis sp2 (Mac) and Amydetes vivianii (Amy) firefly luciferases; (2) the pH-insensitive green-emitting Pyrearinus termitilluminans larval click beetle (Pte) and Aspisoma lineatum (Al2) larval firefly luciferases, and (3) the pH-insensitive red-emitting Phrixotrix hirtus railroadworm (PxRE) luciferase. The most blue-shifted luciferases, independently of pH sensitivity, are thermally more stable at different pHs than the red-shifted ones. The pH-sensitive luciferases undergo increases of α-helices and thermal stability above pH 6. The pH-insensitive Pte luciferase secondary structure remains stable between pH 6 and 8, whereas the Al2 luciferase displays an increase of the β-sheet at pH 8. The PxRE luciferase also displays an increase of α-helices at pH 8. The results indicate that green-yellow emission in beetle luciferases can be attained by: (1) a structurally rigid scaffold which stabilizes a single closed active site conformation in the pH-insensitive luciferases, and (2) active site compaction above pH 7.0 in the more flexible pH-sensitive luciferases.

RNA Structure in the 5' Untranslated Region of Enterovirus D68 Strains with Differing Neurovirulence Phenotypes.

Enterovirus-D68 (EV-D68) is a positive-sense single-stranded RNA virus within the family Picornaviridae. EV-D68 was initially considered a respiratory virus that primarily affected children. However, in 2014, EV-D68 outbreaks occurred causing the expected increase in respiratory illness cases, but also an increase in acute flaccid myelitis cases (AFM). Sequencing of 2014 outbreak isolates revealed variations in the 5' UTR of the genome compared to the historical Fermon strain. The structure of the 5' UTR RNA contributes to enterovirus virulence, including neurovirulence in poliovirus, and could contribute to neurovirulence in contemporary EV-D68 strains. In this study, the secondary and tertiary structures of 5' UTR RNA from the Fermon strain and 2014 isolate KT347251.1 are analyzed and compared. Secondary structures were determined using SHAPE-MaP and TurboFold II and tertiary structures were predicted using 3dRNAv2.0. Comparison of RNA structures between the EV-D68 strains shows significant remodeling at the secondary and tertiary levels. Notable secondary structure changes occurred in domains II, IV and V. Shifts in the secondary structure changed the tertiary structure of the individual domains and the orientation of the domains. Our comparative structural models for EV-D68 5' UTR RNA highlight regions of the molecule that could be targeted for treatment of neurotropic enteroviruses.

Interaction of bioactive kaempferol with HMGB1: Investigation by multi-spectroscopic and molecular simulation methods

Chronic and persistent inflammation associated with excessive high mobility group protein 1 (HMGB1) is a risk factor for various diseases. Dietary intake of kaempferol has been proven to be effective in reducing HMGB1 levels and the degree of inflammation, but the structural mechanism remains unclear. In this context, we first investigated the interaction between bioactive kaempferol and HMGB1 using multi-spectroscopic and molecular simulation techniques. The surface plasmon resonance (SPR) data indicated that kaempferol binds directly to HMGB1 with a Kd value of 2.89 × 10−5 M. Binding of kaempferol with HMGB1 led to the intrinsic fluorescence quenching and modest secondary structure change of HMGB1 supported by fluorescence spectrometry and circular dichroism (CD). Using dynamic light scattering (DLS), it was found that kaempferol induced the aggregation of HMGB1 protein complex to form larger particles. On HMGB1-activated RAW264.7 cells, kaempferol co-incubation exhibited a remarkable inhibitory effect on nitric oxide (NO) release with an IC50 value of 5.02 μM, which was lower than that of quercetin. In silico, kaempferol binds to HMGB1 mainly through hydrogen bonds and hydrophobic forces. Collectively, our study showed kaempferol as a potential HMGB1 inhibitor, mainly acting by direct binding to HMGB1 and inducing its conformational changes, which provides clues for the treatment of chronic inflammation by kaempferol.

Controlling the Adsorption of β-Glucosidase onto Wrinkled SiO2 Nanoparticles To Boost the Yield of Immobilization of an Efficient Biocatalyst.

β-Glucosidase (BG) catalyzes the hydrolysis of cellobiose to glucose, a substrate for fermentation to produce the carbon-neutral fuel bioethanol. Enzyme thermal stability and reusability can be improved through immobilization onto insoluble supports. Moreover, nanoscaled matrixes allow for preserving high reaction rates. In this work, BG was physically immobilized onto wrinkled SiO2 nanoparticles (WSNs). The adsorption procedure was tuned by varying the BG:WSNs weight ratio to achieve the maximum controllability and maximize the yield of immobilization, while different times of immobilization were monitored. Results show that a BG:WSNs ratio equal to 1:6 wt/wt provides for the highest colloidal stability, whereas an immobilization time of 24 h results in the highest enzyme loading (135 mg/g of support) corresponding to 80% yield of immobilization. An enzyme corona is formed in 2 h, which gradually disappears as the protein diffuses within the pores. The adsorption into the silica structure causes little change in the protein secondary structure. Furthermore, supported enzyme exhibits a remarkable gain in thermal stability, retaining complete folding up to 90 °C. Catalytic tests assessed that immobilized BG achieves 100% cellobiose conversion. The improved adsorption protocol provides simultaneously high glucose production, enhanced yield of immobilization, and good reusability, resulting in considerable reduction of enzyme waste in the immobilization stage.

Understanding Conformational Changes in Human Serum Albumin and Its Interactions with Gold Nanorods: Do Flexible Regions Play a Role in Corona Formation?

The importance of protein-nanoparticle (NP) conjugates for biomedical applications has seen an exponential growth in the past few years. The protein corona formation on NPs with human serum albumin (HSA), being the most abundant protein in blood serum, has become one of the most studied protein analyses under NP-protein interactions as HSA is readily adsorbed on the surface of the NPs. Understanding the fate of the NPs in physiological media along with the change in biological responses due to the formation of the protein corona thus becomes important. We analyzed the HSA protein corona formation on gold nanorods (AuNRs) through different spectroscopic studies in addition to the effects of change in the protein concentration on the protein-NP interactions. Different imaging techniques such as high-resolution transmission electron microscopy, field emission scanning electron microscopy, and atomic force microscopy were used to determine the morphology and the dimensions of the nanorods and the protein-nanorod conjugates. Fourier-transform infrared data showed a reduction in the α-helix content and an increase in β-sheet content for the HSA-AuNR conjugate compared to the native protein. A decrease in steady-state fluorescence intensity occurred with instant addition of AuNR to HSA showing better and efficient quenching of Trp fluorescence for the lower concentration of protein. Time-correlated single photon counting results showed greater energy transfer efficiency and faster decay rate for higher concentrations of proteins. The circular dichroism study gives insight into the secondary structural changes due to unfolding, and a greater change was observed for lower concentrations of protein due to a thermodynamically stable protein corona formation. Surface-enhanced Raman spectroscopy (SERS) indicated the presence of aromatic residues such as Phe, Tyr, and Cys that appear to be close to the surface of the AuNRs in addition to hydrophobic interactions between AuNR and the protein. The disordered and flexible regions mapped onto HSA (PDB: 1AO6), predicted by the intrinsically disordered region predictors, point toward the interactions of similar residues with the nanorods observed from SERS and fluorescence studies. These studies could provide a clearer understanding of the interactions between HSA and AuNRs for possible biological applications.

Spectroscopic Studies of Quinobenzothiazine Derivative in Terms of the In Vitro Interaction with Selected Human Plasma Proteins: Part 2.

Synthesis of anticancer substances and studying their binding abilities towards human serum proteins as carriers are important parts of pharmaceutical and medical sciences development. The presented work is a continuation of studies of quinobenzothiazine derivatives binding with serum proteins. The main aim of this work was a spectroscopic analysis of second from benzothiazinium derivatives salt, 9-fluoro-5-alkyl-12(H)-quino [3,4-b][1,4]benzothiazinium chloride (Salt2), its interaction with carrier proteins, i.e., human serum albumin (HSA), α1-acid glycoprotein (AGP), human gamma globulin (HGG), and the study of protein secondary and tertiary structure changes using spectroscopic techniques (spectrofluorescence, UV-Vis and circular dichroism CD spectroscopy). In order to mimic in vivo conditions, control normal serum (CNS) was used. Using the Klotz method, both binding constants (Ka [M-1]) and the number of binding classes (n) were calculated. In addition, the percentage of displacement of binding site markers from HSA and AGP molecules has been defined. Based on the obtained data, it can be concluded that the main binding protein for Salt2 is AGP. HSA and HGG are also involved in the distribution of the studied substance in the bloodstream. Moreover, Salt2 very slightly interacts with CNS, which can cause strong therapeutic as well as toxic effects. The analysis of CD spectra confirms that there are no changes in the secondary structure of the main binding proteins in the presence of Salt2.

Association Between Transforming Growth Factor-β1 Polymorphisms and Ischemic Stroke Susceptibility: A Meta-Analysis.

Epidemiological studies have suggested a potential relationship between the transforming growth factor-β1 (TGF-β1) gene and ischemic stroke (IS) risk; however, the current results are inconsistent. Therefore, we performed this meta-analysis to assess the precise association between TGF-β1 polymorphisms and IS risk. Online databases were searched for themes related to TGF-β1 polymorphisms and ARE risk. Quantitative calculations of odds ratios (ORs) and confidence intervals (CIs) were performed using 5 genetic models of each variant locus. Heterogeneity tests, cumulative analyses, sensitivity analyses, and publication bias were conducted to examine statistical power. Moreover, changes in the secondary structure and minimum free energy (MFE) were explored using in silico analysis. Nineteen case-control studies were included in our meta-analysis on rs1800468 G>A, rs1800469 C>T, and rs1800470 T>C polymorphisms and IS risk. Overall, only a marginal association was found between the rs1800469 C>T polymorphism and IS risk (T vs C: OR = 1.12, 95%CI = 1.00-1.46, P = .05, I2 = 77.0%). Otherwise, no significant association was observed between the rs1800468 G>A and rs1800470 T>C polymorphisms and IS risk in general and stratified analyses. Moreover, no significant changes in secondary structure and MFE were found in any of the 3 polymorphic loci. Current evidence cautiously suggests that TGF-β1 polymorphisms are not associated with IS susceptibility.

Mono-phosphorylation at Ser4 of barrier-to-autointegration factor (Banf1) significantly reduces its DNA binding capability by inducing critical changes in its local conformation and DNA binding surface.

Barrier-to-autointegration factor (Banf1) is a small DNA-bridging protein. The binding status of Banf1 to DNA is regulated by its N-terminal phosphorylation and dephosphorylation, which plays a critical role in cell proliferation. Banf1 can be phosphorylated at Ser4 into mono-phosphorylated Banf1, which is further phosphorylated at Thr3 to form di-phosphorylated Banf1. It was observed decades ago that mono-phosphorylated Banf1 cannot bind to DNA. However, the underlying molecular- and atomic-level mechanisms remain unclear. A clear understanding of these mechanisms will aid in interfering with the cell proliferation process for better global health. Herein, we explored the detailed atomic bases of unphosphorylated Banf1-DNA binding and how mono- and di-phosphorylation of Banf1 impair these atomic bases to eliminate its DNA-binding capability, followed by exploring the DNA-binding capability of mono- and di-phosphorylation Banf1, using comprehensive and systematic molecular modelling and molecular dynamics simulations. This work presented in detail the residue-level binding energies, hydrogen bonds and water bridges between Banf1 and DNA, some of which have not been reported. Moreover, we revealed that mono-phosphorylation of Banf1 causes its N-terminal secondary structure changes, which in turn induce significant changes in Banf1's DNA binding surface, thus eliminating its DNA-binding capability. At the atomic level, we also uncovered the alterations in interactions due to the induction of mono-phosphorylation that result in the N-terminal secondary structure changes of Banf1. Additionally, our modelling showed that phosphorylated Banf1 with their dominant N-terminal secondary structures bind to DNA with a significantly lower affinity and the docked binding pose are not stable in MD simulations. These findings help future studies in predicting effect of mutations in Banf1 on its DNA-binding capability and open a novel avenue for the development of therapeutics such as cancer drugs, targeting cell proliferation by inducing conformational changes in Banf1's N-terminal domain.

Effect of high-intensity ultrasound on the physicochemical properties of Tenebrio Molitor Protein

Insect is an important source of dietary protein, and its application in the food industry has attracted attention. Tenebrio Molitor is rich in water-soluble protein, and the over-hydrophilic nature of water-soluble protein generally limits its industrial application. For the above reasons, this study systematically investigated the effect of high-intensity ultrasound (HIUS) on the physicochemical and physical characteristics of Tenebrio Molitor Protein (TMP). The results show that HIUS treatment might break the non-covalent bonds through the cavitation effect generated by the ultrasound probe, inducing the unfolding and disintegration of TMP soluble aggregates, and resulting in hydrophobic exposure and particle size reduction. HIUS optimize the physical characteristics of TMP (solubility, foamability, foam stability, emulsification, etc.) by changing its secondary/tertiary structure. Furthermore, emulsions stabilized by HIUS-treated TMP (UTMPEs) present smaller particle size and denser structure due to the changes in secondary structure, which plays a dominant role in the protein interface adsorption stabilization. The results of this study are expected to provide new guidance for better application of HIUS-treated TMP in the future food industry. • Modification of Tenebrio Molitor Protein (TMP) using high-intensity ultrasound (HIUS). • HIUS changes the secondary and tertiary structure of TMP. • HIUS enhances the emulsifying ability of TMP.

PH dependence of the assembly mechanism and properties of poly(L-lysine) and poly(L-glutamic acid) complexes.

We show by extensive experimental characterization combined with molecular simulations that pH has a major impact on the assembly mechanism and properties of poly(L-lysine) (PLL) and poly(L-glutamic acid) (PGA) complexes. A combination of dynamic light scattering (DLS) and laser Doppler velocimetry (LDV) is used to assess the complexation, charge state, and other physical characteristics of the complexes, isothermal titration calorimetry (ITC) is used to examine the complexation thermodynamics, and circular dichroism (CD) is used to extract the polypeptides' secondary structure. For enhanced analysis and interpretation of the data, analytical ultracentrifugation (AUC) is used to define the precise molecular weights and solution association of the peptides. Molecular dynamics simulations reveal the associated intra- and intermolecular binding changes in terms of intrinsic vs. extrinsic charge compensation, the role of hydrogen bonding, and secondary structure changes, aiding in the interpretation of the experimental data. We combine the data to reveal the pH dependency of PLL/PGA complexation and the associated molecular level mechanisms. This work shows that not only pH provides a means to control complex formation but also that the associated changes in the secondary structure and binding conformation can be systematically used to control materials assembly. This gives access to rational design of peptide materials via pH control.

Renaturation of Myoglobin Denatured by Sodium Dodecyl Sulfate by Removal of Dodecyl Sulfate Ions Bound to the Protein Using Sodium Cholate.

The secondary and tertiary structures of myoglobin were disrupted by sodium dodecyl sulfate (SDS) but were hardly affected by the bile salt, sodium cholate (NaCho). This disruption was induced by the binding of dodecyl sulfate (DS) ions to the protein. In this study, the removal of DS ions bound to the protein was attempted using NaCho. The extent of removal of DS ions was estimated by the restoration of the secondary and tertiary structures of the protein disrupted by SDS. The secondary structural change was followed by monitoring mean residue ellipticity at 222 nm, [θ]222, which was frequently used as a measure of α-helical content. The tertiary structural change was followed by examining the Soret band absorbance of the protein. Evidently, the magnitude of [θ]222 of myoglobin in the SDS solution initially decreased and then increased back to almost its original value as the NaCho concentration increased. The initial decrease in [θ]222 indicated the cooperation of NaCho and SDS in disrupting the secondary structure at low concentrations of both surfactants. This cooperation was also observed in the tertiary structural change as a shift of the Soret band maximum wavelength, λmax, and a decrease in the molar absorption coefficient, εmax, at λmax. Above a certain NaCho concentration, the position of λmax and the magnitude of εmax were also restored to their original states. The secondary and tertiary structures were simultaneously restored by adding NaCho. These recoveries were attributed to removal of the DS ions bound to the protein. This removal might be due to the ability of cholate anions to strip DS ions bound to the protein. The stripped DS ions are more likely to form SDS-NaCho mixed micelles in bulk than SDS-NaCho mixed aggregates on the protein.

RNA Secondary Structure Alteration Caused by Single Nucleotide Variants.

A point mutation in coding RNA can cause not only an amino acid substitution but also a dynamic change of RNA secondary structure, leading to a dysfunctional RNA. Although in silico structure prediction has been used to detect structure-disrupting point mutations known as riboSNitches, exhaustive simulation of long RNAs is needed to detect a significant enrichment or depletion of riboSNitches in functional RNAs. Here, we have developed a novel algorithm Radiam (RNA secondary structure Analysis with Deletion, Insertion, And substitution Mutations) for a comprehensive riboSNitch analysis of long RNAs. Radiam is based on the ParasoR framework, which efficiently computes local RNA secondary structures for long RNAs. ParasoR can compute a variety of structure scores over globally consistent structures with maximal span constraints for the base pair distance. Using the reusable structure database made by ParasoR, Radiam performs an efficient recomputation of the secondary structures for mutated sequences. An exhaustive simulation of Radiam is expected to find reliable riboSNitch candidates on long RNAs by evaluating their statistical significance in terms of the change of local structure stability.

Characterization of freeze-dried oxidized human red blood cells for pre-transfusion testing by synchrotron FTIR microspectroscopy live-cell analysis.

Oxidative treatment of human red blood cells (RBCs) prior to freeze-drying appears to stabilize the RBCs to withstand dried storage at room temperature. To better understand the effects of oxidation and freeze-drying/rehydration on RBC lipids and proteins, single-cell measurements were performed by synchrotron-based Fourier transform infrared (FTIR) microspectroscopy 'live-cell' (unfixed) analysis. Lipid and protein spectral data of tert-butyl hydroperoxide (TBHP)-oxidized RBCs (oxRBCs), FDoxRBCs and control (untreated) RBCs were compared using principal component analysis (PCA) and band integration ratios. The oxRBCs and FDoxRBCs samples had similar spectral profiles that were clearly different to control RBCs. Spectral changes in the CH stretching region of oxRBCs and FDoxRBCs indicated the presence of increased saturated and shorter-chain lipids, consistent with lipid peroxidation and stiffening of the RBC membrane compared to control RBCs. The PCA loadings plot for the fingerprint region of control RBCs corresponding to the α-helical structure of hemoglobin, shows that oxRBCs and FDoxRBCs have conformational changes in the protein secondary structure to β-pleated sheets and β-turns. Finally, the freeze-drying process did not appear to compound or induce additional changes. In this context, FDoxRBCs could become a stable source of reagent RBCs for pre-transfusion blood serology testing. The synchrotron FTIR microspectroscopic live-cell protocol provides a powerful analytical tool to characterize and contrast the effects of different treatments on RBC chemical composition at the single cell level.

Insight into the interaction between tannin acid and bovine serum albumin from a spectroscopic and molecular docking perspective.

In this study, the interaction mechanism of bovine serum albumin (BSA) with tannic acid (TA) was investigated by spectroscopic and computational approaches and further validated using circular dichroism (CD), differential scanning calorimetry (DSC) and molecular docking techniques. The fluorescence spectra showed that TA bound to BSA and underwent static quenching at a single binding site, which was consistent with the molecular docking results. And the fluorescence quenching of BSA by TA was dose-dependent. Thermodynamic analysis indicated that hydrophobic forces dominated the interaction of BSA with TA. The results of circular dichroism showed that the secondary structure of BSA was slightly changed after coupling with TA. Differential scanning calorimetry showed that the interaction between BSA and TA improved the stability of the BSA-TA complex, and the melting temperature increased to 86.67 °C and the enthalpy increased to 264.1 J g-1 when the ratio of TA to BSA was 1.2 : 1. Molecular docking techniques revealed specific amino acid binding sites for the BSA-TA complex with a docking energy of -12.9 kcal mol-1, which means the TA is non-covalently bound to the BSA active site.

Protective effect of pangasius myosin on thermal stability of lycopene and their interaction mechanism

In this study, the influence of extracted pangasius myosin on the thermal stability of lycopene and the mechanism of their interaction were examined. The addition of pangasius myosin positively affected the thermal stability of lycopene. After adding myosin, under heating conditions, the L* value of lycopene increased by 6.2–10.04%, a* value increased by 20–27%, and ΔE decreased by 42–51%. Lycopene inhibited the fluorescence of ovalbumin by static burst. Binding and thermodynamic parameters demonstrated that lycopene bound spontaneously to myosin through hydrophobic interaction with a complex stoichiometry ratio of 1:1. Circular dichroism and Fourier infrared transform spectroscopy were used to examine the secondary structure changes that occurred in myosin after it bound to lycopene. Particle size and electron microscopy analysis showed that the addition of low concentrations of lycopene resulted in smaller particle size and improve dispersion stability; however, high concentrations of lycopene promoted myosin aggregation. This study provides a theoretical foundation for improving the thermal stability of lycopene in minced fish products.

Conformational Flexibility Is a Key Determinant for the Lytic Activity of the Pore-Forming Protein, Cytolysin A.

Several bacterial infections are mediated by pore-forming toxins (PFTs), a subclass of proteins that oligomerize on mammalian cell membranes forming lytic nanopores. Cytolysin A (ClyA), an α-PFT, undergoes a dramatic conformational change restructuring its two membrane-binding motifs (the β-tongue and the N-terminus helix), during pore formation. A complete molecular picture for this key transition and the driving force behind the secondary structure change upon membrane binding remain elusive. Using all-atom molecular dynamics (MD) simulations of the ClyA monomer and string method based free energy computations with path collective variables, we illustrate that an unfolded β-tongue motif is an on-pathway intermediate during the transition to the helix-turn-helix motif of the protomer. An aggregate of 28 μs of all-atom thermal unfolding MD simulations of wild-type ClyA and its single point mutants reveal that the membrane-binding motifs of the ClyA protein display high structural flexibility in water. However, point mutations in these motifs lead to a distinct reduction in the flexibility, especially in the β-tongue, thereby stabilizing the pretransition secondary structure. Resistance to unfolding was further corroborated by MD simulations of the β-tongue mutant motif in the membrane. Combined with the thermal unfolding simulations, we posit that the β-tongue as well as N-terminal mutants that lower the tendency to unfold and disorder the β-tongue are detrimental to pore formation by ClyA and its lytic activity. Erythrocyte turbidity and vesicle leakage assays indeed reveal a loss of activity for the β-tongue mutant, and delayed kinetics for the N-terminus mutants. On the other hand, a point mutation in the extracellular domain that did not abrogate lytic activity displayed similar unfolding characteristics as the wild type. Thus, attenuation of conformational flexibility in membrane-binding motifs correlates with reduced lytic and leakage activity. Combined with secondary structure changes observed in the membrane bound states, our study shows that the tendency to unfold in the β-tongue region is a critical step in the conformational transition and bistability of the ClyA protein and mutants that disrupt this tendency reduced pore formation. Overall, our finding suggests that inherent flexibility in the protein could play a wider and hitherto unrecognized role in membrane-mediated conformational transitions of PFTs and other membrane protein transformations.

Investigation of novel cold atmospheric plasma sources and their impact on the structural and functional characteristics of pea protein

The impact of three cold atmospheric plasma (CAP) sources, atmospheric pressure plasma jet (APPJ), two- dimension dielectric barrier discharge (2D-DBD), and nanosecond pulsed discharge (ns-pulsed) on the structure, functionality, and amino acid composition of pea protein was evaluated. Different plasma sources and associated reactive species resulted in protein denaturation, increased surface hydrophobicity, formation of soluble aggregates mostly by disulfide linkages, and changes in secondary structures. Enhancement in surface properties, presence of soluble aggregates, and increase in β-sheet contributed to significant improvement in gelation and emulsification. Enhanced emulsion stability was attributed to relatively small droplet sizes and high surface-charge. Differences among CAP-treated samples were attributed to differences in fluence and composition of plasma-produced reactive species. While all three plasma treatments could be appreciable functionalization approaches, 2D-DBD (Ar + O2) treatment for 30 min had insignificant effect on the amino acid composition.